Starting phenix.real_space_refine on Wed Nov 19 21:28:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mjs_3522/11_2025/5mjs_3522.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mjs_3522/11_2025/5mjs_3522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5mjs_3522/11_2025/5mjs_3522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mjs_3522/11_2025/5mjs_3522.map" model { file = "/net/cci-nas-00/data/ceres_data/5mjs_3522/11_2025/5mjs_3522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mjs_3522/11_2025/5mjs_3522.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 190 5.16 5 C 17619 2.51 5 N 4824 2.21 5 O 5461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28114 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3304 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 410} Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1010 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3412 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Chain: "F" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3412 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Chain: "G" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3412 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Chain: "H" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3412 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Chain: "J" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3304 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 410} Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3304 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 410} Chain: "C" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3304 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 410} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.25 Number of scatterers: 28114 At special positions: 0 Unit cell: (113.98, 116.76, 208.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 190 16.00 P 20 15.00 O 5461 8.00 N 4824 7.00 C 17619 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: 2.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6578 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 28 sheets defined 45.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 5.077A pdb=" N GLY A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 79 removed outlier: 4.003A pdb=" N VAL A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 107 through 125 removed outlier: 3.501A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.016A pdb=" N GLY A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.941A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.831A pdb=" N PHE A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 242 removed outlier: 4.030A pdb=" N HIS A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 231 " --> pdb=" O HIS A 227 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.827A pdb=" N ASN A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.680A pdb=" N GLN A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.752A pdb=" N GLN A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.600A pdb=" N PHE A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 403 through 426 removed outlier: 3.573A pdb=" N PHE A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.652A pdb=" N LEU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 16 " --> pdb=" O ILE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 28 removed outlier: 3.552A pdb=" N ASP D 25 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.718A pdb=" N PHE D 36 " --> pdb=" O MET D 32 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 32 through 37' Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.527A pdb=" N TYR D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN D 60 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN D 61 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP D 62 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 63 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 64' Processing helix chain 'D' and resid 64 through 73 removed outlier: 3.765A pdb=" N VAL D 68 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 70 " --> pdb=" O GLN D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.711A pdb=" N LEU D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.975A pdb=" N TRP D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'E' and resid 9 through 27 removed outlier: 3.605A pdb=" N GLY E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 79 through 85 removed outlier: 4.038A pdb=" N ARG E 83 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 114 through 117 Processing helix chain 'E' and resid 118 through 130 removed outlier: 3.635A pdb=" N ARG E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET E 129 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.534A pdb=" N GLU E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 193 removed outlier: 3.828A pdb=" N LEU E 193 " --> pdb=" O TYR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.741A pdb=" N ARG E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 247 removed outlier: 3.608A pdb=" N GLN E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU E 246 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 247 " --> pdb=" O THR E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 262 removed outlier: 4.103A pdb=" N PHE E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 286 removed outlier: 4.095A pdb=" N PHE E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 300 removed outlier: 3.665A pdb=" N GLN E 298 " --> pdb=" O GLU E 294 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.613A pdb=" N ASN E 304 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 340 removed outlier: 4.042A pdb=" N SER E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 403 removed outlier: 4.332A pdb=" N TRP E 392 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 401 " --> pdb=" O HIS E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 414 Processing helix chain 'E' and resid 419 through 441 removed outlier: 4.284A pdb=" N ARG E 426 " --> pdb=" O PHE E 422 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 removed outlier: 3.605A pdb=" N GLY F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY F 17 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU F 22 " --> pdb=" O ASN F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 79 through 85 removed outlier: 4.039A pdb=" N ARG F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 114 through 117 Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.635A pdb=" N ARG F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 166 removed outlier: 3.535A pdb=" N GLU F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 193 removed outlier: 3.828A pdb=" N LEU F 193 " --> pdb=" O TYR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.741A pdb=" N ARG F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 247 removed outlier: 3.609A pdb=" N GLN F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL F 238 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU F 246 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG F 247 " --> pdb=" O THR F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 262 removed outlier: 4.104A pdb=" N PHE F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN F 260 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 removed outlier: 4.095A pdb=" N PHE F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 300 removed outlier: 3.665A pdb=" N GLN F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE F 300 " --> pdb=" O THR F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 removed outlier: 3.613A pdb=" N ASN F 304 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 340 removed outlier: 4.041A pdb=" N SER F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 403 removed outlier: 4.332A pdb=" N TRP F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 401 " --> pdb=" O HIS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 414 Processing helix chain 'F' and resid 419 through 441 removed outlier: 4.284A pdb=" N ARG F 426 " --> pdb=" O PHE F 422 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU F 427 " --> pdb=" O SER F 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 27 removed outlier: 3.604A pdb=" N GLY G 13 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 17 " --> pdb=" O GLY G 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 19 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU G 22 " --> pdb=" O ASN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 55 Processing helix chain 'G' and resid 79 through 85 removed outlier: 4.038A pdb=" N ARG G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 111 Processing helix chain 'G' and resid 114 through 117 Processing helix chain 'G' and resid 118 through 130 removed outlier: 3.635A pdb=" N ARG G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET G 129 " --> pdb=" O ARG G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 166 removed outlier: 3.534A pdb=" N GLU G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET G 163 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 removed outlier: 3.828A pdb=" N LEU G 193 " --> pdb=" O TYR G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 220 removed outlier: 3.741A pdb=" N ARG G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 247 removed outlier: 3.608A pdb=" N GLN G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU G 246 " --> pdb=" O ILE G 242 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 247 " --> pdb=" O THR G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 262 removed outlier: 4.103A pdb=" N PHE G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR G 261 " --> pdb=" O ASN G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 removed outlier: 4.095A pdb=" N PHE G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 300 removed outlier: 3.665A pdb=" N GLN G 298 " --> pdb=" O GLU G 294 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.614A pdb=" N ASN G 304 " --> pdb=" O GLU G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 340 removed outlier: 4.042A pdb=" N SER G 338 " --> pdb=" O ALA G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 403 removed outlier: 4.331A pdb=" N TRP G 392 " --> pdb=" O ILE G 388 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU G 401 " --> pdb=" O HIS G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 414 Processing helix chain 'G' and resid 419 through 441 removed outlier: 4.284A pdb=" N ARG G 426 " --> pdb=" O PHE G 422 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU G 427 " --> pdb=" O SER G 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 removed outlier: 3.604A pdb=" N GLY H 13 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU H 22 " --> pdb=" O ASN H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 79 through 85 removed outlier: 4.038A pdb=" N ARG H 83 " --> pdb=" O ILE H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 111 Processing helix chain 'H' and resid 114 through 117 Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.634A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET H 129 " --> pdb=" O ARG H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 166 removed outlier: 3.534A pdb=" N GLU H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 193 removed outlier: 3.829A pdb=" N LEU H 193 " --> pdb=" O TYR H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 removed outlier: 3.742A pdb=" N ARG H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 247 removed outlier: 3.608A pdb=" N GLN H 237 " --> pdb=" O ARG H 233 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL H 238 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER H 245 " --> pdb=" O SER H 241 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU H 246 " --> pdb=" O ILE H 242 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG H 247 " --> pdb=" O THR H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 262 removed outlier: 4.104A pdb=" N PHE H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR H 261 " --> pdb=" O ASN H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 286 removed outlier: 4.095A pdb=" N PHE H 286 " --> pdb=" O ALA H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 300 removed outlier: 3.665A pdb=" N GLN H 298 " --> pdb=" O GLU H 294 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE H 300 " --> pdb=" O THR H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 removed outlier: 3.614A pdb=" N ASN H 304 " --> pdb=" O GLU H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 340 removed outlier: 4.043A pdb=" N SER H 338 " --> pdb=" O ALA H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 403 removed outlier: 4.332A pdb=" N TRP H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU H 401 " --> pdb=" O HIS H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 414 Processing helix chain 'H' and resid 419 through 441 removed outlier: 4.284A pdb=" N ARG H 426 " --> pdb=" O PHE H 422 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU H 427 " --> pdb=" O SER H 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 removed outlier: 5.078A pdb=" N GLY J 17 " --> pdb=" O GLY J 13 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA J 18 " --> pdb=" O ASN J 14 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 79 removed outlier: 4.002A pdb=" N VAL J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 106 Processing helix chain 'J' and resid 107 through 125 removed outlier: 3.502A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP J 118 " --> pdb=" O ASP J 114 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL J 119 " --> pdb=" O ALA J 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG J 122 " --> pdb=" O ASP J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 157 removed outlier: 4.016A pdb=" N GLY J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 193 removed outlier: 3.941A pdb=" N GLN J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 214 removed outlier: 3.831A pdb=" N PHE J 211 " --> pdb=" O LEU J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 242 removed outlier: 4.030A pdb=" N HIS J 227 " --> pdb=" O ASP J 223 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA J 231 " --> pdb=" O HIS J 227 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET J 233 " --> pdb=" O VAL J 229 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER J 239 " --> pdb=" O GLY J 235 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE J 240 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE J 242 " --> pdb=" O THR J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 256 removed outlier: 3.828A pdb=" N ASN J 256 " --> pdb=" O LYS J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 291 removed outlier: 3.681A pdb=" N GLN J 290 " --> pdb=" O PRO J 286 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN J 291 " --> pdb=" O GLU J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 336 removed outlier: 3.752A pdb=" N GLN J 328 " --> pdb=" O GLU J 324 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR J 334 " --> pdb=" O ARG J 330 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS J 335 " --> pdb=" O SER J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 386 removed outlier: 3.600A pdb=" N PHE J 377 " --> pdb=" O ILE J 373 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG J 379 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN J 383 " --> pdb=" O ARG J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 399 Processing helix chain 'J' and resid 403 through 426 removed outlier: 3.573A pdb=" N PHE J 407 " --> pdb=" O ASP J 403 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA J 410 " --> pdb=" O GLU J 406 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU J 411 " --> pdb=" O PHE J 407 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER J 412 " --> pdb=" O THR J 408 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU J 420 " --> pdb=" O ASP J 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN J 425 " --> pdb=" O TYR J 421 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU J 426 " --> pdb=" O GLN J 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 5.077A pdb=" N GLY B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 79 removed outlier: 4.003A pdb=" N VAL B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 125 removed outlier: 3.502A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 157 removed outlier: 4.016A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.940A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.831A pdb=" N PHE B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 242 removed outlier: 4.030A pdb=" N HIS B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.828A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.682A pdb=" N GLN B 290 " --> pdb=" O PRO B 286 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.752A pdb=" N GLN B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.600A pdb=" N PHE B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 383 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 403 through 426 removed outlier: 3.572A pdb=" N PHE B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU B 411 " --> pdb=" O PHE B 407 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 5.077A pdb=" N GLY C 17 " --> pdb=" O GLY C 13 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA C 18 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 79 removed outlier: 4.002A pdb=" N VAL C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.502A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 157 removed outlier: 4.016A pdb=" N GLY C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.940A pdb=" N GLN C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 214 removed outlier: 3.830A pdb=" N PHE C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 242 removed outlier: 4.029A pdb=" N HIS C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 231 " --> pdb=" O HIS C 227 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET C 233 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 237 " --> pdb=" O MET C 233 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.828A pdb=" N ASN C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 291 removed outlier: 3.681A pdb=" N GLN C 290 " --> pdb=" O PRO C 286 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 removed outlier: 3.752A pdb=" N GLN C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 334 " --> pdb=" O ARG C 330 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.600A pdb=" N PHE C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 383 " --> pdb=" O ARG C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 403 through 426 removed outlier: 3.573A pdb=" N PHE C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU C 411 " --> pdb=" O PHE C 407 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 420 " --> pdb=" O ASP C 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU C 426 " --> pdb=" O GLN C 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.897A pdb=" N ILE A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU A 65 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 66 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU A 3 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE A 133 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 5 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 135 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE A 7 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 9 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLN A 131 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 165 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE A 133 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE A 167 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU A 135 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 169 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N HIS A 137 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 198 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 200 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 199 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 265 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS A 201 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 270 Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 8 removed outlier: 3.665A pdb=" N LEU E 171 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN E 170 " --> pdb=" O CYS E 204 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE E 206 " --> pdb=" O ASN E 170 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLN E 172 " --> pdb=" O PHE E 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 57 through 59 removed outlier: 3.700A pdb=" N SER E 58 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL E 66 " --> pdb=" O SER E 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 72 removed outlier: 5.487A pdb=" N TYR E 71 " --> pdb=" O VAL E 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 275 through 277 removed outlier: 6.428A pdb=" N ALA E 378 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR E 323 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS E 380 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU E 321 " --> pdb=" O CYS E 380 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU E 382 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR E 319 " --> pdb=" O LEU E 382 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN E 384 " --> pdb=" O MET E 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 8 removed outlier: 3.665A pdb=" N LEU F 171 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN F 170 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE F 206 " --> pdb=" O ASN F 170 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN F 172 " --> pdb=" O PHE F 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 57 through 59 removed outlier: 3.700A pdb=" N SER F 58 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 66 " --> pdb=" O SER F 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 71 through 72 removed outlier: 5.487A pdb=" N TYR F 71 " --> pdb=" O VAL F 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 275 through 277 removed outlier: 6.430A pdb=" N ALA F 378 " --> pdb=" O TYR F 323 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR F 323 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS F 380 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU F 321 " --> pdb=" O CYS F 380 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU F 382 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR F 319 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN F 384 " --> pdb=" O MET F 317 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 6 through 8 removed outlier: 3.665A pdb=" N LEU G 171 " --> pdb=" O PHE G 139 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN G 170 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE G 206 " --> pdb=" O ASN G 170 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLN G 172 " --> pdb=" O PHE G 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.700A pdb=" N SER G 58 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL G 66 " --> pdb=" O SER G 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 71 through 72 removed outlier: 5.487A pdb=" N TYR G 71 " --> pdb=" O VAL G 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 275 through 277 removed outlier: 6.429A pdb=" N ALA G 378 " --> pdb=" O TYR G 323 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR G 323 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS G 380 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU G 321 " --> pdb=" O CYS G 380 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 382 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR G 319 " --> pdb=" O LEU G 382 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN G 384 " --> pdb=" O MET G 317 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.666A pdb=" N LEU H 171 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN H 170 " --> pdb=" O CYS H 204 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE H 206 " --> pdb=" O ASN H 170 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN H 172 " --> pdb=" O PHE H 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.700A pdb=" N SER H 58 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL H 66 " --> pdb=" O SER H 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 71 through 72 removed outlier: 5.487A pdb=" N TYR H 71 " --> pdb=" O VAL H 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 275 through 277 removed outlier: 6.429A pdb=" N ALA H 378 " --> pdb=" O TYR H 323 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR H 323 " --> pdb=" O ALA H 378 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS H 380 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU H 321 " --> pdb=" O CYS H 380 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU H 382 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR H 319 " --> pdb=" O LEU H 382 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN H 384 " --> pdb=" O MET H 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 91 through 92 removed outlier: 7.898A pdb=" N ILE J 91 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU J 65 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL J 66 " --> pdb=" O GLN J 8 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU J 3 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE J 133 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL J 5 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU J 135 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE J 7 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS J 137 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA J 9 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN J 131 " --> pdb=" O MET J 163 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA J 165 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE J 133 " --> pdb=" O ALA J 165 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE J 167 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU J 135 " --> pdb=" O PHE J 167 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL J 169 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N HIS J 137 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU J 198 " --> pdb=" O MET J 164 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE J 200 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 199 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE J 265 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS J 201 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=AC4, first strand: chain 'J' and resid 268 through 270 Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 92 removed outlier: 7.898A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 66 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLN B 131 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE B 133 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU B 198 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 200 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 199 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B 265 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS B 201 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AC7, first strand: chain 'B' and resid 268 through 270 Processing sheet with id=AC8, first strand: chain 'C' and resid 91 through 92 removed outlier: 7.898A pdb=" N ILE C 91 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU C 65 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 66 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU C 3 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE C 133 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C 5 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C 135 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE C 7 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS C 137 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA C 9 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN C 131 " --> pdb=" O MET C 163 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA C 165 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE C 133 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE C 167 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU C 135 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL C 169 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS C 137 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU C 198 " --> pdb=" O MET C 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 200 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 199 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE C 265 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS C 201 " --> pdb=" O PHE C 265 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AD1, first strand: chain 'C' and resid 268 through 270 951 hydrogen bonds defined for protein. 2754 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: 5.25 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6719 1.33 - 1.45: 6219 1.45 - 1.57: 15469 1.57 - 1.69: 32 1.69 - 1.81: 313 Bond restraints: 28752 Sorted by residual: bond pdb=" C GLN D 89 " pdb=" N ASP D 90 " ideal model delta sigma weight residual 1.332 1.291 0.041 1.40e-02 5.10e+03 8.73e+00 bond pdb=" CB PHE G 259 " pdb=" CG PHE G 259 " ideal model delta sigma weight residual 1.502 1.445 0.057 2.30e-02 1.89e+03 6.18e+00 bond pdb=" CB PHE F 259 " pdb=" CG PHE F 259 " ideal model delta sigma weight residual 1.502 1.445 0.057 2.30e-02 1.89e+03 6.16e+00 bond pdb=" CB PHE E 259 " pdb=" CG PHE E 259 " ideal model delta sigma weight residual 1.502 1.445 0.057 2.30e-02 1.89e+03 6.14e+00 bond pdb=" CB PHE H 259 " pdb=" CG PHE H 259 " ideal model delta sigma weight residual 1.502 1.446 0.056 2.30e-02 1.89e+03 6.02e+00 ... (remaining 28747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 36619 2.20 - 4.40: 2009 4.40 - 6.60: 295 6.60 - 8.80: 65 8.80 - 11.00: 18 Bond angle restraints: 39006 Sorted by residual: angle pdb=" C MET D 88 " pdb=" N GLN D 89 " pdb=" CA GLN D 89 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C GLY C 98 " pdb=" N ASN C 99 " pdb=" CA ASN C 99 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C GLY A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C GLY J 98 " pdb=" N ASN J 99 " pdb=" CA ASN J 99 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C GLY B 98 " pdb=" N ASN B 99 " pdb=" CA ASN B 99 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 ... (remaining 39001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.54: 16839 31.54 - 63.09: 181 63.09 - 94.63: 41 94.63 - 126.17: 8 126.17 - 157.72: 4 Dihedral angle restraints: 17073 sinusoidal: 6804 harmonic: 10269 Sorted by residual: dihedral pdb=" CA PHE G 347 " pdb=" C PHE G 347 " pdb=" N VAL G 348 " pdb=" CA VAL G 348 " ideal model delta harmonic sigma weight residual 180.00 142.69 37.31 0 5.00e+00 4.00e-02 5.57e+01 dihedral pdb=" CA PHE E 347 " pdb=" C PHE E 347 " pdb=" N VAL E 348 " pdb=" CA VAL E 348 " ideal model delta harmonic sigma weight residual 180.00 142.71 37.29 0 5.00e+00 4.00e-02 5.56e+01 dihedral pdb=" CA PHE F 347 " pdb=" C PHE F 347 " pdb=" N VAL F 348 " pdb=" CA VAL F 348 " ideal model delta harmonic sigma weight residual 180.00 142.73 37.27 0 5.00e+00 4.00e-02 5.56e+01 ... (remaining 17070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2965 0.068 - 0.136: 1052 0.136 - 0.205: 143 0.205 - 0.273: 23 0.273 - 0.341: 17 Chirality restraints: 4200 Sorted by residual: chirality pdb=" CB ILE G 269 " pdb=" CA ILE G 269 " pdb=" CG1 ILE G 269 " pdb=" CG2 ILE G 269 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE E 269 " pdb=" CA ILE E 269 " pdb=" CG1 ILE E 269 " pdb=" CG2 ILE E 269 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB ILE H 269 " pdb=" CA ILE H 269 " pdb=" CG1 ILE H 269 " pdb=" CG2 ILE H 269 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 4197 not shown) Planarity restraints: 5117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 260 " -0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO B 261 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 260 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.25e+01 pdb=" N PRO J 261 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO J 261 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO J 261 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 260 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.25e+01 pdb=" N PRO C 261 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 261 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 261 " -0.049 5.00e-02 4.00e+02 ... (remaining 5114 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1048 2.68 - 3.24: 28002 3.24 - 3.79: 46802 3.79 - 4.35: 59762 4.35 - 4.90: 91997 Nonbonded interactions: 227611 Sorted by model distance: nonbonded pdb=" O ARG A 390 " pdb=" OH TYR F 266 " model vdw 2.131 3.040 nonbonded pdb=" O GLU E 187 " pdb=" OG SER E 191 " model vdw 2.222 3.040 nonbonded pdb=" O GLU H 187 " pdb=" OG SER H 191 " model vdw 2.222 3.040 nonbonded pdb=" O GLU F 187 " pdb=" OG SER F 191 " model vdw 2.222 3.040 nonbonded pdb=" O GLU G 187 " pdb=" OG SER G 191 " model vdw 2.222 3.040 ... (remaining 227606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.100 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.540 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.010 0.101 28752 Z= 0.457 Angle : 1.166 11.005 39006 Z= 0.635 Chirality : 0.069 0.341 4200 Planarity : 0.009 0.089 5117 Dihedral : 12.531 157.716 10495 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.10 % Favored : 89.87 % Rotamer: Outliers : 0.66 % Allowed : 3.66 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -4.35 (0.11), residues: 3543 helix: -3.73 (0.08), residues: 1308 sheet: -1.42 (0.21), residues: 524 loop : -2.60 (0.13), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 46 TYR 0.032 0.004 TYR H 214 PHE 0.059 0.004 PHE E 57 TRP 0.021 0.004 TRP D 97 HIS 0.013 0.004 HIS H 196 Details of bonding type rmsd covalent geometry : bond 0.00981 (28752) covalent geometry : angle 1.16646 (39006) hydrogen bonds : bond 0.32377 ( 951) hydrogen bonds : angle 10.84439 ( 2754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1450 time to evaluate : 1.369 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.8696 (t-90) cc_final: 0.8474 (t-170) REVERT: A 35 ILE cc_start: 0.8902 (tt) cc_final: 0.8230 (tp) REVERT: A 53 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6458 (tm-30) REVERT: A 64 VAL cc_start: 0.9267 (t) cc_final: 0.9065 (t) REVERT: A 88 ASP cc_start: 0.8598 (m-30) cc_final: 0.8241 (p0) REVERT: A 89 ASN cc_start: 0.8921 (m-40) cc_final: 0.8111 (m110) REVERT: A 134 GLN cc_start: 0.6904 (mt0) cc_final: 0.6626 (mt0) REVERT: A 136 THR cc_start: 0.8951 (m) cc_final: 0.8660 (t) REVERT: A 162 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.8314 (mmm160) REVERT: A 204 ASN cc_start: 0.9092 (m-40) cc_final: 0.8706 (p0) REVERT: A 292 MET cc_start: 0.7799 (mtm) cc_final: 0.7541 (mtp) REVERT: A 340 PHE cc_start: 0.7272 (m-80) cc_final: 0.7021 (m-10) REVERT: A 358 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7557 (pttp) REVERT: A 360 LEU cc_start: 0.8674 (mt) cc_final: 0.8395 (mt) REVERT: A 372 SER cc_start: 0.9349 (p) cc_final: 0.8959 (m) REVERT: A 414 MET cc_start: 0.8877 (ttm) cc_final: 0.8545 (ttm) REVERT: D 14 GLN cc_start: 0.7011 (tt0) cc_final: 0.5142 (tp40) REVERT: D 32 MET cc_start: 0.6410 (mmm) cc_final: 0.5533 (mmm) REVERT: D 35 ILE cc_start: 0.8235 (mt) cc_final: 0.8021 (mt) REVERT: D 65 LEU cc_start: 0.9029 (mt) cc_final: 0.8826 (mp) REVERT: D 71 LYS cc_start: 0.7971 (mttt) cc_final: 0.7623 (mmtp) REVERT: D 106 TYR cc_start: 0.5761 (m-10) cc_final: 0.5329 (m-10) REVERT: E 18 ASN cc_start: 0.9208 (m110) cc_final: 0.8871 (m110) REVERT: E 21 TRP cc_start: 0.9254 (m100) cc_final: 0.8983 (m100) REVERT: E 59 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7188 (pt0) REVERT: E 64 LYS cc_start: 0.8772 (pttm) cc_final: 0.7954 (ptpp) REVERT: E 73 ASP cc_start: 0.7785 (t0) cc_final: 0.7358 (t0) REVERT: E 74 LEU cc_start: 0.7883 (mt) cc_final: 0.7649 (mt) REVERT: E 77 ASN cc_start: 0.7851 (m-40) cc_final: 0.7644 (m-40) REVERT: E 94 GLU cc_start: 0.8312 (tt0) cc_final: 0.8079 (tm-30) REVERT: E 100 LYS cc_start: 0.8673 (mttm) cc_final: 0.8335 (mttp) REVERT: E 101 GLU cc_start: 0.8525 (pm20) cc_final: 0.8118 (tm-30) REVERT: E 114 VAL cc_start: 0.9426 (p) cc_final: 0.9130 (m) REVERT: E 119 ILE cc_start: 0.8680 (mm) cc_final: 0.8410 (mm) REVERT: E 120 ASP cc_start: 0.8681 (m-30) cc_final: 0.8361 (m-30) REVERT: E 131 ASP cc_start: 0.8168 (m-30) cc_final: 0.7892 (m-30) REVERT: E 156 LEU cc_start: 0.9238 (tt) cc_final: 0.8972 (tp) REVERT: E 158 LEU cc_start: 0.9331 (mp) cc_final: 0.9023 (mp) REVERT: E 201 ASN cc_start: 0.8644 (m110) cc_final: 0.7702 (t0) REVERT: E 209 ASP cc_start: 0.8214 (t0) cc_final: 0.7574 (t0) REVERT: E 213 CYS cc_start: 0.8796 (t) cc_final: 0.8327 (t) REVERT: E 252 LEU cc_start: 0.9087 (mt) cc_final: 0.8823 (mt) REVERT: E 255 ASP cc_start: 0.8643 (t70) cc_final: 0.7935 (m-30) REVERT: E 257 ASN cc_start: 0.8759 (t0) cc_final: 0.8081 (t0) REVERT: E 270 HIS cc_start: 0.8338 (p-80) cc_final: 0.8065 (p-80) REVERT: E 295 ILE cc_start: 0.9098 (mt) cc_final: 0.8797 (tp) REVERT: E 308 LYS cc_start: 0.8580 (tptp) cc_final: 0.7835 (mmtp) REVERT: E 309 CYS cc_start: 0.8962 (m) cc_final: 0.8726 (p) REVERT: E 365 GLN cc_start: 0.9266 (tp40) cc_final: 0.9033 (tp40) REVERT: E 374 LYS cc_start: 0.8495 (tttm) cc_final: 0.7936 (tptp) REVERT: E 402 MET cc_start: 0.8946 (mmt) cc_final: 0.8183 (mmt) REVERT: E 415 GLU cc_start: 0.6830 (pt0) cc_final: 0.6475 (pt0) REVERT: F 18 ASN cc_start: 0.9094 (m110) cc_final: 0.8796 (m110) REVERT: F 21 TRP cc_start: 0.8863 (m100) cc_final: 0.8148 (m100) REVERT: F 30 ILE cc_start: 0.9205 (mt) cc_final: 0.8859 (mt) REVERT: F 59 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7621 (pt0) REVERT: F 82 VAL cc_start: 0.8654 (t) cc_final: 0.8400 (p) REVERT: F 131 ASP cc_start: 0.7605 (m-30) cc_final: 0.7199 (m-30) REVERT: F 149 THR cc_start: 0.9213 (m) cc_final: 0.8794 (p) REVERT: F 168 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8861 (mmmm) REVERT: F 219 ARG cc_start: 0.7123 (mtm110) cc_final: 0.6799 (tmm-80) REVERT: F 225 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7683 (mtt-85) REVERT: F 255 ASP cc_start: 0.8425 (t70) cc_final: 0.8057 (m-30) REVERT: F 256 LEU cc_start: 0.9378 (mt) cc_final: 0.8940 (mm) REVERT: F 260 GLN cc_start: 0.8492 (pt0) cc_final: 0.8247 (pm20) REVERT: F 268 ARG cc_start: 0.8497 (mmt90) cc_final: 0.7678 (mmm-85) REVERT: F 270 HIS cc_start: 0.8752 (p-80) cc_final: 0.8110 (p-80) REVERT: F 287 HIS cc_start: 0.7968 (m170) cc_final: 0.7543 (m170) REVERT: F 308 LYS cc_start: 0.8275 (tptp) cc_final: 0.8016 (mmtp) REVERT: F 330 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7793 (tpp-160) REVERT: F 344 THR cc_start: 0.9340 (t) cc_final: 0.9132 (p) REVERT: F 382 LEU cc_start: 0.9002 (mt) cc_final: 0.8799 (mp) REVERT: F 415 GLU cc_start: 0.6685 (pt0) cc_final: 0.6217 (pt0) REVERT: G 59 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6353 (pt0) REVERT: G 64 LYS cc_start: 0.8413 (pttm) cc_final: 0.7811 (ptpp) REVERT: G 67 PRO cc_start: 0.9549 (Cg_endo) cc_final: 0.9242 (Cg_exo) REVERT: G 73 ASP cc_start: 0.8751 (t0) cc_final: 0.8435 (t0) REVERT: G 82 VAL cc_start: 0.8913 (t) cc_final: 0.8684 (p) REVERT: G 90 LEU cc_start: 0.9238 (tp) cc_final: 0.8940 (tp) REVERT: G 116 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8538 (ptmt) REVERT: G 129 MET cc_start: 0.9299 (mmt) cc_final: 0.9024 (mmm) REVERT: G 133 CYS cc_start: 0.8559 (m) cc_final: 0.8344 (m) REVERT: G 140 LEU cc_start: 0.9065 (tp) cc_final: 0.8674 (tp) REVERT: G 143 HIS cc_start: 0.8513 (p90) cc_final: 0.8182 (p90) REVERT: G 159 GLU cc_start: 0.8452 (pt0) cc_final: 0.7892 (pt0) REVERT: G 209 ASP cc_start: 0.7854 (t0) cc_final: 0.7520 (t0) REVERT: G 215 ASP cc_start: 0.7825 (t0) cc_final: 0.7235 (m-30) REVERT: G 237 GLN cc_start: 0.8787 (mt0) cc_final: 0.8544 (mt0) REVERT: G 242 ILE cc_start: 0.9361 (mt) cc_final: 0.9160 (tp) REVERT: G 270 HIS cc_start: 0.8800 (p-80) cc_final: 0.8460 (p-80) REVERT: G 295 ILE cc_start: 0.9332 (mt) cc_final: 0.9000 (tp) REVERT: G 306 MET cc_start: 0.8415 (mmt) cc_final: 0.8213 (mmt) REVERT: G 343 ARG cc_start: 0.8580 (ptm160) cc_final: 0.7956 (mtt180) REVERT: G 365 GLN cc_start: 0.9063 (tp40) cc_final: 0.8624 (tp-100) REVERT: G 374 LYS cc_start: 0.8415 (tttm) cc_final: 0.8084 (tptp) REVERT: G 380 CYS cc_start: 0.9086 (t) cc_final: 0.8673 (t) REVERT: G 382 LEU cc_start: 0.9671 (mt) cc_final: 0.9288 (mp) REVERT: G 396 ASP cc_start: 0.9214 (t0) cc_final: 0.8264 (t0) REVERT: G 403 TYR cc_start: 0.8360 (t80) cc_final: 0.8096 (t80) REVERT: G 424 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7903 (pt0) REVERT: G 441 GLN cc_start: 0.9048 (mm110) cc_final: 0.8206 (tm-30) REVERT: H 15 GLN cc_start: 0.8741 (mt0) cc_final: 0.8341 (mt0) REVERT: H 21 TRP cc_start: 0.8684 (m100) cc_final: 0.8386 (m100) REVERT: H 70 ILE cc_start: 0.8389 (tp) cc_final: 0.7340 (mt) REVERT: H 73 ASP cc_start: 0.8608 (t0) cc_final: 0.8287 (t0) REVERT: H 79 ILE cc_start: 0.9199 (mm) cc_final: 0.8729 (tp) REVERT: H 94 GLU cc_start: 0.8389 (tt0) cc_final: 0.7924 (tm-30) REVERT: H 97 VAL cc_start: 0.9470 (p) cc_final: 0.9073 (m) REVERT: H 116 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8531 (ptpt) REVERT: H 137 GLN cc_start: 0.8546 (mt0) cc_final: 0.8123 (mm-40) REVERT: H 143 HIS cc_start: 0.8503 (p90) cc_final: 0.7878 (p90) REVERT: H 149 THR cc_start: 0.9129 (m) cc_final: 0.8754 (p) REVERT: H 206 PHE cc_start: 0.8876 (m-80) cc_final: 0.8515 (m-80) REVERT: H 243 THR cc_start: 0.9060 (p) cc_final: 0.8067 (p) REVERT: H 247 ARG cc_start: 0.7232 (mmt90) cc_final: 0.4981 (mmt90) REVERT: H 270 HIS cc_start: 0.8806 (p-80) cc_final: 0.7726 (p-80) REVERT: H 275 THR cc_start: 0.7145 (m) cc_final: 0.6711 (m) REVERT: H 287 HIS cc_start: 0.7643 (m170) cc_final: 0.6994 (m170) REVERT: H 308 LYS cc_start: 0.8878 (tptp) cc_final: 0.8459 (mmtp) REVERT: H 344 THR cc_start: 0.9285 (t) cc_final: 0.9076 (m) REVERT: H 353 THR cc_start: 0.9274 (m) cc_final: 0.8987 (p) REVERT: H 374 LYS cc_start: 0.9035 (tttm) cc_final: 0.8596 (ttmm) REVERT: H 382 LEU cc_start: 0.9552 (mt) cc_final: 0.9048 (mp) REVERT: H 396 ASP cc_start: 0.9127 (t0) cc_final: 0.8463 (t0) REVERT: H 415 GLU cc_start: 0.6336 (pt0) cc_final: 0.6049 (pt0) REVERT: H 424 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8050 (pt0) REVERT: H 441 GLN cc_start: 0.8891 (mm110) cc_final: 0.7754 (tm-30) REVERT: J 6 HIS cc_start: 0.8748 (t-90) cc_final: 0.8523 (t70) REVERT: J 51 PHE cc_start: 0.9146 (m-80) cc_final: 0.8866 (m-80) REVERT: J 53 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7702 (tm-30) REVERT: J 130 LEU cc_start: 0.9384 (mt) cc_final: 0.9077 (mp) REVERT: J 134 GLN cc_start: 0.8430 (mt0) cc_final: 0.7977 (mt0) REVERT: J 136 THR cc_start: 0.9065 (m) cc_final: 0.8861 (m) REVERT: J 150 LEU cc_start: 0.9504 (tt) cc_final: 0.9242 (tp) REVERT: J 167 PHE cc_start: 0.9194 (m-80) cc_final: 0.8994 (m-10) REVERT: J 181 GLU cc_start: 0.7564 (tt0) cc_final: 0.7104 (tt0) REVERT: J 190 HIS cc_start: 0.8695 (t70) cc_final: 0.8459 (t-90) REVERT: J 198 GLU cc_start: 0.8161 (pt0) cc_final: 0.7479 (tp30) REVERT: J 204 ASN cc_start: 0.8917 (m-40) cc_final: 0.8532 (p0) REVERT: J 233 MET cc_start: 0.9227 (mtm) cc_final: 0.8991 (mtm) REVERT: J 265 PHE cc_start: 0.7380 (p90) cc_final: 0.6462 (p90) REVERT: J 294 ASP cc_start: 0.8546 (m-30) cc_final: 0.8188 (m-30) REVERT: J 297 ASN cc_start: 0.8822 (m110) cc_final: 0.8591 (t0) REVERT: J 339 TYR cc_start: 0.8341 (m-80) cc_final: 0.8138 (m-80) REVERT: J 365 THR cc_start: 0.8280 (m) cc_final: 0.7835 (p) REVERT: B 53 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7362 (tm-30) REVERT: B 64 VAL cc_start: 0.9265 (t) cc_final: 0.9064 (t) REVERT: B 65 LEU cc_start: 0.9247 (mp) cc_final: 0.8653 (mp) REVERT: B 84 LEU cc_start: 0.9055 (mt) cc_final: 0.8709 (mt) REVERT: B 85 PHE cc_start: 0.8233 (m-80) cc_final: 0.7827 (m-80) REVERT: B 101 TRP cc_start: 0.9063 (t60) cc_final: 0.8690 (t60) REVERT: B 117 LEU cc_start: 0.9003 (mp) cc_final: 0.8645 (mp) REVERT: B 127 CYS cc_start: 0.8154 (t) cc_final: 0.5686 (t) REVERT: B 130 LEU cc_start: 0.9604 (mt) cc_final: 0.8723 (mp) REVERT: B 154 LYS cc_start: 0.8908 (mttt) cc_final: 0.8633 (mtmt) REVERT: B 181 GLU cc_start: 0.8003 (tt0) cc_final: 0.7297 (tt0) REVERT: B 186 THR cc_start: 0.9171 (m) cc_final: 0.8838 (p) REVERT: B 221 SER cc_start: 0.9097 (t) cc_final: 0.8744 (p) REVERT: B 233 MET cc_start: 0.9443 (mtm) cc_final: 0.9149 (mtm) REVERT: B 247 ASN cc_start: 0.7155 (m110) cc_final: 0.6903 (m-40) REVERT: B 315 LEU cc_start: 0.9253 (mt) cc_final: 0.8813 (mt) REVERT: B 319 LYS cc_start: 0.8909 (tppt) cc_final: 0.8611 (tptm) REVERT: B 352 VAL cc_start: 0.9115 (t) cc_final: 0.8039 (t) REVERT: B 358 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7632 (pttm) REVERT: B 372 SER cc_start: 0.9035 (p) cc_final: 0.8480 (m) REVERT: B 405 MET cc_start: 0.7837 (ttm) cc_final: 0.7213 (tmm) REVERT: B 408 THR cc_start: 0.8701 (p) cc_final: 0.8348 (p) REVERT: C 1 MET cc_start: 0.8175 (mmp) cc_final: 0.7737 (mmm) REVERT: C 6 HIS cc_start: 0.8986 (t-90) cc_final: 0.8346 (t70) REVERT: C 30 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7510 (tp) REVERT: C 35 ILE cc_start: 0.8592 (tt) cc_final: 0.8335 (tp) REVERT: C 53 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6825 (tm-30) REVERT: C 65 LEU cc_start: 0.8970 (mp) cc_final: 0.8532 (mp) REVERT: C 101 TRP cc_start: 0.8898 (t60) cc_final: 0.8383 (t60) REVERT: C 154 LYS cc_start: 0.8711 (mttt) cc_final: 0.8485 (mtmt) REVERT: C 177 ASP cc_start: 0.7369 (t0) cc_final: 0.7100 (t0) REVERT: C 186 THR cc_start: 0.9399 (m) cc_final: 0.9087 (p) REVERT: C 187 LEU cc_start: 0.9362 (mm) cc_final: 0.8836 (mm) REVERT: C 233 MET cc_start: 0.9379 (mtm) cc_final: 0.8891 (mtm) REVERT: C 315 LEU cc_start: 0.9149 (mt) cc_final: 0.8538 (mt) REVERT: C 339 TYR cc_start: 0.8474 (m-80) cc_final: 0.8118 (m-80) REVERT: C 343 TRP cc_start: 0.6605 (m100) cc_final: 0.6322 (m100) outliers start: 20 outliers final: 3 residues processed: 1459 average time/residue: 0.2063 time to fit residues: 465.8935 Evaluate side-chains 948 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 944 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 195 ASN A 306 HIS D 53 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 89 GLN D 91 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 210 ASN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 201 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 GLN G 8 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 201 ASN ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 HIS ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN H 210 ASN H 304 ASN J 6 HIS J 14 ASN J 99 ASN J 131 GLN J 195 ASN J 328 GLN J 415 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 6 HIS C 14 ASN C 131 GLN C 195 ASN ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 328 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.120880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105030 restraints weight = 58777.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108633 restraints weight = 33785.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111073 restraints weight = 21431.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112820 restraints weight = 14600.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114025 restraints weight = 10521.882| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 28752 Z= 0.175 Angle : 0.722 9.027 39006 Z= 0.378 Chirality : 0.050 0.216 4200 Planarity : 0.007 0.084 5117 Dihedral : 10.691 155.782 3979 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.53 % Allowed : 3.76 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.12 (0.12), residues: 3543 helix: -2.32 (0.11), residues: 1450 sheet: -0.58 (0.23), residues: 488 loop : -2.21 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 315 TYR 0.022 0.002 TYR E 165 PHE 0.022 0.002 PHE A 242 TRP 0.030 0.003 TRP F 411 HIS 0.006 0.001 HIS C 263 Details of bonding type rmsd covalent geometry : bond 0.00376 (28752) covalent geometry : angle 0.72180 (39006) hydrogen bonds : bond 0.05481 ( 951) hydrogen bonds : angle 6.53646 ( 2754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1192 time to evaluate : 1.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.8899 (t-90) cc_final: 0.8215 (t-170) REVERT: A 88 ASP cc_start: 0.8603 (m-30) cc_final: 0.8350 (p0) REVERT: A 89 ASN cc_start: 0.8827 (m-40) cc_final: 0.8138 (m-40) REVERT: A 136 THR cc_start: 0.8695 (m) cc_final: 0.8407 (t) REVERT: A 162 ARG cc_start: 0.8469 (mmt-90) cc_final: 0.7838 (mmt-90) REVERT: A 164 MET cc_start: 0.7985 (mmp) cc_final: 0.6779 (mmp) REVERT: A 169 VAL cc_start: 0.9150 (m) cc_final: 0.8816 (p) REVERT: A 202 ILE cc_start: 0.8978 (mm) cc_final: 0.8752 (mm) REVERT: A 257 MET cc_start: 0.8219 (mmp) cc_final: 0.8001 (mmp) REVERT: A 280 PHE cc_start: 0.7527 (m-10) cc_final: 0.7315 (m-10) REVERT: A 292 MET cc_start: 0.7699 (mtm) cc_final: 0.7456 (mtp) REVERT: A 330 ARG cc_start: 0.9102 (mtm180) cc_final: 0.8793 (mtp85) REVERT: A 340 PHE cc_start: 0.7226 (m-80) cc_final: 0.6845 (m-80) REVERT: A 352 VAL cc_start: 0.8761 (m) cc_final: 0.8362 (m) REVERT: A 372 SER cc_start: 0.9266 (p) cc_final: 0.9003 (m) REVERT: D 32 MET cc_start: 0.7819 (mmm) cc_final: 0.7415 (mmm) REVERT: D 71 LYS cc_start: 0.7967 (mttt) cc_final: 0.7685 (mmtp) REVERT: D 106 TYR cc_start: 0.6474 (m-10) cc_final: 0.6219 (m-10) REVERT: E 21 TRP cc_start: 0.9067 (m100) cc_final: 0.8525 (m100) REVERT: E 59 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6394 (pt0) REVERT: E 64 LYS cc_start: 0.8605 (pttm) cc_final: 0.7723 (ptpp) REVERT: E 65 PHE cc_start: 0.7355 (p90) cc_final: 0.6506 (p90) REVERT: E 73 ASP cc_start: 0.7741 (t0) cc_final: 0.7329 (t0) REVERT: E 80 ASP cc_start: 0.8226 (m-30) cc_final: 0.7882 (m-30) REVERT: E 156 LEU cc_start: 0.9552 (tt) cc_final: 0.9004 (tp) REVERT: E 158 LEU cc_start: 0.9049 (mp) cc_final: 0.8644 (mp) REVERT: E 192 VAL cc_start: 0.8924 (p) cc_final: 0.8656 (m) REVERT: E 201 ASN cc_start: 0.8006 (m-40) cc_final: 0.7398 (t0) REVERT: E 213 CYS cc_start: 0.8177 (t) cc_final: 0.7840 (t) REVERT: E 237 GLN cc_start: 0.8531 (mt0) cc_final: 0.8169 (mt0) REVERT: E 243 THR cc_start: 0.8747 (p) cc_final: 0.8538 (p) REVERT: E 255 ASP cc_start: 0.8748 (t70) cc_final: 0.8098 (t70) REVERT: E 256 LEU cc_start: 0.9200 (mt) cc_final: 0.8819 (mt) REVERT: E 270 HIS cc_start: 0.8609 (p-80) cc_final: 0.8345 (p-80) REVERT: E 308 LYS cc_start: 0.8422 (tptp) cc_final: 0.7859 (mmtp) REVERT: E 377 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8060 (mtm180) REVERT: E 381 MET cc_start: 0.8707 (ttt) cc_final: 0.8225 (ttp) REVERT: E 402 MET cc_start: 0.9248 (mmt) cc_final: 0.8445 (mmt) REVERT: E 406 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7984 (mtp85) REVERT: E 415 GLU cc_start: 0.6815 (pt0) cc_final: 0.6534 (pt0) REVERT: F 18 ASN cc_start: 0.8999 (m110) cc_final: 0.8715 (m110) REVERT: F 21 TRP cc_start: 0.8811 (m100) cc_final: 0.8026 (m100) REVERT: F 24 TYR cc_start: 0.8901 (m-10) cc_final: 0.8130 (m-10) REVERT: F 30 ILE cc_start: 0.9266 (mt) cc_final: 0.8887 (mt) REVERT: F 59 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7208 (pt0) REVERT: F 65 PHE cc_start: 0.7470 (p90) cc_final: 0.6155 (p90) REVERT: F 73 ASP cc_start: 0.8229 (t0) cc_final: 0.7946 (t0) REVERT: F 94 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7569 (tp30) REVERT: F 131 ASP cc_start: 0.7611 (m-30) cc_final: 0.7299 (m-30) REVERT: F 153 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8535 (tt) REVERT: F 196 HIS cc_start: 0.8261 (m-70) cc_final: 0.6798 (t70) REVERT: F 204 CYS cc_start: 0.8600 (t) cc_final: 0.8389 (t) REVERT: F 225 ARG cc_start: 0.7839 (ptp90) cc_final: 0.7169 (mtt-85) REVERT: F 243 THR cc_start: 0.8874 (p) cc_final: 0.8581 (p) REVERT: F 256 LEU cc_start: 0.9459 (mt) cc_final: 0.8933 (mt) REVERT: F 270 HIS cc_start: 0.8832 (p-80) cc_final: 0.8101 (p-80) REVERT: F 276 TYR cc_start: 0.8783 (t80) cc_final: 0.8546 (t80) REVERT: F 441 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8075 (tm-30) REVERT: G 59 GLU cc_start: 0.6382 (mt-10) cc_final: 0.5373 (pt0) REVERT: G 64 LYS cc_start: 0.8403 (pttm) cc_final: 0.7923 (ptpp) REVERT: G 65 PHE cc_start: 0.7313 (p90) cc_final: 0.6088 (p90) REVERT: G 94 GLU cc_start: 0.8208 (tt0) cc_final: 0.7621 (tp30) REVERT: G 97 VAL cc_start: 0.9481 (p) cc_final: 0.9277 (m) REVERT: G 133 CYS cc_start: 0.8953 (m) cc_final: 0.8556 (m) REVERT: G 159 GLU cc_start: 0.8479 (pt0) cc_final: 0.8154 (pt0) REVERT: G 215 ASP cc_start: 0.8313 (t0) cc_final: 0.8103 (m-30) REVERT: G 237 GLN cc_start: 0.8979 (mt0) cc_final: 0.8771 (tt0) REVERT: G 270 HIS cc_start: 0.8681 (p-80) cc_final: 0.8430 (p-80) REVERT: G 301 GLU cc_start: 0.8904 (tt0) cc_final: 0.7998 (tt0) REVERT: G 306 MET cc_start: 0.8450 (mmt) cc_final: 0.8148 (mmt) REVERT: G 351 CYS cc_start: 0.8458 (t) cc_final: 0.8014 (t) REVERT: G 374 LYS cc_start: 0.8561 (tttm) cc_final: 0.8206 (tmtt) REVERT: G 381 MET cc_start: 0.9095 (tmm) cc_final: 0.8646 (tmm) REVERT: G 382 LEU cc_start: 0.9384 (mt) cc_final: 0.9155 (mp) REVERT: G 408 PHE cc_start: 0.6806 (m-10) cc_final: 0.6100 (m-10) REVERT: G 424 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8409 (pt0) REVERT: G 441 GLN cc_start: 0.9003 (mm110) cc_final: 0.8308 (tm-30) REVERT: H 77 ASN cc_start: 0.8229 (t0) cc_final: 0.7721 (t0) REVERT: H 80 ASP cc_start: 0.8717 (m-30) cc_final: 0.8502 (p0) REVERT: H 94 GLU cc_start: 0.8116 (tt0) cc_final: 0.7602 (tp30) REVERT: H 109 ARG cc_start: 0.5942 (ptp90) cc_final: 0.5556 (ptp-110) REVERT: H 137 GLN cc_start: 0.8440 (mt0) cc_final: 0.7917 (mm-40) REVERT: H 142 PHE cc_start: 0.8262 (m-80) cc_final: 0.8043 (m-10) REVERT: H 167 LYS cc_start: 0.8889 (ptmt) cc_final: 0.8489 (mmtp) REVERT: H 192 VAL cc_start: 0.9230 (p) cc_final: 0.9016 (m) REVERT: H 196 HIS cc_start: 0.7996 (m-70) cc_final: 0.7773 (m-70) REVERT: H 206 PHE cc_start: 0.8739 (m-80) cc_final: 0.8479 (m-80) REVERT: H 211 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7811 (tm-30) REVERT: H 237 GLN cc_start: 0.8994 (mt0) cc_final: 0.8484 (mt0) REVERT: H 247 ARG cc_start: 0.7206 (mmt90) cc_final: 0.4910 (mmt90) REVERT: H 268 ARG cc_start: 0.8739 (mmt90) cc_final: 0.8382 (mmm-85) REVERT: H 270 HIS cc_start: 0.8717 (p-80) cc_final: 0.7700 (p-80) REVERT: H 287 HIS cc_start: 0.7627 (m170) cc_final: 0.7360 (m170) REVERT: H 304 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8440 (t0) REVERT: H 317 MET cc_start: 0.7165 (mmm) cc_final: 0.6630 (tpt) REVERT: H 343 ARG cc_start: 0.8192 (ptt180) cc_final: 0.7760 (mtt180) REVERT: H 374 LYS cc_start: 0.9026 (tttm) cc_final: 0.8544 (tmtt) REVERT: H 399 PHE cc_start: 0.8566 (t80) cc_final: 0.8226 (t80) REVERT: H 402 MET cc_start: 0.8600 (mmp) cc_final: 0.8384 (mmp) REVERT: H 424 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8346 (pt0) REVERT: H 441 GLN cc_start: 0.8758 (mm110) cc_final: 0.7808 (tm-30) REVERT: J 14 ASN cc_start: 0.9207 (m110) cc_final: 0.8851 (m-40) REVERT: J 21 TRP cc_start: 0.9136 (m100) cc_final: 0.8802 (m100) REVERT: J 31 ASP cc_start: 0.7925 (p0) cc_final: 0.7517 (p0) REVERT: J 50 TYR cc_start: 0.8116 (m-10) cc_final: 0.7749 (m-10) REVERT: J 51 PHE cc_start: 0.8922 (m-80) cc_final: 0.8248 (m-80) REVERT: J 53 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7666 (tm-30) REVERT: J 67 ASP cc_start: 0.8278 (t0) cc_final: 0.7861 (p0) REVERT: J 134 GLN cc_start: 0.8629 (mt0) cc_final: 0.8084 (mt0) REVERT: J 147 MET cc_start: 0.7613 (tmm) cc_final: 0.7365 (tmm) REVERT: J 164 MET cc_start: 0.8117 (mmp) cc_final: 0.7847 (mmm) REVERT: J 222 TYR cc_start: 0.8800 (m-10) cc_final: 0.8443 (m-80) REVERT: J 257 MET cc_start: 0.8298 (mmp) cc_final: 0.8092 (mmp) REVERT: J 297 ASN cc_start: 0.8990 (m110) cc_final: 0.8774 (t0) REVERT: J 330 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8735 (mmm160) REVERT: J 343 TRP cc_start: 0.8065 (m100) cc_final: 0.7733 (m100) REVERT: J 394 LEU cc_start: 0.8829 (tp) cc_final: 0.8511 (tt) REVERT: J 405 MET cc_start: 0.8445 (tpp) cc_final: 0.8226 (tpp) REVERT: J 406 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8364 (mt-10) REVERT: B 6 HIS cc_start: 0.8900 (t70) cc_final: 0.8621 (t-170) REVERT: B 20 PHE cc_start: 0.8415 (t80) cc_final: 0.8051 (t80) REVERT: B 53 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7196 (tm-30) REVERT: B 62 ARG cc_start: 0.9135 (mtt180) cc_final: 0.8739 (mtm-85) REVERT: B 83 ASN cc_start: 0.8452 (m-40) cc_final: 0.8203 (m110) REVERT: B 84 LEU cc_start: 0.8799 (mt) cc_final: 0.8218 (mt) REVERT: B 85 PHE cc_start: 0.7763 (m-80) cc_final: 0.7202 (m-80) REVERT: B 101 TRP cc_start: 0.8690 (t60) cc_final: 0.8430 (t60) REVERT: B 103 LYS cc_start: 0.8642 (tttp) cc_final: 0.8254 (tttp) REVERT: B 164 MET cc_start: 0.7711 (mmp) cc_final: 0.6603 (mmp) REVERT: B 181 GLU cc_start: 0.7814 (tt0) cc_final: 0.7551 (tt0) REVERT: B 221 SER cc_start: 0.9182 (t) cc_final: 0.8542 (p) REVERT: B 222 TYR cc_start: 0.8580 (m-10) cc_final: 0.8364 (m-80) REVERT: B 245 GLU cc_start: 0.7644 (mp0) cc_final: 0.7431 (mp0) REVERT: B 336 ASN cc_start: 0.8280 (m110) cc_final: 0.8044 (m110) REVERT: B 358 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7781 (pttm) REVERT: B 372 SER cc_start: 0.8801 (p) cc_final: 0.8432 (m) REVERT: B 376 ILE cc_start: 0.8828 (mm) cc_final: 0.8575 (mm) REVERT: B 394 LEU cc_start: 0.8529 (tt) cc_final: 0.8295 (tp) REVERT: B 414 MET cc_start: 0.8017 (ttt) cc_final: 0.7188 (tpp) REVERT: C 2 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6604 (mtp85) REVERT: C 6 HIS cc_start: 0.8824 (t70) cc_final: 0.8254 (t70) REVERT: C 53 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6708 (tm-30) REVERT: C 101 TRP cc_start: 0.8989 (t60) cc_final: 0.8120 (t60) REVERT: C 174 LYS cc_start: 0.8913 (mppt) cc_final: 0.8697 (mppt) REVERT: C 233 MET cc_start: 0.9345 (mtm) cc_final: 0.8936 (ttp) REVERT: C 280 PHE cc_start: 0.7851 (m-10) cc_final: 0.7639 (m-80) REVERT: C 335 LYS cc_start: 0.8019 (mttp) cc_final: 0.7554 (ptpp) REVERT: C 339 TYR cc_start: 0.8487 (m-80) cc_final: 0.8223 (m-80) REVERT: C 406 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8486 (mt-10) REVERT: C 412 SER cc_start: 0.9256 (m) cc_final: 0.8963 (p) REVERT: C 414 MET cc_start: 0.8479 (ttt) cc_final: 0.7810 (tpp) REVERT: C 415 ASN cc_start: 0.8331 (m110) cc_final: 0.8052 (t0) REVERT: C 420 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7619 (mm-30) outliers start: 16 outliers final: 1 residues processed: 1199 average time/residue: 0.1936 time to fit residues: 364.7390 Evaluate side-chains 947 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 944 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 235 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN A 297 ASN A 422 GLN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 95 GLN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 GLN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN C 195 ASN ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 297 ASN C 422 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.105096 restraints weight = 58609.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108545 restraints weight = 34185.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.110867 restraints weight = 21969.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112589 restraints weight = 15124.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113760 restraints weight = 10965.379| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28752 Z= 0.140 Angle : 0.658 9.289 39006 Z= 0.335 Chirality : 0.048 0.230 4200 Planarity : 0.006 0.080 5117 Dihedral : 9.910 159.153 3979 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.17 % Allowed : 3.69 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % 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: -2.46 (0.13), residues: 3543 helix: -1.52 (0.12), residues: 1448 sheet: -0.42 (0.23), residues: 488 loop : -2.06 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 46 TYR 0.014 0.001 TYR E 24 PHE 0.021 0.002 PHE A 167 TRP 0.024 0.002 TRP E 350 HIS 0.011 0.001 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00309 (28752) covalent geometry : angle 0.65836 (39006) hydrogen bonds : bond 0.04464 ( 951) hydrogen bonds : angle 5.69070 ( 2754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1136 time to evaluate : 1.112 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.8640 (t-90) cc_final: 0.8232 (t-170) REVERT: A 14 ASN cc_start: 0.9142 (m-40) cc_final: 0.8902 (m-40) REVERT: A 89 ASN cc_start: 0.8909 (m-40) cc_final: 0.8199 (m110) REVERT: A 130 LEU cc_start: 0.9352 (mt) cc_final: 0.9126 (tt) REVERT: A 134 GLN cc_start: 0.8010 (mt0) cc_final: 0.7284 (mt0) REVERT: A 136 THR cc_start: 0.8699 (m) cc_final: 0.8472 (t) REVERT: A 164 MET cc_start: 0.8057 (mmp) cc_final: 0.6743 (mmp) REVERT: A 166 THR cc_start: 0.8723 (t) cc_final: 0.8410 (p) REVERT: A 169 VAL cc_start: 0.9101 (m) cc_final: 0.8881 (t) REVERT: A 196 SER cc_start: 0.9569 (t) cc_final: 0.9017 (p) REVERT: A 197 ASP cc_start: 0.8442 (t70) cc_final: 0.8062 (t0) REVERT: A 202 ILE cc_start: 0.8982 (mm) cc_final: 0.8746 (mm) REVERT: A 292 MET cc_start: 0.7562 (mtm) cc_final: 0.7358 (mtp) REVERT: A 330 ARG cc_start: 0.9022 (mtm180) cc_final: 0.8694 (mtp85) REVERT: A 340 PHE cc_start: 0.7432 (m-80) cc_final: 0.7090 (m-10) REVERT: A 365 THR cc_start: 0.8686 (m) cc_final: 0.8448 (p) REVERT: A 372 SER cc_start: 0.9380 (p) cc_final: 0.8992 (m) REVERT: A 380 LEU cc_start: 0.9386 (mm) cc_final: 0.8962 (tt) REVERT: A 405 MET cc_start: 0.7991 (mmt) cc_final: 0.7608 (tpp) REVERT: A 408 THR cc_start: 0.8569 (p) cc_final: 0.8297 (p) REVERT: D 41 GLN cc_start: 0.8227 (tp40) cc_final: 0.8018 (tp40) REVERT: D 47 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8480 (mtpt) REVERT: D 66 GLN cc_start: 0.7918 (mp10) cc_final: 0.7669 (mp10) REVERT: D 71 LYS cc_start: 0.7785 (mttt) cc_final: 0.7549 (mmtp) REVERT: D 106 TYR cc_start: 0.6692 (m-10) cc_final: 0.6351 (m-10) REVERT: E 18 ASN cc_start: 0.9267 (m110) cc_final: 0.9041 (m110) REVERT: E 21 TRP cc_start: 0.8846 (m100) cc_final: 0.8533 (m100) REVERT: E 59 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6285 (pt0) REVERT: E 64 LYS cc_start: 0.8753 (pttm) cc_final: 0.8230 (ptpp) REVERT: E 65 PHE cc_start: 0.7327 (p90) cc_final: 0.5820 (p90) REVERT: E 69 SER cc_start: 0.8663 (p) cc_final: 0.8364 (p) REVERT: E 94 GLU cc_start: 0.6871 (pp20) cc_final: 0.6517 (tm-30) REVERT: E 116 LYS cc_start: 0.8936 (tmmt) cc_final: 0.8535 (ttpt) REVERT: E 118 MET cc_start: 0.8664 (mmm) cc_final: 0.8320 (mmm) REVERT: E 131 ASP cc_start: 0.8081 (m-30) cc_final: 0.7771 (m-30) REVERT: E 201 ASN cc_start: 0.7962 (m-40) cc_final: 0.7568 (m-40) REVERT: E 213 CYS cc_start: 0.8302 (t) cc_final: 0.8057 (t) REVERT: E 237 GLN cc_start: 0.8745 (mt0) cc_final: 0.8528 (mt0) REVERT: E 255 ASP cc_start: 0.8361 (t70) cc_final: 0.8030 (m-30) REVERT: E 270 HIS cc_start: 0.8525 (p-80) cc_final: 0.8232 (p-80) REVERT: E 344 THR cc_start: 0.8916 (t) cc_final: 0.8422 (p) REVERT: E 377 ARG cc_start: 0.8515 (mtm180) cc_final: 0.7995 (mtm180) REVERT: E 381 MET cc_start: 0.8859 (ttt) cc_final: 0.8436 (ttp) REVERT: E 399 PHE cc_start: 0.8032 (t80) cc_final: 0.7812 (t80) REVERT: E 402 MET cc_start: 0.9305 (mmt) cc_final: 0.8573 (mmt) REVERT: E 415 GLU cc_start: 0.7320 (pt0) cc_final: 0.6840 (pt0) REVERT: E 441 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 14 VAL cc_start: 0.9530 (t) cc_final: 0.9305 (t) REVERT: F 16 ILE cc_start: 0.9247 (mm) cc_final: 0.8914 (mm) REVERT: F 21 TRP cc_start: 0.8711 (m100) cc_final: 0.7874 (m100) REVERT: F 24 TYR cc_start: 0.8863 (m-10) cc_final: 0.8097 (m-10) REVERT: F 27 GLU cc_start: 0.8574 (tt0) cc_final: 0.8258 (tt0) REVERT: F 30 ILE cc_start: 0.9279 (mt) cc_final: 0.9049 (mm) REVERT: F 56 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.6117 (m-10) REVERT: F 59 GLU cc_start: 0.7771 (mt-10) cc_final: 0.6846 (pt0) REVERT: F 65 PHE cc_start: 0.7876 (p90) cc_final: 0.6318 (p90) REVERT: F 79 ILE cc_start: 0.9231 (mm) cc_final: 0.8954 (tp) REVERT: F 81 GLN cc_start: 0.7796 (mt0) cc_final: 0.7510 (mt0) REVERT: F 94 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7557 (tm-30) REVERT: F 131 ASP cc_start: 0.7738 (m-30) cc_final: 0.7491 (m-30) REVERT: F 225 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7359 (mtt-85) REVERT: F 237 GLN cc_start: 0.8859 (mt0) cc_final: 0.8129 (tt0) REVERT: F 247 ARG cc_start: 0.6558 (mmt90) cc_final: 0.4812 (mmt90) REVERT: F 270 HIS cc_start: 0.8628 (p-80) cc_final: 0.7659 (p-80) REVERT: F 274 VAL cc_start: 0.9329 (t) cc_final: 0.9116 (t) REVERT: F 275 THR cc_start: 0.7824 (m) cc_final: 0.6199 (m) REVERT: F 276 TYR cc_start: 0.8449 (t80) cc_final: 0.7596 (t80) REVERT: F 301 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8008 (mt-10) REVERT: G 23 LEU cc_start: 0.9131 (tp) cc_final: 0.8423 (tp) REVERT: G 27 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7634 (mt-10) REVERT: G 59 GLU cc_start: 0.6570 (mt-10) cc_final: 0.5765 (pt0) REVERT: G 90 LEU cc_start: 0.9223 (tp) cc_final: 0.8955 (tp) REVERT: G 94 GLU cc_start: 0.8026 (tt0) cc_final: 0.7786 (tm-30) REVERT: G 96 MET cc_start: 0.7470 (tmm) cc_final: 0.6877 (tmm) REVERT: G 125 ARG cc_start: 0.8613 (mtt90) cc_final: 0.6982 (mtt90) REVERT: G 206 PHE cc_start: 0.9285 (m-80) cc_final: 0.8815 (m-80) REVERT: G 211 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8361 (mm-30) REVERT: G 220 ASN cc_start: 0.9289 (m-40) cc_final: 0.8962 (m110) REVERT: G 237 GLN cc_start: 0.8990 (mt0) cc_final: 0.8723 (tt0) REVERT: G 241 SER cc_start: 0.9437 (m) cc_final: 0.9034 (p) REVERT: G 270 HIS cc_start: 0.8804 (p-80) cc_final: 0.8397 (p-80) REVERT: G 305 GLN cc_start: 0.9040 (mp-120) cc_final: 0.8648 (mm-40) REVERT: G 306 MET cc_start: 0.8317 (mmt) cc_final: 0.8038 (mmt) REVERT: G 308 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8542 (mmtt) REVERT: G 351 CYS cc_start: 0.8455 (t) cc_final: 0.7894 (t) REVERT: G 374 LYS cc_start: 0.8680 (tttm) cc_final: 0.8339 (tptp) REVERT: G 381 MET cc_start: 0.9037 (tmm) cc_final: 0.8673 (tmm) REVERT: G 424 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8435 (pt0) REVERT: G 441 GLN cc_start: 0.8755 (mm110) cc_final: 0.8398 (tm-30) REVERT: H 15 GLN cc_start: 0.8556 (mt0) cc_final: 0.8247 (mt0) REVERT: H 20 CYS cc_start: 0.8742 (m) cc_final: 0.8481 (m) REVERT: H 94 GLU cc_start: 0.8052 (tt0) cc_final: 0.7723 (tp30) REVERT: H 131 ASP cc_start: 0.8287 (m-30) cc_final: 0.8062 (m-30) REVERT: H 137 GLN cc_start: 0.8282 (mt0) cc_final: 0.7760 (mm-40) REVERT: H 142 PHE cc_start: 0.8228 (m-80) cc_final: 0.8012 (m-10) REVERT: H 143 HIS cc_start: 0.8873 (p90) cc_final: 0.8571 (p90) REVERT: H 171 LEU cc_start: 0.7355 (mt) cc_final: 0.5505 (mt) REVERT: H 196 HIS cc_start: 0.7669 (m-70) cc_final: 0.7374 (m-70) REVERT: H 215 ASP cc_start: 0.7691 (m-30) cc_final: 0.7130 (m-30) REVERT: H 247 ARG cc_start: 0.6929 (mmt90) cc_final: 0.4833 (mmt90) REVERT: H 270 HIS cc_start: 0.8663 (p-80) cc_final: 0.8335 (p-80) REVERT: H 276 TYR cc_start: 0.8286 (t80) cc_final: 0.7700 (t80) REVERT: H 287 HIS cc_start: 0.7510 (m170) cc_final: 0.7142 (m170) REVERT: H 308 LYS cc_start: 0.8682 (tptp) cc_final: 0.8425 (mttt) REVERT: H 343 ARG cc_start: 0.8359 (ptt180) cc_final: 0.7924 (mtt180) REVERT: H 402 MET cc_start: 0.8844 (mmp) cc_final: 0.8420 (mmp) REVERT: H 415 GLU cc_start: 0.6035 (pt0) cc_final: 0.5539 (pt0) REVERT: H 441 GLN cc_start: 0.8625 (mm110) cc_final: 0.7985 (tm-30) REVERT: J 6 HIS cc_start: 0.9049 (t-170) cc_final: 0.8618 (t-170) REVERT: J 21 TRP cc_start: 0.9028 (m100) cc_final: 0.8556 (m100) REVERT: J 31 ASP cc_start: 0.7616 (p0) cc_final: 0.7267 (p0) REVERT: J 53 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7581 (tm-30) REVERT: J 83 ASN cc_start: 0.8897 (m-40) cc_final: 0.8505 (m-40) REVERT: J 84 LEU cc_start: 0.9221 (mt) cc_final: 0.8840 (mt) REVERT: J 92 TYR cc_start: 0.8312 (p90) cc_final: 0.8051 (p90) REVERT: J 101 TRP cc_start: 0.9109 (t60) cc_final: 0.8810 (t60) REVERT: J 130 LEU cc_start: 0.9100 (mt) cc_final: 0.8534 (mp) REVERT: J 147 MET cc_start: 0.8842 (tmm) cc_final: 0.8472 (tmm) REVERT: J 149 THR cc_start: 0.9207 (p) cc_final: 0.8970 (p) REVERT: J 162 ARG cc_start: 0.7894 (mmt-90) cc_final: 0.7001 (mmt180) REVERT: J 164 MET cc_start: 0.7921 (mmp) cc_final: 0.6467 (mmp) REVERT: J 174 LYS cc_start: 0.9081 (mppt) cc_final: 0.8520 (mttp) REVERT: J 189 MET cc_start: 0.8548 (mmt) cc_final: 0.8056 (mmp) REVERT: J 233 MET cc_start: 0.9050 (mtm) cc_final: 0.8727 (ttp) REVERT: J 297 ASN cc_start: 0.8986 (m110) cc_final: 0.8783 (t0) REVERT: J 322 MET cc_start: 0.8822 (mmm) cc_final: 0.8366 (mmp) REVERT: J 326 ASP cc_start: 0.8959 (m-30) cc_final: 0.8645 (m-30) REVERT: J 405 MET cc_start: 0.8504 (tpp) cc_final: 0.7889 (tpp) REVERT: J 408 THR cc_start: 0.9183 (p) cc_final: 0.8958 (p) REVERT: J 415 ASN cc_start: 0.8577 (m-40) cc_final: 0.8075 (t0) REVERT: B 6 HIS cc_start: 0.8824 (t70) cc_final: 0.8435 (t-170) REVERT: B 14 ASN cc_start: 0.8849 (m-40) cc_final: 0.8374 (m-40) REVERT: B 20 PHE cc_start: 0.8158 (t80) cc_final: 0.7867 (t80) REVERT: B 49 VAL cc_start: 0.9080 (m) cc_final: 0.8843 (m) REVERT: B 50 TYR cc_start: 0.8210 (m-80) cc_final: 0.7597 (m-10) REVERT: B 62 ARG cc_start: 0.8958 (mtt180) cc_final: 0.8589 (mtm-85) REVERT: B 80 LYS cc_start: 0.9102 (ptmm) cc_final: 0.8863 (ptmm) REVERT: B 85 PHE cc_start: 0.7827 (m-80) cc_final: 0.7385 (m-10) REVERT: B 88 ASP cc_start: 0.8730 (m-30) cc_final: 0.8513 (p0) REVERT: B 103 LYS cc_start: 0.8690 (tttp) cc_final: 0.8117 (tttm) REVERT: B 135 LEU cc_start: 0.9300 (mp) cc_final: 0.8845 (mp) REVERT: B 164 MET cc_start: 0.7316 (mmp) cc_final: 0.6537 (mmp) REVERT: B 166 THR cc_start: 0.8758 (t) cc_final: 0.8375 (p) REVERT: B 181 GLU cc_start: 0.7864 (tt0) cc_final: 0.7606 (tt0) REVERT: B 189 MET cc_start: 0.8515 (tpt) cc_final: 0.7998 (tpt) REVERT: B 193 VAL cc_start: 0.8625 (t) cc_final: 0.7028 (t) REVERT: B 221 SER cc_start: 0.9308 (t) cc_final: 0.8485 (p) REVERT: B 245 GLU cc_start: 0.7708 (mp0) cc_final: 0.7363 (mp0) REVERT: B 247 ASN cc_start: 0.5103 (m110) cc_final: 0.4561 (m110) REVERT: B 358 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7889 (pttm) REVERT: B 372 SER cc_start: 0.8932 (p) cc_final: 0.8562 (m) REVERT: B 395 HIS cc_start: 0.8826 (p-80) cc_final: 0.8188 (p-80) REVERT: B 405 MET cc_start: 0.8008 (ttm) cc_final: 0.7605 (tpt) REVERT: B 412 SER cc_start: 0.9430 (m) cc_final: 0.9207 (t) REVERT: C 6 HIS cc_start: 0.9000 (t70) cc_final: 0.7628 (t-170) REVERT: C 8 GLN cc_start: 0.7321 (mt0) cc_final: 0.6745 (mt0) REVERT: C 30 LEU cc_start: 0.8631 (tp) cc_final: 0.8307 (tp) REVERT: C 50 TYR cc_start: 0.8436 (m-80) cc_final: 0.7807 (m-10) REVERT: C 53 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6807 (tm-30) REVERT: C 62 ARG cc_start: 0.8794 (mtt180) cc_final: 0.8112 (mtt90) REVERT: C 147 MET cc_start: 0.8417 (ppp) cc_final: 0.8151 (ppp) REVERT: C 233 MET cc_start: 0.9247 (mtm) cc_final: 0.8994 (ttp) REVERT: C 352 VAL cc_start: 0.8713 (m) cc_final: 0.8401 (m) REVERT: C 412 SER cc_start: 0.9347 (m) cc_final: 0.9135 (p) REVERT: C 420 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7677 (mm-30) outliers start: 5 outliers final: 0 residues processed: 1137 average time/residue: 0.1853 time to fit residues: 336.8132 Evaluate side-chains 930 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 929 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 83 optimal weight: 0.0870 chunk 225 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 324 optimal weight: 40.0000 chunk 204 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 206 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 HIS A 226 ASN A 328 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 262 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 137 HIS J 226 ASN B 83 ASN B 89 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN C 37 HIS ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104351 restraints weight = 60358.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107804 restraints weight = 35346.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110207 restraints weight = 22714.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111883 restraints weight = 15582.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.113059 restraints weight = 11315.487| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28752 Z= 0.148 Angle : 0.659 10.652 39006 Z= 0.333 Chirality : 0.049 0.259 4200 Planarity : 0.005 0.080 5117 Dihedral : 9.712 157.812 3979 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % 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: -1.91 (0.14), residues: 3543 helix: -1.02 (0.13), residues: 1434 sheet: -0.08 (0.24), residues: 476 loop : -1.80 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 426 TYR 0.021 0.001 TYR H 107 PHE 0.023 0.002 PHE F 408 TRP 0.035 0.002 TRP A 396 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00328 (28752) covalent geometry : angle 0.65906 (39006) hydrogen bonds : bond 0.04048 ( 951) hydrogen bonds : angle 5.40055 ( 2754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1070 time to evaluate : 1.630 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.8874 (t-90) cc_final: 0.8114 (t-170) REVERT: A 14 ASN cc_start: 0.9227 (m-40) cc_final: 0.8785 (m-40) REVERT: A 88 ASP cc_start: 0.7488 (p0) cc_final: 0.6963 (p0) REVERT: A 89 ASN cc_start: 0.8636 (m-40) cc_final: 0.8266 (m-40) REVERT: A 130 LEU cc_start: 0.9250 (mt) cc_final: 0.9009 (tt) REVERT: A 136 THR cc_start: 0.8718 (m) cc_final: 0.8419 (t) REVERT: A 139 LEU cc_start: 0.8813 (mt) cc_final: 0.8540 (mt) REVERT: A 157 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 164 MET cc_start: 0.8215 (mmp) cc_final: 0.6962 (mmp) REVERT: A 169 VAL cc_start: 0.9218 (m) cc_final: 0.8973 (p) REVERT: A 181 GLU cc_start: 0.9458 (pp20) cc_final: 0.8861 (pp20) REVERT: A 189 MET cc_start: 0.8831 (mmp) cc_final: 0.8630 (mmt) REVERT: A 196 SER cc_start: 0.9497 (t) cc_final: 0.9035 (p) REVERT: A 197 ASP cc_start: 0.8518 (t70) cc_final: 0.8104 (t0) REVERT: A 202 ILE cc_start: 0.8924 (mm) cc_final: 0.8684 (mm) REVERT: A 227 HIS cc_start: 0.8173 (t-90) cc_final: 0.7922 (t-90) REVERT: A 247 ASN cc_start: 0.5830 (m-40) cc_final: 0.5608 (m110) REVERT: A 252 LYS cc_start: 0.9031 (mptt) cc_final: 0.8606 (mptt) REVERT: A 293 PHE cc_start: 0.6807 (t80) cc_final: 0.6394 (t80) REVERT: A 315 LEU cc_start: 0.9049 (mt) cc_final: 0.8720 (mt) REVERT: A 330 ARG cc_start: 0.8972 (mtm180) cc_final: 0.8598 (mtp85) REVERT: A 340 PHE cc_start: 0.7576 (m-80) cc_final: 0.7249 (m-10) REVERT: A 352 VAL cc_start: 0.8572 (m) cc_final: 0.8367 (m) REVERT: A 375 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 380 LEU cc_start: 0.9431 (mm) cc_final: 0.8883 (tt) REVERT: D 5 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7520 (ttp80) REVERT: D 32 MET cc_start: 0.7926 (mmm) cc_final: 0.7189 (mmm) REVERT: D 35 ILE cc_start: 0.8817 (mt) cc_final: 0.8604 (mt) REVERT: D 71 LYS cc_start: 0.7768 (mttt) cc_final: 0.7490 (mmtp) REVERT: D 106 TYR cc_start: 0.6828 (m-10) cc_final: 0.5855 (m-10) REVERT: E 21 TRP cc_start: 0.8930 (m100) cc_final: 0.8461 (m100) REVERT: E 59 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6336 (pt0) REVERT: E 64 LYS cc_start: 0.8781 (pttm) cc_final: 0.8499 (ptpp) REVERT: E 69 SER cc_start: 0.8939 (p) cc_final: 0.8582 (p) REVERT: E 75 GLU cc_start: 0.8498 (tp30) cc_final: 0.8131 (tp30) REVERT: E 116 LYS cc_start: 0.8906 (tmmt) cc_final: 0.8428 (ttmt) REVERT: E 131 ASP cc_start: 0.7969 (m-30) cc_final: 0.7584 (m-30) REVERT: E 201 ASN cc_start: 0.8051 (m-40) cc_final: 0.7850 (m-40) REVERT: E 237 GLN cc_start: 0.8783 (mt0) cc_final: 0.8473 (mt0) REVERT: E 255 ASP cc_start: 0.8463 (t70) cc_final: 0.7981 (m-30) REVERT: E 270 HIS cc_start: 0.8563 (p-80) cc_final: 0.8186 (p-80) REVERT: E 308 LYS cc_start: 0.8280 (tptp) cc_final: 0.7884 (tttm) REVERT: E 350 TRP cc_start: 0.7016 (m-10) cc_final: 0.6387 (m-10) REVERT: E 381 MET cc_start: 0.8863 (ttt) cc_final: 0.8520 (ttp) REVERT: E 399 PHE cc_start: 0.8308 (t80) cc_final: 0.8100 (t80) REVERT: E 402 MET cc_start: 0.9318 (mmt) cc_final: 0.8710 (mmt) REVERT: E 415 GLU cc_start: 0.6796 (pt0) cc_final: 0.6417 (pt0) REVERT: E 439 VAL cc_start: 0.7806 (t) cc_final: 0.7514 (t) REVERT: F 21 TRP cc_start: 0.8684 (m100) cc_final: 0.7962 (m100) REVERT: F 24 TYR cc_start: 0.8839 (m-10) cc_final: 0.7891 (m-10) REVERT: F 30 ILE cc_start: 0.9272 (mt) cc_final: 0.9035 (mt) REVERT: F 59 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6703 (pt0) REVERT: F 65 PHE cc_start: 0.7777 (p90) cc_final: 0.5711 (p90) REVERT: F 94 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7427 (tm-30) REVERT: F 131 ASP cc_start: 0.7716 (m-30) cc_final: 0.7458 (m-30) REVERT: F 173 PHE cc_start: 0.8603 (m-80) cc_final: 0.8289 (m-80) REVERT: F 210 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8531 (m-40) REVERT: F 225 ARG cc_start: 0.7963 (ptp90) cc_final: 0.7638 (mtt-85) REVERT: F 237 GLN cc_start: 0.8833 (mt0) cc_final: 0.8210 (tt0) REVERT: F 239 VAL cc_start: 0.8915 (t) cc_final: 0.8676 (t) REVERT: F 247 ARG cc_start: 0.7025 (mmt90) cc_final: 0.4711 (mmt90) REVERT: F 255 ASP cc_start: 0.8332 (t70) cc_final: 0.8059 (m-30) REVERT: F 260 GLN cc_start: 0.8833 (pm20) cc_final: 0.8566 (pm20) REVERT: F 270 HIS cc_start: 0.8524 (p-80) cc_final: 0.7704 (p-80) REVERT: F 301 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7979 (mt-10) REVERT: F 308 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8197 (mmtm) REVERT: F 317 MET cc_start: 0.7475 (tpt) cc_final: 0.7075 (tpt) REVERT: F 328 ILE cc_start: 0.9203 (mm) cc_final: 0.8886 (pt) REVERT: F 351 CYS cc_start: 0.8712 (t) cc_final: 0.6799 (p) REVERT: F 429 LEU cc_start: 0.9263 (tp) cc_final: 0.8498 (tp) REVERT: F 441 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8061 (tm-30) REVERT: G 23 LEU cc_start: 0.9149 (tp) cc_final: 0.8542 (tt) REVERT: G 27 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7574 (mt-10) REVERT: G 59 GLU cc_start: 0.6464 (mt-10) cc_final: 0.5366 (pt0) REVERT: G 65 PHE cc_start: 0.7540 (p90) cc_final: 0.6605 (p90) REVERT: G 80 ASP cc_start: 0.8423 (m-30) cc_final: 0.8145 (m-30) REVERT: G 90 LEU cc_start: 0.9228 (tp) cc_final: 0.8981 (tp) REVERT: G 124 GLU cc_start: 0.8394 (tt0) cc_final: 0.7639 (tt0) REVERT: G 125 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7205 (mtt90) REVERT: G 129 MET cc_start: 0.9083 (mmm) cc_final: 0.8844 (mmm) REVERT: G 137 GLN cc_start: 0.6553 (mm-40) cc_final: 0.5996 (mp10) REVERT: G 206 PHE cc_start: 0.9192 (m-80) cc_final: 0.8935 (m-10) REVERT: G 306 MET cc_start: 0.8281 (mmt) cc_final: 0.7905 (mmt) REVERT: G 351 CYS cc_start: 0.8333 (t) cc_final: 0.7807 (t) REVERT: G 374 LYS cc_start: 0.8778 (tttm) cc_final: 0.8368 (tmtt) REVERT: G 381 MET cc_start: 0.9055 (tmm) cc_final: 0.8718 (tmm) REVERT: G 419 GLU cc_start: 0.8735 (pm20) cc_final: 0.8532 (pm20) REVERT: G 434 ARG cc_start: 0.8901 (mpt-90) cc_final: 0.8525 (mtt90) REVERT: G 441 GLN cc_start: 0.8776 (mm110) cc_final: 0.8346 (tm-30) REVERT: H 65 PHE cc_start: 0.6618 (p90) cc_final: 0.5723 (p90) REVERT: H 94 GLU cc_start: 0.8045 (tt0) cc_final: 0.7833 (tp30) REVERT: H 102 ASP cc_start: 0.8582 (t0) cc_final: 0.8246 (t0) REVERT: H 131 ASP cc_start: 0.8293 (m-30) cc_final: 0.8068 (m-30) REVERT: H 137 GLN cc_start: 0.8402 (mt0) cc_final: 0.8165 (mp10) REVERT: H 140 LEU cc_start: 0.8564 (tp) cc_final: 0.8032 (mm) REVERT: H 142 PHE cc_start: 0.8395 (m-80) cc_final: 0.7957 (m-10) REVERT: H 143 HIS cc_start: 0.8827 (p90) cc_final: 0.8482 (p90) REVERT: H 187 GLU cc_start: 0.8656 (tt0) cc_final: 0.8277 (tp30) REVERT: H 213 CYS cc_start: 0.8449 (t) cc_final: 0.8223 (t) REVERT: H 237 GLN cc_start: 0.8715 (mt0) cc_final: 0.7860 (tt0) REVERT: H 247 ARG cc_start: 0.6913 (mmt90) cc_final: 0.4772 (mmt90) REVERT: H 270 HIS cc_start: 0.8792 (p-80) cc_final: 0.8436 (p-80) REVERT: H 276 TYR cc_start: 0.8132 (t80) cc_final: 0.7045 (t80) REVERT: H 287 HIS cc_start: 0.7782 (m170) cc_final: 0.7359 (m170) REVERT: H 308 LYS cc_start: 0.8669 (tptp) cc_final: 0.8403 (mttt) REVERT: H 343 ARG cc_start: 0.8400 (ptt180) cc_final: 0.8008 (mtt180) REVERT: H 415 GLU cc_start: 0.6500 (pt0) cc_final: 0.6029 (pt0) REVERT: H 434 ARG cc_start: 0.9127 (mtt90) cc_final: 0.8903 (mtt90) REVERT: H 441 GLN cc_start: 0.8665 (mm110) cc_final: 0.8092 (tm-30) REVERT: J 1 MET cc_start: 0.8637 (tpt) cc_final: 0.8337 (tpp) REVERT: J 6 HIS cc_start: 0.8715 (t-170) cc_final: 0.8484 (t-170) REVERT: J 21 TRP cc_start: 0.9112 (m100) cc_final: 0.8680 (m100) REVERT: J 31 ASP cc_start: 0.7821 (p0) cc_final: 0.7294 (p0) REVERT: J 50 TYR cc_start: 0.7955 (m-10) cc_final: 0.7613 (m-10) REVERT: J 83 ASN cc_start: 0.8945 (m-40) cc_final: 0.8543 (m-40) REVERT: J 101 TRP cc_start: 0.9096 (t60) cc_final: 0.8826 (t60) REVERT: J 130 LEU cc_start: 0.9140 (mt) cc_final: 0.8802 (mp) REVERT: J 147 MET cc_start: 0.8710 (tmm) cc_final: 0.8095 (tmm) REVERT: J 149 THR cc_start: 0.9212 (p) cc_final: 0.8901 (p) REVERT: J 162 ARG cc_start: 0.7429 (mmt-90) cc_final: 0.7179 (mmt180) REVERT: J 164 MET cc_start: 0.8122 (mmp) cc_final: 0.6910 (mmp) REVERT: J 167 PHE cc_start: 0.9107 (m-80) cc_final: 0.8819 (m-80) REVERT: J 174 LYS cc_start: 0.9083 (mppt) cc_final: 0.8535 (mttp) REVERT: J 190 HIS cc_start: 0.8329 (t-90) cc_final: 0.8024 (t-90) REVERT: J 191 GLN cc_start: 0.8765 (mp10) cc_final: 0.8271 (mp10) REVERT: J 196 SER cc_start: 0.9458 (t) cc_final: 0.9026 (p) REVERT: J 216 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8754 (mmmt) REVERT: J 257 MET cc_start: 0.8696 (mmp) cc_final: 0.8318 (mmp) REVERT: J 297 ASN cc_start: 0.9061 (m110) cc_final: 0.8659 (t0) REVERT: J 322 MET cc_start: 0.8942 (mmm) cc_final: 0.8675 (mmm) REVERT: J 365 THR cc_start: 0.8594 (m) cc_final: 0.8141 (p) REVERT: J 405 MET cc_start: 0.8170 (tpp) cc_final: 0.7473 (mmm) REVERT: J 408 THR cc_start: 0.9184 (p) cc_final: 0.8870 (p) REVERT: J 412 SER cc_start: 0.9086 (m) cc_final: 0.8808 (p) REVERT: J 415 ASN cc_start: 0.8528 (m-40) cc_final: 0.8063 (t0) REVERT: B 14 ASN cc_start: 0.8921 (m-40) cc_final: 0.8681 (m-40) REVERT: B 20 PHE cc_start: 0.8189 (t80) cc_final: 0.7626 (t80) REVERT: B 53 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7205 (tm-30) REVERT: B 62 ARG cc_start: 0.8940 (mtt180) cc_final: 0.8613 (mtm-85) REVERT: B 85 PHE cc_start: 0.7782 (m-80) cc_final: 0.7506 (m-80) REVERT: B 88 ASP cc_start: 0.8622 (m-30) cc_final: 0.8357 (p0) REVERT: B 103 LYS cc_start: 0.8770 (tttp) cc_final: 0.8210 (tttp) REVERT: B 164 MET cc_start: 0.7392 (mmp) cc_final: 0.6521 (mmp) REVERT: B 166 THR cc_start: 0.8934 (t) cc_final: 0.8566 (p) REVERT: B 181 GLU cc_start: 0.8081 (tt0) cc_final: 0.7799 (tt0) REVERT: B 205 GLU cc_start: 0.9286 (tt0) cc_final: 0.9017 (mt-10) REVERT: B 221 SER cc_start: 0.9396 (t) cc_final: 0.8504 (p) REVERT: B 224 ASP cc_start: 0.9381 (m-30) cc_final: 0.9173 (m-30) REVERT: B 225 LEU cc_start: 0.9512 (mp) cc_final: 0.9193 (mp) REVERT: B 245 GLU cc_start: 0.7699 (mp0) cc_final: 0.7434 (mp0) REVERT: B 247 ASN cc_start: 0.4889 (m110) cc_final: 0.4390 (m110) REVERT: B 394 LEU cc_start: 0.8687 (tt) cc_final: 0.8474 (tt) REVERT: B 395 HIS cc_start: 0.8815 (p-80) cc_final: 0.8311 (p-80) REVERT: C 6 HIS cc_start: 0.8991 (t70) cc_final: 0.7685 (t-170) REVERT: C 8 GLN cc_start: 0.7621 (mt0) cc_final: 0.6755 (mt0) REVERT: C 53 GLU cc_start: 0.7724 (mt-10) cc_final: 0.6962 (tm-30) REVERT: C 157 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8655 (tm-30) REVERT: C 174 LYS cc_start: 0.8951 (mppt) cc_final: 0.8701 (mppt) REVERT: C 190 HIS cc_start: 0.8330 (t-90) cc_final: 0.7800 (t-90) REVERT: C 233 MET cc_start: 0.9229 (mtm) cc_final: 0.8928 (ttp) REVERT: C 252 LYS cc_start: 0.8873 (mptt) cc_final: 0.8553 (mptt) REVERT: C 257 MET cc_start: 0.8238 (mmm) cc_final: 0.7986 (mmp) REVERT: C 343 TRP cc_start: 0.7040 (m100) cc_final: 0.6668 (m100) REVERT: C 397 TYR cc_start: 0.8798 (m-80) cc_final: 0.8458 (m-80) REVERT: C 405 MET cc_start: 0.8021 (tpp) cc_final: 0.7285 (tpt) REVERT: C 408 THR cc_start: 0.8664 (p) cc_final: 0.7660 (p) REVERT: C 420 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7659 (mm-30) outliers start: 2 outliers final: 0 residues processed: 1072 average time/residue: 0.1846 time to fit residues: 317.0444 Evaluate side-chains 890 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 889 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 83 optimal weight: 0.0030 chunk 89 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 340 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 196 optimal weight: 0.4980 chunk 341 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 173 optimal weight: 20.0000 chunk 188 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 overall best weight: 2.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 204 ASN A 226 ASN D 13 ASN D 66 GLN D 91 ASN E 15 GLN E 210 ASN E 262 ASN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN G 210 ASN ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 226 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 134 GLN B 263 HIS ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107480 restraints weight = 59417.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.111059 restraints weight = 34776.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.113529 restraints weight = 22274.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115306 restraints weight = 15289.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116540 restraints weight = 11065.361| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28752 Z= 0.118 Angle : 0.632 10.546 39006 Z= 0.314 Chirality : 0.047 0.186 4200 Planarity : 0.005 0.058 5117 Dihedral : 9.370 159.167 3979 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % 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: -1.73 (0.14), residues: 3543 helix: -0.79 (0.13), residues: 1484 sheet: 0.00 (0.24), residues: 488 loop : -1.83 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 426 TYR 0.017 0.001 TYR H 107 PHE 0.021 0.001 PHE B 280 TRP 0.036 0.002 TRP A 396 HIS 0.009 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00265 (28752) covalent geometry : angle 0.63208 (39006) hydrogen bonds : bond 0.03671 ( 951) hydrogen bonds : angle 5.07087 ( 2754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1100 time to evaluate : 1.117 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.8733 (t-90) cc_final: 0.8333 (t-170) REVERT: A 14 ASN cc_start: 0.9324 (m-40) cc_final: 0.8966 (m-40) REVERT: A 88 ASP cc_start: 0.7534 (p0) cc_final: 0.6962 (p0) REVERT: A 89 ASN cc_start: 0.8633 (m-40) cc_final: 0.8418 (m-40) REVERT: A 136 THR cc_start: 0.8605 (m) cc_final: 0.8185 (t) REVERT: A 139 LEU cc_start: 0.8864 (mt) cc_final: 0.8520 (mt) REVERT: A 145 SER cc_start: 0.8937 (m) cc_final: 0.8614 (p) REVERT: A 166 THR cc_start: 0.8351 (t) cc_final: 0.7900 (p) REVERT: A 169 VAL cc_start: 0.9270 (m) cc_final: 0.9061 (t) REVERT: A 196 SER cc_start: 0.9501 (t) cc_final: 0.8880 (p) REVERT: A 197 ASP cc_start: 0.8576 (t70) cc_final: 0.8376 (t0) REVERT: A 218 LYS cc_start: 0.8569 (tptp) cc_final: 0.8290 (tptp) REVERT: A 233 MET cc_start: 0.9184 (mtp) cc_final: 0.8448 (ttp) REVERT: A 252 LYS cc_start: 0.9065 (mptt) cc_final: 0.8586 (mptt) REVERT: A 293 PHE cc_start: 0.6899 (t80) cc_final: 0.6684 (t80) REVERT: A 297 ASN cc_start: 0.9206 (m-40) cc_final: 0.8675 (t0) REVERT: A 330 ARG cc_start: 0.8932 (mtm180) cc_final: 0.8616 (mtp85) REVERT: A 380 LEU cc_start: 0.9350 (mm) cc_final: 0.8912 (tp) REVERT: A 405 MET cc_start: 0.7544 (mmt) cc_final: 0.7189 (mmm) REVERT: A 408 THR cc_start: 0.8606 (p) cc_final: 0.8041 (p) REVERT: D 5 ARG cc_start: 0.8006 (ttp-110) cc_final: 0.7579 (ttp80) REVERT: D 32 MET cc_start: 0.7841 (mmm) cc_final: 0.7325 (mmm) REVERT: D 71 LYS cc_start: 0.7675 (mttt) cc_final: 0.7415 (mmtp) REVERT: E 21 TRP cc_start: 0.8952 (m100) cc_final: 0.8578 (m100) REVERT: E 59 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6250 (pt0) REVERT: E 65 PHE cc_start: 0.7550 (p90) cc_final: 0.5415 (p90) REVERT: E 116 LYS cc_start: 0.9089 (tmmt) cc_final: 0.8709 (ttmt) REVERT: E 161 LEU cc_start: 0.8515 (pp) cc_final: 0.8249 (pp) REVERT: E 255 ASP cc_start: 0.8451 (t70) cc_final: 0.7984 (m-30) REVERT: E 270 HIS cc_start: 0.8489 (p-80) cc_final: 0.7999 (p-80) REVERT: E 356 LYS cc_start: 0.8893 (tptm) cc_final: 0.8530 (tppt) REVERT: E 361 TYR cc_start: 0.8115 (m-80) cc_final: 0.7846 (m-80) REVERT: E 381 MET cc_start: 0.8897 (ttt) cc_final: 0.8501 (ttp) REVERT: E 396 ASP cc_start: 0.9400 (t0) cc_final: 0.8985 (t0) REVERT: E 402 MET cc_start: 0.9287 (mmt) cc_final: 0.8611 (mmt) REVERT: F 18 ASN cc_start: 0.9075 (m110) cc_final: 0.8868 (m110) REVERT: F 21 TRP cc_start: 0.8566 (m100) cc_final: 0.7806 (m100) REVERT: F 24 TYR cc_start: 0.8553 (m-10) cc_final: 0.7917 (m-10) REVERT: F 30 ILE cc_start: 0.9245 (mt) cc_final: 0.8941 (mm) REVERT: F 59 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6750 (pt0) REVERT: F 118 MET cc_start: 0.8527 (mmm) cc_final: 0.8244 (mmm) REVERT: F 131 ASP cc_start: 0.7689 (m-30) cc_final: 0.7367 (m-30) REVERT: F 173 PHE cc_start: 0.8675 (m-80) cc_final: 0.8426 (m-80) REVERT: F 187 GLU cc_start: 0.9054 (tt0) cc_final: 0.8326 (tp30) REVERT: F 225 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7760 (mtt-85) REVERT: F 239 VAL cc_start: 0.8814 (t) cc_final: 0.8551 (t) REVERT: F 247 ARG cc_start: 0.6649 (mmt90) cc_final: 0.5010 (mmt90) REVERT: F 255 ASP cc_start: 0.8495 (t70) cc_final: 0.8193 (m-30) REVERT: F 308 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8218 (mmtp) REVERT: F 317 MET cc_start: 0.6923 (tpt) cc_final: 0.6395 (tpt) REVERT: F 328 ILE cc_start: 0.9284 (mm) cc_final: 0.8926 (pt) REVERT: F 351 CYS cc_start: 0.8753 (t) cc_final: 0.6911 (p) REVERT: F 381 MET cc_start: 0.9025 (tmm) cc_final: 0.8149 (tmm) REVERT: F 399 PHE cc_start: 0.8592 (t80) cc_final: 0.8267 (t80) REVERT: F 441 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8216 (tm-30) REVERT: G 23 LEU cc_start: 0.9144 (tp) cc_final: 0.8497 (tt) REVERT: G 27 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7765 (mt-10) REVERT: G 59 GLU cc_start: 0.6624 (mt-10) cc_final: 0.5092 (pt0) REVERT: G 65 PHE cc_start: 0.7629 (p90) cc_final: 0.6351 (p90) REVERT: G 70 ILE cc_start: 0.8810 (tp) cc_final: 0.8578 (pt) REVERT: G 94 GLU cc_start: 0.7782 (tp30) cc_final: 0.7326 (tp30) REVERT: G 206 PHE cc_start: 0.9154 (m-80) cc_final: 0.8926 (m-10) REVERT: G 211 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8560 (mt-10) REVERT: G 220 ASN cc_start: 0.9260 (m-40) cc_final: 0.9005 (m110) REVERT: G 257 ASN cc_start: 0.7583 (t0) cc_final: 0.7317 (t0) REVERT: G 306 MET cc_start: 0.8210 (mmt) cc_final: 0.7832 (mmt) REVERT: G 308 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8446 (mmtt) REVERT: G 351 CYS cc_start: 0.8297 (t) cc_final: 0.7805 (t) REVERT: G 356 LYS cc_start: 0.8249 (tppt) cc_final: 0.7731 (tppt) REVERT: G 374 LYS cc_start: 0.8790 (tttm) cc_final: 0.8369 (tmtt) REVERT: G 380 CYS cc_start: 0.9011 (t) cc_final: 0.8609 (t) REVERT: G 381 MET cc_start: 0.8902 (tmm) cc_final: 0.8701 (tmm) REVERT: G 441 GLN cc_start: 0.8799 (mm110) cc_final: 0.8421 (tm-30) REVERT: H 18 ASN cc_start: 0.8878 (m110) cc_final: 0.8674 (m110) REVERT: H 20 CYS cc_start: 0.8825 (m) cc_final: 0.8491 (m) REVERT: H 65 PHE cc_start: 0.6552 (p90) cc_final: 0.5739 (p90) REVERT: H 73 ASP cc_start: 0.8078 (t0) cc_final: 0.7721 (t0) REVERT: H 131 ASP cc_start: 0.8196 (m-30) cc_final: 0.7995 (m-30) REVERT: H 187 GLU cc_start: 0.8691 (tt0) cc_final: 0.8146 (tp30) REVERT: H 237 GLN cc_start: 0.8798 (mt0) cc_final: 0.7918 (tt0) REVERT: H 270 HIS cc_start: 0.8622 (p-80) cc_final: 0.8233 (p-80) REVERT: H 276 TYR cc_start: 0.7845 (t80) cc_final: 0.6994 (t80) REVERT: H 308 LYS cc_start: 0.8673 (tptp) cc_final: 0.8387 (mttt) REVERT: H 324 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7514 (mtp-110) REVERT: H 343 ARG cc_start: 0.8407 (ptt180) cc_final: 0.8065 (mtt180) REVERT: H 374 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8906 (tptp) REVERT: H 375 VAL cc_start: 0.9087 (t) cc_final: 0.8833 (p) REVERT: H 415 GLU cc_start: 0.6271 (pt0) cc_final: 0.5453 (pt0) REVERT: H 418 GLU cc_start: 0.8178 (pt0) cc_final: 0.7613 (mp0) REVERT: H 441 GLN cc_start: 0.8754 (mm110) cc_final: 0.8261 (tm-30) REVERT: J 6 HIS cc_start: 0.9137 (t-170) cc_final: 0.8532 (t-170) REVERT: J 21 TRP cc_start: 0.9110 (m100) cc_final: 0.8669 (m100) REVERT: J 53 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7292 (tm-30) REVERT: J 83 ASN cc_start: 0.8933 (m-40) cc_final: 0.8468 (m-40) REVERT: J 84 LEU cc_start: 0.9150 (mt) cc_final: 0.8928 (mm) REVERT: J 147 MET cc_start: 0.8783 (tmm) cc_final: 0.8196 (tmm) REVERT: J 149 THR cc_start: 0.9209 (p) cc_final: 0.8113 (p) REVERT: J 151 LEU cc_start: 0.9659 (mp) cc_final: 0.9401 (mp) REVERT: J 157 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7998 (tm-30) REVERT: J 162 ARG cc_start: 0.7269 (mmt-90) cc_final: 0.6692 (mmt180) REVERT: J 164 MET cc_start: 0.8082 (mmp) cc_final: 0.6994 (mmp) REVERT: J 174 LYS cc_start: 0.9078 (mppt) cc_final: 0.8448 (mttp) REVERT: J 190 HIS cc_start: 0.8352 (t-90) cc_final: 0.8100 (t-90) REVERT: J 196 SER cc_start: 0.9489 (t) cc_final: 0.8973 (p) REVERT: J 198 GLU cc_start: 0.8474 (pm20) cc_final: 0.7784 (tp30) REVERT: J 216 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8780 (mmmt) REVERT: J 257 MET cc_start: 0.8628 (mmp) cc_final: 0.8270 (mmp) REVERT: J 265 PHE cc_start: 0.7780 (p90) cc_final: 0.7184 (p90) REVERT: J 297 ASN cc_start: 0.9113 (m110) cc_final: 0.8694 (t0) REVERT: J 322 MET cc_start: 0.8817 (mmm) cc_final: 0.8456 (mmp) REVERT: J 405 MET cc_start: 0.8588 (tpp) cc_final: 0.8167 (tpp) REVERT: J 412 SER cc_start: 0.9095 (m) cc_final: 0.8823 (p) REVERT: J 415 ASN cc_start: 0.8410 (m-40) cc_final: 0.8035 (t0) REVERT: B 31 ASP cc_start: 0.7899 (p0) cc_final: 0.7477 (p0) REVERT: B 35 ILE cc_start: 0.8858 (mp) cc_final: 0.8577 (mm) REVERT: B 49 VAL cc_start: 0.8980 (m) cc_final: 0.8654 (m) REVERT: B 51 PHE cc_start: 0.9185 (m-80) cc_final: 0.8595 (m-80) REVERT: B 85 PHE cc_start: 0.7759 (m-80) cc_final: 0.7377 (m-10) REVERT: B 164 MET cc_start: 0.7463 (mmp) cc_final: 0.6541 (mmt) REVERT: B 181 GLU cc_start: 0.7974 (tt0) cc_final: 0.7622 (tt0) REVERT: B 202 ILE cc_start: 0.8936 (mp) cc_final: 0.8641 (mp) REVERT: B 205 GLU cc_start: 0.9191 (tt0) cc_final: 0.8820 (mt-10) REVERT: B 233 MET cc_start: 0.9111 (mtm) cc_final: 0.8543 (mmm) REVERT: B 245 GLU cc_start: 0.7626 (mp0) cc_final: 0.7414 (mp0) REVERT: B 247 ASN cc_start: 0.5805 (m110) cc_final: 0.5212 (m110) REVERT: B 395 HIS cc_start: 0.8836 (p-80) cc_final: 0.8279 (p-80) REVERT: B 414 MET cc_start: 0.8454 (tpp) cc_final: 0.8210 (tpp) REVERT: C 6 HIS cc_start: 0.8913 (t70) cc_final: 0.7946 (t-170) REVERT: C 8 GLN cc_start: 0.7248 (mt0) cc_final: 0.6473 (mt0) REVERT: C 20 PHE cc_start: 0.8021 (t80) cc_final: 0.7662 (t80) REVERT: C 21 TRP cc_start: 0.9127 (m100) cc_final: 0.8896 (m100) REVERT: C 50 TYR cc_start: 0.8157 (m-10) cc_final: 0.7522 (m-10) REVERT: C 53 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6991 (tm-30) REVERT: C 157 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8591 (tm-30) REVERT: C 174 LYS cc_start: 0.8927 (mppt) cc_final: 0.8715 (mppt) REVERT: C 224 ASP cc_start: 0.9080 (m-30) cc_final: 0.8831 (m-30) REVERT: C 252 LYS cc_start: 0.8991 (mptt) cc_final: 0.8352 (mptt) REVERT: C 257 MET cc_start: 0.8210 (mmm) cc_final: 0.7958 (mmp) REVERT: C 288 LEU cc_start: 0.9129 (mt) cc_final: 0.8893 (mt) REVERT: C 394 LEU cc_start: 0.8845 (tp) cc_final: 0.8615 (tp) REVERT: C 397 TYR cc_start: 0.8645 (m-80) cc_final: 0.8332 (m-80) REVERT: C 408 THR cc_start: 0.8812 (p) cc_final: 0.8308 (p) REVERT: C 420 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7777 (mm-30) outliers start: 2 outliers final: 0 residues processed: 1102 average time/residue: 0.1855 time to fit residues: 327.0776 Evaluate side-chains 888 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 888 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 321 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 292 optimal weight: 3.9990 chunk 255 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 317 optimal weight: 30.0000 chunk 184 optimal weight: 20.0000 chunk 263 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 204 ASN A 281 GLN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 162 ASN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** H 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN J 191 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 134 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN C 134 GLN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105497 restraints weight = 59000.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109057 restraints weight = 34417.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111509 restraints weight = 22065.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113274 restraints weight = 15124.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.114484 restraints weight = 10894.501| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28752 Z= 0.138 Angle : 0.654 8.927 39006 Z= 0.327 Chirality : 0.048 0.216 4200 Planarity : 0.005 0.063 5117 Dihedral : 9.329 159.523 3979 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % 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: -1.57 (0.14), residues: 3543 helix: -0.66 (0.13), residues: 1519 sheet: 0.10 (0.23), residues: 520 loop : -1.78 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 426 TYR 0.023 0.001 TYR A 222 PHE 0.039 0.002 PHE E 408 TRP 0.030 0.002 TRP E 350 HIS 0.008 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00313 (28752) covalent geometry : angle 0.65425 (39006) hydrogen bonds : bond 0.03690 ( 951) hydrogen bonds : angle 4.98268 ( 2754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1064 time to evaluate : 1.091 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.8784 (t-90) cc_final: 0.8403 (t-170) REVERT: A 14 ASN cc_start: 0.9243 (m-40) cc_final: 0.8866 (m-40) REVERT: A 20 PHE cc_start: 0.8257 (t80) cc_final: 0.7578 (t80) REVERT: A 73 MET cc_start: 0.7988 (mmm) cc_final: 0.7747 (mmt) REVERT: A 88 ASP cc_start: 0.7573 (p0) cc_final: 0.7053 (p0) REVERT: A 89 ASN cc_start: 0.8605 (m-40) cc_final: 0.8395 (m110) REVERT: A 136 THR cc_start: 0.8591 (m) cc_final: 0.8278 (t) REVERT: A 145 SER cc_start: 0.8906 (m) cc_final: 0.8636 (p) REVERT: A 147 MET cc_start: 0.8224 (ppp) cc_final: 0.7795 (ppp) REVERT: A 151 LEU cc_start: 0.9472 (mt) cc_final: 0.9213 (mt) REVERT: A 166 THR cc_start: 0.8342 (t) cc_final: 0.8032 (p) REVERT: A 169 VAL cc_start: 0.9231 (m) cc_final: 0.8962 (t) REVERT: A 181 GLU cc_start: 0.9316 (pp20) cc_final: 0.8980 (pp20) REVERT: A 196 SER cc_start: 0.9486 (t) cc_final: 0.8998 (p) REVERT: A 197 ASP cc_start: 0.8659 (t70) cc_final: 0.8393 (t0) REVERT: A 202 ILE cc_start: 0.8763 (mm) cc_final: 0.8563 (mm) REVERT: A 247 ASN cc_start: 0.6257 (m-40) cc_final: 0.4447 (t0) REVERT: A 252 LYS cc_start: 0.8982 (mptt) cc_final: 0.8576 (mptt) REVERT: A 257 MET cc_start: 0.8465 (mmm) cc_final: 0.8207 (mmm) REVERT: A 293 PHE cc_start: 0.6903 (t80) cc_final: 0.6678 (t80) REVERT: A 297 ASN cc_start: 0.9173 (m-40) cc_final: 0.8536 (t0) REVERT: A 330 ARG cc_start: 0.8821 (mtm180) cc_final: 0.8500 (mtp85) REVERT: A 340 PHE cc_start: 0.7408 (m-80) cc_final: 0.7054 (m-10) REVERT: A 365 THR cc_start: 0.8704 (t) cc_final: 0.8404 (p) REVERT: A 375 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 380 LEU cc_start: 0.9341 (mm) cc_final: 0.8803 (tt) REVERT: A 405 MET cc_start: 0.7955 (mmt) cc_final: 0.7687 (mmm) REVERT: A 408 THR cc_start: 0.8540 (p) cc_final: 0.7866 (p) REVERT: A 423 GLN cc_start: 0.8135 (mt0) cc_final: 0.7323 (mp10) REVERT: D 5 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7572 (ttp80) REVERT: D 24 GLU cc_start: 0.6605 (mm-30) cc_final: 0.5588 (mm-30) REVERT: D 32 MET cc_start: 0.7909 (mmm) cc_final: 0.7488 (mmm) REVERT: D 71 LYS cc_start: 0.7686 (mttt) cc_final: 0.7343 (mmtp) REVERT: D 88 MET cc_start: 0.7695 (mmp) cc_final: 0.5692 (ttm) REVERT: E 21 TRP cc_start: 0.9048 (m100) cc_final: 0.8633 (m100) REVERT: E 24 TYR cc_start: 0.8525 (m-10) cc_final: 0.8254 (m-10) REVERT: E 59 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6173 (pt0) REVERT: E 65 PHE cc_start: 0.7359 (p90) cc_final: 0.6701 (p90) REVERT: E 116 LYS cc_start: 0.8998 (tmmt) cc_final: 0.8550 (ttmt) REVERT: E 131 ASP cc_start: 0.7880 (m-30) cc_final: 0.7664 (m-30) REVERT: E 161 LEU cc_start: 0.8523 (pp) cc_final: 0.8262 (pp) REVERT: E 186 VAL cc_start: 0.9400 (m) cc_final: 0.9141 (p) REVERT: E 192 VAL cc_start: 0.9247 (p) cc_final: 0.9016 (p) REVERT: E 237 GLN cc_start: 0.9248 (mm110) cc_final: 0.8421 (mm-40) REVERT: E 255 ASP cc_start: 0.8464 (t70) cc_final: 0.8060 (m-30) REVERT: E 270 HIS cc_start: 0.8431 (p-80) cc_final: 0.7982 (p-80) REVERT: E 350 TRP cc_start: 0.7040 (m-90) cc_final: 0.6240 (m-90) REVERT: E 381 MET cc_start: 0.8866 (ttt) cc_final: 0.8444 (ttm) REVERT: E 402 MET cc_start: 0.9239 (mmt) cc_final: 0.8582 (mmt) REVERT: E 426 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.7765 (tpp80) REVERT: F 1 MET cc_start: 0.7993 (ptp) cc_final: 0.7204 (ptt) REVERT: F 21 TRP cc_start: 0.8474 (m100) cc_final: 0.7665 (m100) REVERT: F 24 TYR cc_start: 0.8802 (m-10) cc_final: 0.7864 (m-10) REVERT: F 30 ILE cc_start: 0.9275 (mt) cc_final: 0.8978 (mt) REVERT: F 59 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6616 (pt0) REVERT: F 65 PHE cc_start: 0.7464 (p90) cc_final: 0.6116 (p90) REVERT: F 94 GLU cc_start: 0.7787 (pp20) cc_final: 0.7540 (pp20) REVERT: F 118 MET cc_start: 0.8519 (mmm) cc_final: 0.8209 (mmm) REVERT: F 131 ASP cc_start: 0.7880 (m-30) cc_final: 0.7590 (m-30) REVERT: F 136 LEU cc_start: 0.8457 (tp) cc_final: 0.8040 (tt) REVERT: F 173 PHE cc_start: 0.8896 (m-80) cc_final: 0.8631 (m-80) REVERT: F 225 ARG cc_start: 0.8272 (ptp90) cc_final: 0.8062 (ptp-170) REVERT: F 237 GLN cc_start: 0.9269 (mm110) cc_final: 0.8423 (mm-40) REVERT: F 239 VAL cc_start: 0.8841 (t) cc_final: 0.8529 (t) REVERT: F 247 ARG cc_start: 0.6859 (mmt90) cc_final: 0.5484 (mmt90) REVERT: F 255 ASP cc_start: 0.8593 (t70) cc_final: 0.8385 (m-30) REVERT: F 270 HIS cc_start: 0.8333 (p-80) cc_final: 0.7619 (p-80) REVERT: F 279 ILE cc_start: 0.8996 (mm) cc_final: 0.8755 (mm) REVERT: F 361 TYR cc_start: 0.8154 (m-80) cc_final: 0.7936 (m-80) REVERT: F 381 MET cc_start: 0.9028 (tmm) cc_final: 0.8191 (tmm) REVERT: F 441 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8303 (tm-30) REVERT: G 23 LEU cc_start: 0.9195 (tp) cc_final: 0.8527 (tt) REVERT: G 27 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7783 (mt-10) REVERT: G 59 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5048 (pt0) REVERT: G 65 PHE cc_start: 0.7661 (p90) cc_final: 0.6275 (p90) REVERT: G 94 GLU cc_start: 0.7780 (tp30) cc_final: 0.7193 (tp30) REVERT: G 129 MET cc_start: 0.8936 (mmm) cc_final: 0.8589 (mmm) REVERT: G 133 CYS cc_start: 0.8741 (m) cc_final: 0.8314 (m) REVERT: G 161 LEU cc_start: 0.9019 (pp) cc_final: 0.8818 (pp) REVERT: G 206 PHE cc_start: 0.9237 (m-80) cc_final: 0.8817 (m-10) REVERT: G 306 MET cc_start: 0.8338 (mmt) cc_final: 0.7767 (mmt) REVERT: G 308 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8292 (mmtt) REVERT: G 351 CYS cc_start: 0.8329 (t) cc_final: 0.7885 (t) REVERT: G 356 LYS cc_start: 0.8129 (tppt) cc_final: 0.7664 (tppt) REVERT: G 374 LYS cc_start: 0.8955 (tttm) cc_final: 0.8371 (tptp) REVERT: G 380 CYS cc_start: 0.9026 (t) cc_final: 0.8624 (t) REVERT: G 441 GLN cc_start: 0.8766 (mm110) cc_final: 0.8472 (tm-30) REVERT: H 18 ASN cc_start: 0.8942 (m110) cc_final: 0.8693 (m110) REVERT: H 20 CYS cc_start: 0.8770 (m) cc_final: 0.8505 (m) REVERT: H 73 ASP cc_start: 0.8210 (t0) cc_final: 0.7818 (t0) REVERT: H 94 GLU cc_start: 0.8217 (tp30) cc_final: 0.7632 (tp30) REVERT: H 131 ASP cc_start: 0.8231 (m-30) cc_final: 0.8005 (m-30) REVERT: H 143 HIS cc_start: 0.8731 (p90) cc_final: 0.8505 (p90) REVERT: H 187 GLU cc_start: 0.8551 (tt0) cc_final: 0.8154 (tp30) REVERT: H 237 GLN cc_start: 0.8767 (mt0) cc_final: 0.7996 (tt0) REVERT: H 270 HIS cc_start: 0.8486 (p-80) cc_final: 0.8198 (p-80) REVERT: H 276 TYR cc_start: 0.7982 (t80) cc_final: 0.6735 (t80) REVERT: H 301 GLU cc_start: 0.8621 (tt0) cc_final: 0.8144 (tm-30) REVERT: H 308 LYS cc_start: 0.8697 (tptp) cc_final: 0.8375 (mttt) REVERT: H 343 ARG cc_start: 0.8458 (ptt180) cc_final: 0.8192 (mtt180) REVERT: H 346 GLN cc_start: 0.7801 (mp10) cc_final: 0.7241 (mm-40) REVERT: H 418 GLU cc_start: 0.8245 (pt0) cc_final: 0.7719 (mp0) REVERT: H 441 GLN cc_start: 0.8823 (mm110) cc_final: 0.8367 (tm-30) REVERT: J 6 HIS cc_start: 0.9076 (t-170) cc_final: 0.8470 (t-170) REVERT: J 21 TRP cc_start: 0.9148 (m100) cc_final: 0.8767 (m100) REVERT: J 31 ASP cc_start: 0.7889 (p0) cc_final: 0.7543 (p0) REVERT: J 50 TYR cc_start: 0.8170 (m-10) cc_final: 0.7757 (m-10) REVERT: J 53 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7317 (tm-30) REVERT: J 83 ASN cc_start: 0.8885 (m-40) cc_final: 0.8350 (m110) REVERT: J 86 ARG cc_start: 0.6813 (ptp-170) cc_final: 0.6530 (ptp-170) REVERT: J 147 MET cc_start: 0.8482 (tmm) cc_final: 0.7408 (tmm) REVERT: J 157 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8086 (tm-30) REVERT: J 162 ARG cc_start: 0.7193 (mmt-90) cc_final: 0.6732 (mmt180) REVERT: J 164 MET cc_start: 0.8139 (mmp) cc_final: 0.7041 (mmp) REVERT: J 174 LYS cc_start: 0.8975 (mppt) cc_final: 0.8307 (mttp) REVERT: J 198 GLU cc_start: 0.8687 (pm20) cc_final: 0.7742 (tp30) REVERT: J 216 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8771 (mmmt) REVERT: J 253 LEU cc_start: 0.9433 (tt) cc_final: 0.9187 (tt) REVERT: J 257 MET cc_start: 0.8722 (mmp) cc_final: 0.8290 (mmp) REVERT: J 265 PHE cc_start: 0.7768 (p90) cc_final: 0.7103 (p90) REVERT: J 266 MET cc_start: 0.8536 (mtp) cc_final: 0.8264 (mtp) REVERT: J 287 GLU cc_start: 0.8675 (tt0) cc_final: 0.8376 (tt0) REVERT: J 297 ASN cc_start: 0.9143 (m110) cc_final: 0.8672 (t0) REVERT: J 322 MET cc_start: 0.8772 (mmm) cc_final: 0.8536 (mmm) REVERT: J 394 LEU cc_start: 0.8671 (tt) cc_final: 0.8450 (tt) REVERT: J 412 SER cc_start: 0.9113 (m) cc_final: 0.8890 (p) REVERT: J 415 ASN cc_start: 0.8435 (m-40) cc_final: 0.8025 (t0) REVERT: B 6 HIS cc_start: 0.9176 (t-170) cc_final: 0.8827 (t-170) REVERT: B 14 ASN cc_start: 0.8953 (m-40) cc_final: 0.8531 (m-40) REVERT: B 20 PHE cc_start: 0.8471 (t80) cc_final: 0.7798 (t80) REVERT: B 21 TRP cc_start: 0.9133 (m100) cc_final: 0.8358 (m100) REVERT: B 85 PHE cc_start: 0.7671 (m-80) cc_final: 0.7402 (m-10) REVERT: B 101 TRP cc_start: 0.7708 (t60) cc_final: 0.7381 (t60) REVERT: B 130 LEU cc_start: 0.9187 (tp) cc_final: 0.8931 (tp) REVERT: B 147 MET cc_start: 0.8303 (tmm) cc_final: 0.7760 (tmm) REVERT: B 151 LEU cc_start: 0.9586 (mt) cc_final: 0.9155 (mt) REVERT: B 164 MET cc_start: 0.7463 (mmp) cc_final: 0.6384 (mmp) REVERT: B 181 GLU cc_start: 0.8038 (tt0) cc_final: 0.7703 (tt0) REVERT: B 205 GLU cc_start: 0.9222 (tt0) cc_final: 0.8982 (mt-10) REVERT: B 247 ASN cc_start: 0.5891 (m110) cc_final: 0.5346 (m110) REVERT: B 280 PHE cc_start: 0.5855 (t80) cc_final: 0.5567 (t80) REVERT: B 299 MET cc_start: 0.9085 (mmp) cc_final: 0.8695 (mmt) REVERT: B 344 ILE cc_start: 0.8927 (mt) cc_final: 0.8711 (mt) REVERT: B 358 LYS cc_start: 0.7828 (pttm) cc_final: 0.7468 (pttm) REVERT: B 359 ASP cc_start: 0.9290 (m-30) cc_final: 0.9029 (m-30) REVERT: B 395 HIS cc_start: 0.8807 (p-80) cc_final: 0.8387 (p-80) REVERT: C 6 HIS cc_start: 0.8957 (t70) cc_final: 0.7817 (t-170) REVERT: C 8 GLN cc_start: 0.7380 (mt0) cc_final: 0.6486 (mt0) REVERT: C 20 PHE cc_start: 0.8120 (t80) cc_final: 0.7523 (t80) REVERT: C 53 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6711 (tm-30) REVERT: C 157 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8530 (tm-30) REVERT: C 174 LYS cc_start: 0.8976 (mppt) cc_final: 0.8747 (mppt) REVERT: C 189 MET cc_start: 0.8539 (tpp) cc_final: 0.8328 (mpp) REVERT: C 252 LYS cc_start: 0.8982 (mptt) cc_final: 0.8321 (mmtp) REVERT: C 257 MET cc_start: 0.8231 (mmm) cc_final: 0.8011 (mmp) REVERT: C 297 ASN cc_start: 0.9084 (m-40) cc_final: 0.8795 (t0) REVERT: C 394 LEU cc_start: 0.8887 (tp) cc_final: 0.8661 (tp) REVERT: C 408 THR cc_start: 0.8845 (p) cc_final: 0.8471 (p) REVERT: C 420 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7730 (mm-30) outliers start: 0 outliers final: 0 residues processed: 1064 average time/residue: 0.1776 time to fit residues: 303.7032 Evaluate side-chains 865 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 865 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 307 optimal weight: 20.0000 chunk 245 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 252 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 338 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 204 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 111 HIS E 210 ASN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN ** H 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 191 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.120243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104803 restraints weight = 60382.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108210 restraints weight = 35856.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110550 restraints weight = 23213.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112151 restraints weight = 16063.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.113388 restraints weight = 11791.701| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28752 Z= 0.139 Angle : 0.665 8.982 39006 Z= 0.331 Chirality : 0.048 0.173 4200 Planarity : 0.005 0.065 5117 Dihedral : 9.231 159.732 3979 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % 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: -1.44 (0.14), residues: 3543 helix: -0.57 (0.13), residues: 1535 sheet: 0.23 (0.24), residues: 520 loop : -1.74 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 426 TYR 0.030 0.001 TYR H 107 PHE 0.031 0.002 PHE G 408 TRP 0.019 0.002 TRP C 396 HIS 0.009 0.001 HIS J 190 Details of bonding type rmsd covalent geometry : bond 0.00317 (28752) covalent geometry : angle 0.66487 (39006) hydrogen bonds : bond 0.03663 ( 951) hydrogen bonds : angle 4.96175 ( 2754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1042 time to evaluate : 1.080 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9183 (m-40) cc_final: 0.8754 (m-40) REVERT: A 20 PHE cc_start: 0.8228 (t80) cc_final: 0.7575 (t80) REVERT: A 35 ILE cc_start: 0.8630 (mp) cc_final: 0.8218 (mm) REVERT: A 51 PHE cc_start: 0.8977 (m-80) cc_final: 0.8611 (m-80) REVERT: A 88 ASP cc_start: 0.7673 (p0) cc_final: 0.7141 (p0) REVERT: A 89 ASN cc_start: 0.8667 (m-40) cc_final: 0.8442 (m110) REVERT: A 136 THR cc_start: 0.8619 (m) cc_final: 0.8280 (t) REVERT: A 139 LEU cc_start: 0.8998 (mt) cc_final: 0.8768 (mt) REVERT: A 145 SER cc_start: 0.9004 (m) cc_final: 0.8626 (p) REVERT: A 147 MET cc_start: 0.8266 (ppp) cc_final: 0.7766 (ppp) REVERT: A 151 LEU cc_start: 0.9495 (mt) cc_final: 0.9228 (mt) REVERT: A 166 THR cc_start: 0.8474 (t) cc_final: 0.7831 (p) REVERT: A 181 GLU cc_start: 0.9221 (pp20) cc_final: 0.8889 (pp20) REVERT: A 198 GLU cc_start: 0.8404 (pm20) cc_final: 0.8072 (tp30) REVERT: A 202 ILE cc_start: 0.8769 (mm) cc_final: 0.8516 (mm) REVERT: A 227 HIS cc_start: 0.8090 (t-90) cc_final: 0.7856 (t-90) REVERT: A 233 MET cc_start: 0.9160 (mtp) cc_final: 0.8352 (mtp) REVERT: A 257 MET cc_start: 0.8471 (mmm) cc_final: 0.8093 (mmm) REVERT: A 265 PHE cc_start: 0.7931 (p90) cc_final: 0.7199 (p90) REVERT: A 288 LEU cc_start: 0.9458 (mt) cc_final: 0.9232 (mt) REVERT: A 293 PHE cc_start: 0.7056 (t80) cc_final: 0.6779 (t80) REVERT: A 297 ASN cc_start: 0.9073 (m-40) cc_final: 0.8602 (t0) REVERT: A 330 ARG cc_start: 0.8989 (mtm180) cc_final: 0.8603 (mtp85) REVERT: A 340 PHE cc_start: 0.7471 (m-80) cc_final: 0.7127 (m-10) REVERT: A 365 THR cc_start: 0.8762 (t) cc_final: 0.8468 (p) REVERT: A 380 LEU cc_start: 0.9403 (mm) cc_final: 0.8881 (tt) REVERT: A 423 GLN cc_start: 0.8115 (mt0) cc_final: 0.7647 (mt0) REVERT: D 5 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7025 (ttp80) REVERT: D 24 GLU cc_start: 0.7010 (mm-30) cc_final: 0.5704 (mm-30) REVERT: D 32 MET cc_start: 0.7808 (mmm) cc_final: 0.7506 (mmm) REVERT: D 54 ASN cc_start: 0.7081 (m-40) cc_final: 0.6292 (p0) REVERT: D 71 LYS cc_start: 0.7616 (mttt) cc_final: 0.7357 (mmtp) REVERT: D 88 MET cc_start: 0.7717 (mmp) cc_final: 0.5701 (ttm) REVERT: E 21 TRP cc_start: 0.9000 (m100) cc_final: 0.8546 (m100) REVERT: E 24 TYR cc_start: 0.8576 (m-10) cc_final: 0.8074 (m-10) REVERT: E 27 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7490 (mt-10) REVERT: E 59 GLU cc_start: 0.7452 (mt-10) cc_final: 0.5875 (pt0) REVERT: E 65 PHE cc_start: 0.6911 (p90) cc_final: 0.5808 (p90) REVERT: E 75 GLU cc_start: 0.8435 (tp30) cc_final: 0.8112 (tp30) REVERT: E 116 LYS cc_start: 0.8947 (tmmt) cc_final: 0.8501 (ttmt) REVERT: E 131 ASP cc_start: 0.8061 (m-30) cc_final: 0.7802 (m-30) REVERT: E 161 LEU cc_start: 0.8645 (pp) cc_final: 0.8443 (pp) REVERT: E 201 ASN cc_start: 0.7970 (m-40) cc_final: 0.7671 (t0) REVERT: E 243 THR cc_start: 0.8359 (p) cc_final: 0.8151 (p) REVERT: E 255 ASP cc_start: 0.8481 (t70) cc_final: 0.8080 (m-30) REVERT: E 270 HIS cc_start: 0.8302 (p-80) cc_final: 0.7901 (p-80) REVERT: E 350 TRP cc_start: 0.7114 (m-90) cc_final: 0.6383 (m-90) REVERT: E 381 MET cc_start: 0.8854 (ttt) cc_final: 0.8421 (ttp) REVERT: E 402 MET cc_start: 0.9242 (mmt) cc_final: 0.8624 (mmt) REVERT: E 426 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.7464 (mmm-85) REVERT: F 21 TRP cc_start: 0.8476 (m100) cc_final: 0.7593 (m100) REVERT: F 24 TYR cc_start: 0.8683 (m-10) cc_final: 0.7988 (m-10) REVERT: F 30 ILE cc_start: 0.9263 (mt) cc_final: 0.8979 (mm) REVERT: F 59 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6341 (pt0) REVERT: F 69 SER cc_start: 0.9391 (p) cc_final: 0.8664 (p) REVERT: F 77 ASN cc_start: 0.8885 (t0) cc_final: 0.8626 (t0) REVERT: F 118 MET cc_start: 0.8474 (mmm) cc_final: 0.8211 (mmm) REVERT: F 131 ASP cc_start: 0.7858 (m-30) cc_final: 0.7542 (m-30) REVERT: F 237 GLN cc_start: 0.9206 (mm110) cc_final: 0.8600 (mm-40) REVERT: F 247 ARG cc_start: 0.6615 (mmt90) cc_final: 0.4845 (mmt90) REVERT: F 270 HIS cc_start: 0.8248 (p-80) cc_final: 0.7610 (p-80) REVERT: F 276 TYR cc_start: 0.7971 (t80) cc_final: 0.7131 (t80) REVERT: F 349 ASP cc_start: 0.6902 (t0) cc_final: 0.6606 (p0) REVERT: F 351 CYS cc_start: 0.8437 (t) cc_final: 0.6554 (p) REVERT: F 381 MET cc_start: 0.9006 (tmm) cc_final: 0.8166 (tmm) REVERT: F 441 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8308 (tm-30) REVERT: G 23 LEU cc_start: 0.9122 (tp) cc_final: 0.8443 (tt) REVERT: G 27 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7460 (mt-10) REVERT: G 59 GLU cc_start: 0.6699 (mt-10) cc_final: 0.5096 (pt0) REVERT: G 65 PHE cc_start: 0.7242 (p90) cc_final: 0.5957 (p90) REVERT: G 94 GLU cc_start: 0.7699 (tp30) cc_final: 0.7004 (tp30) REVERT: G 161 LEU cc_start: 0.9073 (pp) cc_final: 0.8829 (pp) REVERT: G 206 PHE cc_start: 0.9283 (m-80) cc_final: 0.8806 (m-80) REVERT: G 260 GLN cc_start: 0.6967 (pm20) cc_final: 0.6274 (tm-30) REVERT: G 305 GLN cc_start: 0.8582 (mp-120) cc_final: 0.7984 (mp10) REVERT: G 306 MET cc_start: 0.8350 (mmt) cc_final: 0.7674 (mmt) REVERT: G 351 CYS cc_start: 0.8235 (t) cc_final: 0.7126 (p) REVERT: G 356 LYS cc_start: 0.7939 (tppt) cc_final: 0.7628 (tppt) REVERT: G 374 LYS cc_start: 0.8990 (tttm) cc_final: 0.8378 (tptp) REVERT: G 377 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7913 (mtm110) REVERT: G 380 CYS cc_start: 0.8925 (t) cc_final: 0.8312 (p) REVERT: G 381 MET cc_start: 0.8871 (tmm) cc_final: 0.8286 (tmm) REVERT: G 402 MET cc_start: 0.8863 (mmm) cc_final: 0.8441 (mmp) REVERT: G 441 GLN cc_start: 0.8753 (mm110) cc_final: 0.8438 (tm-30) REVERT: H 20 CYS cc_start: 0.8771 (m) cc_final: 0.8405 (m) REVERT: H 73 ASP cc_start: 0.8284 (t0) cc_final: 0.7833 (t0) REVERT: H 80 ASP cc_start: 0.8609 (p0) cc_final: 0.8362 (p0) REVERT: H 94 GLU cc_start: 0.7954 (tp30) cc_final: 0.7422 (tp30) REVERT: H 102 ASP cc_start: 0.8830 (t70) cc_final: 0.8428 (t70) REVERT: H 131 ASP cc_start: 0.8219 (m-30) cc_final: 0.7987 (m-30) REVERT: H 140 LEU cc_start: 0.8444 (tp) cc_final: 0.8124 (mm) REVERT: H 143 HIS cc_start: 0.8865 (p90) cc_final: 0.8420 (p90) REVERT: H 187 GLU cc_start: 0.8552 (tt0) cc_final: 0.8083 (tp30) REVERT: H 237 GLN cc_start: 0.8624 (mt0) cc_final: 0.7753 (tt0) REVERT: H 276 TYR cc_start: 0.7969 (t80) cc_final: 0.6552 (t80) REVERT: H 301 GLU cc_start: 0.8293 (tt0) cc_final: 0.7728 (tm-30) REVERT: H 343 ARG cc_start: 0.8499 (ptt180) cc_final: 0.8176 (mtt180) REVERT: H 346 GLN cc_start: 0.7919 (mp10) cc_final: 0.7419 (mm-40) REVERT: H 415 GLU cc_start: 0.6798 (pt0) cc_final: 0.6366 (pt0) REVERT: H 441 GLN cc_start: 0.8705 (mm110) cc_final: 0.8395 (tm-30) REVERT: J 6 HIS cc_start: 0.9129 (t-170) cc_final: 0.8787 (t-170) REVERT: J 21 TRP cc_start: 0.9165 (m100) cc_final: 0.8609 (m100) REVERT: J 31 ASP cc_start: 0.7915 (p0) cc_final: 0.7580 (p0) REVERT: J 53 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7281 (tm-30) REVERT: J 83 ASN cc_start: 0.8716 (m-40) cc_final: 0.8260 (m110) REVERT: J 84 LEU cc_start: 0.9058 (mt) cc_final: 0.8598 (mt) REVERT: J 86 ARG cc_start: 0.6729 (ptp-170) cc_final: 0.6483 (ptp-170) REVERT: J 111 GLU cc_start: 0.8286 (tt0) cc_final: 0.8047 (tp30) REVERT: J 147 MET cc_start: 0.8412 (tmm) cc_final: 0.7810 (tmm) REVERT: J 157 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8144 (tm-30) REVERT: J 162 ARG cc_start: 0.7231 (mmt-90) cc_final: 0.6799 (mmt-90) REVERT: J 164 MET cc_start: 0.8191 (mmp) cc_final: 0.6934 (mmp) REVERT: J 174 LYS cc_start: 0.8936 (mppt) cc_final: 0.8315 (mttp) REVERT: J 198 GLU cc_start: 0.8790 (pm20) cc_final: 0.7814 (tp30) REVERT: J 215 LEU cc_start: 0.9109 (mm) cc_final: 0.8702 (mm) REVERT: J 216 LYS cc_start: 0.9196 (mmtt) cc_final: 0.8801 (mmmt) REVERT: J 233 MET cc_start: 0.9238 (mtp) cc_final: 0.8588 (ttm) REVERT: J 241 ARG cc_start: 0.7246 (mtm110) cc_final: 0.6206 (mtm110) REVERT: J 265 PHE cc_start: 0.7832 (p90) cc_final: 0.7009 (p90) REVERT: J 297 ASN cc_start: 0.9200 (m110) cc_final: 0.8624 (t0) REVERT: J 322 MET cc_start: 0.8737 (mmm) cc_final: 0.8515 (mmp) REVERT: J 365 THR cc_start: 0.8758 (m) cc_final: 0.8532 (p) REVERT: J 394 LEU cc_start: 0.8679 (tt) cc_final: 0.8424 (tt) REVERT: J 412 SER cc_start: 0.9140 (m) cc_final: 0.8880 (p) REVERT: J 415 ASN cc_start: 0.8563 (m-40) cc_final: 0.8160 (t0) REVERT: B 6 HIS cc_start: 0.9239 (t-170) cc_final: 0.8938 (t70) REVERT: B 14 ASN cc_start: 0.8980 (m-40) cc_final: 0.8774 (m-40) REVERT: B 20 PHE cc_start: 0.8522 (t80) cc_final: 0.8040 (t80) REVERT: B 21 TRP cc_start: 0.9216 (m100) cc_final: 0.8390 (m100) REVERT: B 50 TYR cc_start: 0.7742 (m-10) cc_final: 0.7133 (m-10) REVERT: B 51 PHE cc_start: 0.9014 (m-80) cc_final: 0.8795 (m-80) REVERT: B 53 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7193 (tm-30) REVERT: B 85 PHE cc_start: 0.7688 (m-80) cc_final: 0.7481 (m-10) REVERT: B 101 TRP cc_start: 0.7817 (t60) cc_final: 0.7418 (t60) REVERT: B 130 LEU cc_start: 0.9203 (tp) cc_final: 0.8960 (tp) REVERT: B 147 MET cc_start: 0.8304 (tmm) cc_final: 0.7824 (tmm) REVERT: B 151 LEU cc_start: 0.9604 (mt) cc_final: 0.9316 (mt) REVERT: B 164 MET cc_start: 0.7780 (mmp) cc_final: 0.6516 (mmp) REVERT: B 181 GLU cc_start: 0.8083 (tt0) cc_final: 0.7873 (tt0) REVERT: B 198 GLU cc_start: 0.8726 (pm20) cc_final: 0.8454 (pm20) REVERT: B 223 ASP cc_start: 0.8706 (m-30) cc_final: 0.7848 (t70) REVERT: B 233 MET cc_start: 0.9383 (mtm) cc_final: 0.8707 (mmm) REVERT: B 247 ASN cc_start: 0.5797 (m110) cc_final: 0.5110 (m110) REVERT: B 344 ILE cc_start: 0.9008 (mt) cc_final: 0.8779 (mt) REVERT: B 359 ASP cc_start: 0.9294 (m-30) cc_final: 0.9011 (m-30) REVERT: B 372 SER cc_start: 0.8891 (p) cc_final: 0.8685 (p) REVERT: B 395 HIS cc_start: 0.8865 (p-80) cc_final: 0.8449 (p-80) REVERT: B 408 THR cc_start: 0.9105 (p) cc_final: 0.8740 (p) REVERT: B 414 MET cc_start: 0.8259 (mmm) cc_final: 0.7971 (tpt) REVERT: C 6 HIS cc_start: 0.8991 (t70) cc_final: 0.7845 (t-170) REVERT: C 8 GLN cc_start: 0.7402 (mt0) cc_final: 0.6453 (mt0) REVERT: C 20 PHE cc_start: 0.8155 (t80) cc_final: 0.7503 (t80) REVERT: C 53 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6891 (tm-30) REVERT: C 157 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8506 (tm-30) REVERT: C 252 LYS cc_start: 0.8974 (mptt) cc_final: 0.8414 (mmtp) REVERT: C 253 LEU cc_start: 0.9467 (tp) cc_final: 0.9155 (tp) REVERT: C 257 MET cc_start: 0.8334 (mmm) cc_final: 0.7965 (mmp) REVERT: C 297 ASN cc_start: 0.9159 (m-40) cc_final: 0.8832 (t0) REVERT: C 394 LEU cc_start: 0.8902 (tp) cc_final: 0.8535 (tt) REVERT: C 405 MET cc_start: 0.8378 (tpt) cc_final: 0.8158 (tpp) REVERT: C 408 THR cc_start: 0.8913 (p) cc_final: 0.8485 (p) REVERT: C 420 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7576 (mm-30) outliers start: 0 outliers final: 0 residues processed: 1042 average time/residue: 0.1828 time to fit residues: 304.9862 Evaluate side-chains 837 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 837 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 170 optimal weight: 30.0000 chunk 241 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 190 optimal weight: 0.1980 chunk 276 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 262 ASN F 210 ASN ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** H 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN B 44 HIS B 83 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.103472 restraints weight = 59671.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106969 restraints weight = 34771.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.109410 restraints weight = 22297.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111144 restraints weight = 15280.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.112344 restraints weight = 11048.062| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28752 Z= 0.147 Angle : 0.674 11.233 39006 Z= 0.336 Chirality : 0.049 0.185 4200 Planarity : 0.005 0.083 5117 Dihedral : 9.172 160.898 3979 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.07 % Allowed : 1.16 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.39 (0.14), residues: 3543 helix: -0.53 (0.13), residues: 1528 sheet: 0.42 (0.24), residues: 508 loop : -1.76 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 426 TYR 0.034 0.002 TYR H 107 PHE 0.033 0.002 PHE E 408 TRP 0.028 0.002 TRP A 21 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00333 (28752) covalent geometry : angle 0.67391 (39006) hydrogen bonds : bond 0.03661 ( 951) hydrogen bonds : angle 4.84881 ( 2754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1035 time to evaluate : 1.111 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: symmetry clash REVERT: A 6 HIS cc_start: 0.9094 (t-170) cc_final: 0.8810 (t-170) REVERT: A 20 PHE cc_start: 0.8096 (t80) cc_final: 0.7486 (t80) REVERT: A 51 PHE cc_start: 0.8966 (m-80) cc_final: 0.8629 (m-80) REVERT: A 88 ASP cc_start: 0.7915 (p0) cc_final: 0.7676 (p0) REVERT: A 136 THR cc_start: 0.8483 (m) cc_final: 0.8237 (t) REVERT: A 145 SER cc_start: 0.8983 (m) cc_final: 0.8589 (p) REVERT: A 147 MET cc_start: 0.8347 (ppp) cc_final: 0.7830 (ppp) REVERT: A 151 LEU cc_start: 0.9473 (mt) cc_final: 0.9218 (mt) REVERT: A 181 GLU cc_start: 0.9259 (pp20) cc_final: 0.8864 (pp20) REVERT: A 198 GLU cc_start: 0.8446 (pm20) cc_final: 0.7726 (tp30) REVERT: A 202 ILE cc_start: 0.8793 (mm) cc_final: 0.8538 (mm) REVERT: A 215 LEU cc_start: 0.9205 (mp) cc_final: 0.8984 (mp) REVERT: A 265 PHE cc_start: 0.7882 (p90) cc_final: 0.7070 (p90) REVERT: A 288 LEU cc_start: 0.9470 (mt) cc_final: 0.9269 (mt) REVERT: A 330 ARG cc_start: 0.9019 (mtm180) cc_final: 0.8717 (mtp180) REVERT: A 340 PHE cc_start: 0.7463 (m-80) cc_final: 0.7182 (m-10) REVERT: A 365 THR cc_start: 0.8884 (t) cc_final: 0.8631 (p) REVERT: A 380 LEU cc_start: 0.9417 (mm) cc_final: 0.8874 (tt) REVERT: A 387 MET cc_start: 0.9183 (mmm) cc_final: 0.8788 (mmm) REVERT: A 405 MET cc_start: 0.7324 (mmt) cc_final: 0.7076 (tpp) REVERT: A 414 MET cc_start: 0.8170 (ttp) cc_final: 0.7903 (ptt) REVERT: A 423 GLN cc_start: 0.8149 (mt0) cc_final: 0.7671 (mt0) REVERT: D 5 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.7271 (ttp80) REVERT: D 32 MET cc_start: 0.7695 (mmm) cc_final: 0.7326 (mmm) REVERT: D 54 ASN cc_start: 0.7070 (m-40) cc_final: 0.6325 (p0) REVERT: D 66 GLN cc_start: 0.8199 (mp10) cc_final: 0.7498 (mp10) REVERT: E 21 TRP cc_start: 0.9007 (m100) cc_final: 0.8498 (m100) REVERT: E 23 LEU cc_start: 0.9197 (tt) cc_final: 0.8526 (tp) REVERT: E 24 TYR cc_start: 0.8597 (m-10) cc_final: 0.8152 (m-10) REVERT: E 27 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7158 (mt-10) REVERT: E 59 GLU cc_start: 0.7548 (mt-10) cc_final: 0.5784 (pt0) REVERT: E 65 PHE cc_start: 0.7408 (p90) cc_final: 0.5897 (p90) REVERT: E 73 ASP cc_start: 0.8112 (t0) cc_final: 0.7868 (t0) REVERT: E 116 LYS cc_start: 0.8942 (tmmt) cc_final: 0.8395 (ttpt) REVERT: E 131 ASP cc_start: 0.8004 (m-30) cc_final: 0.7672 (m-30) REVERT: E 219 ARG cc_start: 0.7129 (mtm110) cc_final: 0.6693 (ttp-170) REVERT: E 237 GLN cc_start: 0.8919 (mm110) cc_final: 0.8628 (mm-40) REVERT: E 243 THR cc_start: 0.8439 (p) cc_final: 0.8096 (p) REVERT: E 270 HIS cc_start: 0.8456 (p-80) cc_final: 0.7963 (p-80) REVERT: E 350 TRP cc_start: 0.7130 (m-90) cc_final: 0.6311 (m-10) REVERT: E 381 MET cc_start: 0.8840 (ttt) cc_final: 0.8302 (ttp) REVERT: E 396 ASP cc_start: 0.9422 (t0) cc_final: 0.8940 (t0) REVERT: E 402 MET cc_start: 0.9229 (mmt) cc_final: 0.8783 (mmt) REVERT: F 1 MET cc_start: 0.8000 (ptp) cc_final: 0.7517 (ptt) REVERT: F 21 TRP cc_start: 0.8454 (m100) cc_final: 0.7713 (m100) REVERT: F 24 TYR cc_start: 0.8802 (m-10) cc_final: 0.8152 (m-10) REVERT: F 30 ILE cc_start: 0.9220 (mt) cc_final: 0.9009 (mm) REVERT: F 55 THR cc_start: 0.8420 (p) cc_final: 0.8112 (p) REVERT: F 59 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6309 (pt0) REVERT: F 69 SER cc_start: 0.9415 (p) cc_final: 0.9038 (p) REVERT: F 94 GLU cc_start: 0.7819 (pp20) cc_final: 0.7264 (pp20) REVERT: F 131 ASP cc_start: 0.7886 (m-30) cc_final: 0.7549 (m-30) REVERT: F 247 ARG cc_start: 0.6756 (mmt90) cc_final: 0.4748 (mmt90) REVERT: F 270 HIS cc_start: 0.8306 (p-80) cc_final: 0.7676 (p-80) REVERT: F 351 CYS cc_start: 0.8425 (t) cc_final: 0.6567 (p) REVERT: F 381 MET cc_start: 0.8983 (tmm) cc_final: 0.8184 (tmm) REVERT: F 441 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8418 (tm-30) REVERT: G 2 ARG cc_start: 0.5643 (mtp180) cc_final: 0.5214 (mtt180) REVERT: G 23 LEU cc_start: 0.8894 (tp) cc_final: 0.8341 (tp) REVERT: G 27 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7486 (mt-10) REVERT: G 59 GLU cc_start: 0.6765 (mt-10) cc_final: 0.5216 (pt0) REVERT: G 65 PHE cc_start: 0.7481 (p90) cc_final: 0.6045 (p90) REVERT: G 94 GLU cc_start: 0.7672 (tp30) cc_final: 0.7010 (tp30) REVERT: G 129 MET cc_start: 0.8937 (mmm) cc_final: 0.8704 (mmm) REVERT: G 143 HIS cc_start: 0.8591 (p90) cc_final: 0.8339 (p90) REVERT: G 167 LYS cc_start: 0.8006 (mptt) cc_final: 0.7632 (ptpt) REVERT: G 305 GLN cc_start: 0.8498 (mp-120) cc_final: 0.7891 (mp-120) REVERT: G 351 CYS cc_start: 0.8307 (t) cc_final: 0.7188 (p) REVERT: G 356 LYS cc_start: 0.8268 (tppt) cc_final: 0.7898 (tppt) REVERT: G 374 LYS cc_start: 0.9027 (tttm) cc_final: 0.8406 (tptp) REVERT: G 377 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7913 (mtm110) REVERT: G 380 CYS cc_start: 0.9011 (t) cc_final: 0.8325 (p) REVERT: G 381 MET cc_start: 0.8916 (tmm) cc_final: 0.8317 (tmm) REVERT: G 441 GLN cc_start: 0.8760 (mm110) cc_final: 0.8470 (tm-30) REVERT: H 20 CYS cc_start: 0.8836 (m) cc_final: 0.8404 (m) REVERT: H 73 ASP cc_start: 0.8423 (t0) cc_final: 0.7893 (t0) REVERT: H 94 GLU cc_start: 0.7865 (tp30) cc_final: 0.7370 (tp30) REVERT: H 102 ASP cc_start: 0.8794 (t70) cc_final: 0.7535 (t70) REVERT: H 131 ASP cc_start: 0.8232 (m-30) cc_final: 0.7973 (m-30) REVERT: H 140 LEU cc_start: 0.8410 (tp) cc_final: 0.8154 (mm) REVERT: H 142 PHE cc_start: 0.8150 (m-10) cc_final: 0.7895 (m-10) REVERT: H 143 HIS cc_start: 0.8886 (p90) cc_final: 0.8326 (p90) REVERT: H 187 GLU cc_start: 0.8712 (tt0) cc_final: 0.8169 (tp30) REVERT: H 209 ASP cc_start: 0.8190 (t0) cc_final: 0.7926 (t0) REVERT: H 237 GLN cc_start: 0.8554 (mt0) cc_final: 0.7996 (tt0) REVERT: H 276 TYR cc_start: 0.8060 (t80) cc_final: 0.6783 (t80) REVERT: H 301 GLU cc_start: 0.8452 (tt0) cc_final: 0.7780 (tm-30) REVERT: H 305 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8958 (mm-40) REVERT: H 306 MET cc_start: 0.8893 (mtp) cc_final: 0.8033 (tpp) REVERT: H 308 LYS cc_start: 0.8672 (tptp) cc_final: 0.8348 (mmtt) REVERT: H 343 ARG cc_start: 0.8537 (ptt180) cc_final: 0.8231 (mtt180) REVERT: H 346 GLN cc_start: 0.7950 (mp10) cc_final: 0.7535 (mm-40) REVERT: H 415 GLU cc_start: 0.6683 (pt0) cc_final: 0.6360 (pt0) REVERT: H 419 GLU cc_start: 0.8773 (pm20) cc_final: 0.8505 (pm20) REVERT: H 441 GLN cc_start: 0.8774 (mm110) cc_final: 0.8497 (tm-30) REVERT: J 6 HIS cc_start: 0.9192 (t-170) cc_final: 0.8840 (t-170) REVERT: J 21 TRP cc_start: 0.9214 (m100) cc_final: 0.8656 (m100) REVERT: J 31 ASP cc_start: 0.7867 (p0) cc_final: 0.7522 (p0) REVERT: J 53 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7299 (tm-30) REVERT: J 83 ASN cc_start: 0.8695 (m-40) cc_final: 0.8233 (m110) REVERT: J 84 LEU cc_start: 0.8915 (mt) cc_final: 0.8370 (mt) REVERT: J 86 ARG cc_start: 0.7060 (ptp-170) cc_final: 0.6825 (ptp-170) REVERT: J 111 GLU cc_start: 0.8305 (tt0) cc_final: 0.8061 (tp30) REVERT: J 147 MET cc_start: 0.8413 (tmm) cc_final: 0.7821 (tmm) REVERT: J 157 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8164 (tm-30) REVERT: J 162 ARG cc_start: 0.7134 (mmt-90) cc_final: 0.6797 (mmt-90) REVERT: J 164 MET cc_start: 0.8316 (mmp) cc_final: 0.7044 (mmp) REVERT: J 169 VAL cc_start: 0.8725 (m) cc_final: 0.8413 (t) REVERT: J 174 LYS cc_start: 0.8972 (mppt) cc_final: 0.8327 (mttp) REVERT: J 189 MET cc_start: 0.8690 (mmp) cc_final: 0.8351 (mmp) REVERT: J 198 GLU cc_start: 0.8811 (pm20) cc_final: 0.7815 (tp30) REVERT: J 215 LEU cc_start: 0.8884 (mm) cc_final: 0.8429 (mm) REVERT: J 216 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8744 (mmmt) REVERT: J 265 PHE cc_start: 0.7851 (p90) cc_final: 0.6824 (p90) REVERT: J 297 ASN cc_start: 0.9196 (m110) cc_final: 0.8731 (t0) REVERT: J 365 THR cc_start: 0.8760 (m) cc_final: 0.8530 (p) REVERT: J 412 SER cc_start: 0.9139 (m) cc_final: 0.8889 (p) REVERT: J 415 ASN cc_start: 0.8548 (m-40) cc_final: 0.8176 (t0) REVERT: B 6 HIS cc_start: 0.8818 (t-170) cc_final: 0.8429 (t-170) REVERT: B 20 PHE cc_start: 0.8502 (t80) cc_final: 0.8085 (t80) REVERT: B 21 TRP cc_start: 0.9206 (m100) cc_final: 0.8496 (m100) REVERT: B 51 PHE cc_start: 0.9023 (m-80) cc_final: 0.8778 (m-80) REVERT: B 53 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7094 (tm-30) REVERT: B 64 VAL cc_start: 0.9667 (t) cc_final: 0.9374 (t) REVERT: B 83 ASN cc_start: 0.8394 (m-40) cc_final: 0.8117 (m110) REVERT: B 84 LEU cc_start: 0.9041 (mt) cc_final: 0.8637 (mt) REVERT: B 85 PHE cc_start: 0.7570 (m-80) cc_final: 0.7363 (m-10) REVERT: B 101 TRP cc_start: 0.7741 (t60) cc_final: 0.7398 (t60) REVERT: B 147 MET cc_start: 0.8268 (tmm) cc_final: 0.7803 (tmm) REVERT: B 151 LEU cc_start: 0.9618 (mt) cc_final: 0.9311 (mt) REVERT: B 164 MET cc_start: 0.7967 (mmp) cc_final: 0.6602 (mmp) REVERT: B 174 LYS cc_start: 0.8977 (mppt) cc_final: 0.8678 (mppt) REVERT: B 181 GLU cc_start: 0.8174 (tt0) cc_final: 0.7877 (tt0) REVERT: B 198 GLU cc_start: 0.8742 (pm20) cc_final: 0.8409 (pm20) REVERT: B 233 MET cc_start: 0.9269 (mtm) cc_final: 0.8670 (mmm) REVERT: B 247 ASN cc_start: 0.5859 (m110) cc_final: 0.5278 (m110) REVERT: B 344 ILE cc_start: 0.9012 (mt) cc_final: 0.8767 (mt) REVERT: C 6 HIS cc_start: 0.9023 (t70) cc_final: 0.7891 (t-170) REVERT: C 20 PHE cc_start: 0.8172 (t80) cc_final: 0.7430 (t80) REVERT: C 35 ILE cc_start: 0.8775 (mp) cc_final: 0.8353 (mm) REVERT: C 53 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6917 (tm-30) REVERT: C 147 MET cc_start: 0.8206 (ppp) cc_final: 0.7450 (ppp) REVERT: C 157 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8556 (tm-30) REVERT: C 223 ASP cc_start: 0.8822 (m-30) cc_final: 0.8037 (t70) REVERT: C 297 ASN cc_start: 0.9241 (m-40) cc_final: 0.8791 (t0) REVERT: C 394 LEU cc_start: 0.8918 (tp) cc_final: 0.8594 (tt) REVERT: C 408 THR cc_start: 0.8945 (p) cc_final: 0.8663 (p) outliers start: 2 outliers final: 0 residues processed: 1037 average time/residue: 0.1845 time to fit residues: 305.5235 Evaluate side-chains 851 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 851 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 343 optimal weight: 40.0000 chunk 175 optimal weight: 30.0000 chunk 190 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 342 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 131 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN D 91 ASN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 HIS ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN C 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.116818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101434 restraints weight = 60426.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104789 restraints weight = 35225.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.107139 restraints weight = 22640.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108764 restraints weight = 15584.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.109966 restraints weight = 11402.024| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28752 Z= 0.172 Angle : 0.709 10.245 39006 Z= 0.355 Chirality : 0.050 0.247 4200 Planarity : 0.005 0.091 5117 Dihedral : 9.216 160.041 3979 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.40 (0.14), residues: 3543 helix: -0.50 (0.13), residues: 1531 sheet: 0.39 (0.24), residues: 520 loop : -1.82 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 2 TYR 0.037 0.002 TYR H 107 PHE 0.039 0.002 PHE E 408 TRP 0.044 0.002 TRP A 21 HIS 0.009 0.001 HIS J 44 Details of bonding type rmsd covalent geometry : bond 0.00385 (28752) covalent geometry : angle 0.70863 (39006) hydrogen bonds : bond 0.03786 ( 951) hydrogen bonds : angle 4.91616 ( 2754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1000 time to evaluate : 1.088 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.9202 (t-170) cc_final: 0.8722 (t-170) REVERT: A 20 PHE cc_start: 0.8158 (t80) cc_final: 0.7813 (t80) REVERT: A 53 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7046 (tm-30) REVERT: A 136 THR cc_start: 0.8500 (m) cc_final: 0.8275 (t) REVERT: A 145 SER cc_start: 0.8953 (m) cc_final: 0.8569 (p) REVERT: A 147 MET cc_start: 0.8198 (ppp) cc_final: 0.7728 (ppp) REVERT: A 151 LEU cc_start: 0.9490 (mt) cc_final: 0.9191 (mt) REVERT: A 157 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 166 THR cc_start: 0.8566 (t) cc_final: 0.7990 (p) REVERT: A 181 GLU cc_start: 0.9224 (pp20) cc_final: 0.8788 (pp20) REVERT: A 198 GLU cc_start: 0.8517 (pm20) cc_final: 0.7749 (tp30) REVERT: A 202 ILE cc_start: 0.8903 (mm) cc_final: 0.8639 (mm) REVERT: A 218 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8509 (tmtt) REVERT: A 233 MET cc_start: 0.9168 (mtp) cc_final: 0.8725 (mtp) REVERT: A 252 LYS cc_start: 0.8980 (mptt) cc_final: 0.8264 (mppt) REVERT: A 265 PHE cc_start: 0.8057 (p90) cc_final: 0.7167 (p90) REVERT: A 293 PHE cc_start: 0.7060 (t80) cc_final: 0.6610 (t80) REVERT: A 297 ASN cc_start: 0.9196 (p0) cc_final: 0.8930 (p0) REVERT: A 330 ARG cc_start: 0.9102 (mtm180) cc_final: 0.8750 (mtp180) REVERT: A 340 PHE cc_start: 0.7355 (m-80) cc_final: 0.7069 (m-10) REVERT: A 355 VAL cc_start: 0.8169 (p) cc_final: 0.7863 (p) REVERT: A 365 THR cc_start: 0.8941 (t) cc_final: 0.8712 (p) REVERT: A 387 MET cc_start: 0.9133 (mmm) cc_final: 0.8385 (mmm) REVERT: A 405 MET cc_start: 0.7417 (mmt) cc_final: 0.7178 (mmm) REVERT: A 414 MET cc_start: 0.8266 (ttp) cc_final: 0.7899 (ptt) REVERT: A 423 GLN cc_start: 0.8148 (mt0) cc_final: 0.7796 (mt0) REVERT: D 5 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7377 (ttp80) REVERT: D 32 MET cc_start: 0.7792 (mmm) cc_final: 0.7527 (mmm) REVERT: D 54 ASN cc_start: 0.7035 (m-40) cc_final: 0.6289 (p0) REVERT: E 21 TRP cc_start: 0.9010 (m100) cc_final: 0.8498 (m100) REVERT: E 24 TYR cc_start: 0.8734 (m-10) cc_final: 0.8271 (m-10) REVERT: E 27 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7125 (mt-10) REVERT: E 59 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6010 (pt0) REVERT: E 116 LYS cc_start: 0.8977 (tmmt) cc_final: 0.8589 (ttpt) REVERT: E 131 ASP cc_start: 0.8012 (m-30) cc_final: 0.7719 (m-30) REVERT: E 219 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6272 (ttp-170) REVERT: E 231 LEU cc_start: 0.9568 (mp) cc_final: 0.9345 (mp) REVERT: E 270 HIS cc_start: 0.8287 (p-80) cc_final: 0.7855 (p-80) REVERT: E 303 TYR cc_start: 0.8821 (m-10) cc_final: 0.8619 (m-10) REVERT: E 356 LYS cc_start: 0.9040 (tptm) cc_final: 0.8388 (tppt) REVERT: E 381 MET cc_start: 0.8959 (ttt) cc_final: 0.8095 (tmm) REVERT: E 402 MET cc_start: 0.9013 (mmt) cc_final: 0.8728 (mmt) REVERT: E 426 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7799 (tpp80) REVERT: F 1 MET cc_start: 0.7934 (ptp) cc_final: 0.7359 (ptt) REVERT: F 21 TRP cc_start: 0.8498 (m100) cc_final: 0.7808 (m100) REVERT: F 24 TYR cc_start: 0.8870 (m-10) cc_final: 0.8061 (m-10) REVERT: F 30 ILE cc_start: 0.9289 (mt) cc_final: 0.9004 (mm) REVERT: F 59 GLU cc_start: 0.7644 (mt-10) cc_final: 0.6325 (pt0) REVERT: F 69 SER cc_start: 0.9438 (p) cc_final: 0.9074 (p) REVERT: F 131 ASP cc_start: 0.7976 (m-30) cc_final: 0.7621 (m-30) REVERT: F 204 CYS cc_start: 0.9065 (t) cc_final: 0.8722 (t) REVERT: F 239 VAL cc_start: 0.8986 (t) cc_final: 0.8649 (t) REVERT: F 247 ARG cc_start: 0.7041 (mmt90) cc_final: 0.4472 (mmt90) REVERT: F 270 HIS cc_start: 0.8233 (p-80) cc_final: 0.7682 (p-80) REVERT: F 381 MET cc_start: 0.9016 (tmm) cc_final: 0.8408 (tmm) REVERT: F 415 GLU cc_start: 0.6837 (pt0) cc_final: 0.6320 (pt0) REVERT: F 426 ARG cc_start: 0.8913 (mmp80) cc_final: 0.8547 (mmp80) REVERT: F 441 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8558 (tm-30) REVERT: G 23 LEU cc_start: 0.9158 (tp) cc_final: 0.8417 (tt) REVERT: G 27 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7479 (mt-10) REVERT: G 59 GLU cc_start: 0.6791 (mt-10) cc_final: 0.5594 (pt0) REVERT: G 94 GLU cc_start: 0.7735 (tp30) cc_final: 0.7090 (tp30) REVERT: G 167 LYS cc_start: 0.7976 (mptt) cc_final: 0.7625 (ptpt) REVERT: G 214 TYR cc_start: 0.8822 (m-80) cc_final: 0.8395 (m-80) REVERT: G 219 ARG cc_start: 0.7380 (mtm110) cc_final: 0.6932 (ttp-170) REVERT: G 351 CYS cc_start: 0.8219 (t) cc_final: 0.7887 (t) REVERT: G 356 LYS cc_start: 0.8608 (tppt) cc_final: 0.8167 (tppt) REVERT: G 374 LYS cc_start: 0.9101 (tttm) cc_final: 0.8436 (tptp) REVERT: G 377 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7943 (mtm110) REVERT: G 380 CYS cc_start: 0.9104 (t) cc_final: 0.8471 (p) REVERT: G 381 MET cc_start: 0.8836 (tmm) cc_final: 0.8301 (tmm) REVERT: G 434 ARG cc_start: 0.8885 (mtt90) cc_final: 0.8614 (mtt90) REVERT: G 441 GLN cc_start: 0.8751 (mm110) cc_final: 0.8439 (tm-30) REVERT: H 20 CYS cc_start: 0.8737 (m) cc_final: 0.8492 (m) REVERT: H 57 PHE cc_start: 0.8044 (m-80) cc_final: 0.7008 (m-80) REVERT: H 73 ASP cc_start: 0.8447 (t0) cc_final: 0.8151 (t0) REVERT: H 94 GLU cc_start: 0.7833 (tp30) cc_final: 0.7353 (tp30) REVERT: H 102 ASP cc_start: 0.8754 (t70) cc_final: 0.7255 (t70) REVERT: H 131 ASP cc_start: 0.8174 (m-30) cc_final: 0.7963 (m-30) REVERT: H 140 LEU cc_start: 0.8413 (tp) cc_final: 0.8087 (mm) REVERT: H 142 PHE cc_start: 0.8200 (m-10) cc_final: 0.7880 (m-10) REVERT: H 143 HIS cc_start: 0.8833 (p90) cc_final: 0.8220 (p90) REVERT: H 145 PHE cc_start: 0.8912 (m-80) cc_final: 0.8686 (m-80) REVERT: H 187 GLU cc_start: 0.8843 (tt0) cc_final: 0.8229 (tp30) REVERT: H 301 GLU cc_start: 0.8484 (tt0) cc_final: 0.8164 (tm-30) REVERT: H 343 ARG cc_start: 0.8725 (ptt180) cc_final: 0.7917 (mtt180) REVERT: H 419 GLU cc_start: 0.8732 (pm20) cc_final: 0.8493 (pm20) REVERT: H 426 ARG cc_start: 0.8994 (mmm160) cc_final: 0.8232 (mmm160) REVERT: H 441 GLN cc_start: 0.8787 (mm110) cc_final: 0.8517 (tm-30) REVERT: J 6 HIS cc_start: 0.9191 (t-170) cc_final: 0.8895 (t-170) REVERT: J 21 TRP cc_start: 0.9170 (m100) cc_final: 0.8684 (m100) REVERT: J 31 ASP cc_start: 0.7972 (p0) cc_final: 0.7554 (p0) REVERT: J 53 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7312 (tm-30) REVERT: J 83 ASN cc_start: 0.8523 (m-40) cc_final: 0.8127 (m110) REVERT: J 84 LEU cc_start: 0.8920 (mt) cc_final: 0.8478 (mm) REVERT: J 111 GLU cc_start: 0.8238 (tt0) cc_final: 0.7943 (tp30) REVERT: J 147 MET cc_start: 0.8433 (tmm) cc_final: 0.7765 (tmm) REVERT: J 151 LEU cc_start: 0.9626 (mp) cc_final: 0.9387 (mp) REVERT: J 157 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8274 (tm-30) REVERT: J 162 ARG cc_start: 0.7137 (mmt-90) cc_final: 0.6751 (mmt-90) REVERT: J 164 MET cc_start: 0.8354 (mmp) cc_final: 0.7079 (mmp) REVERT: J 189 MET cc_start: 0.8786 (mmp) cc_final: 0.8364 (mmp) REVERT: J 198 GLU cc_start: 0.8828 (pm20) cc_final: 0.7825 (tp30) REVERT: J 216 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8730 (mmmt) REVERT: J 228 LEU cc_start: 0.9329 (tp) cc_final: 0.9103 (tp) REVERT: J 233 MET cc_start: 0.9035 (mtp) cc_final: 0.8779 (ttm) REVERT: J 265 PHE cc_start: 0.7714 (p90) cc_final: 0.6596 (p90) REVERT: J 288 LEU cc_start: 0.9265 (mt) cc_final: 0.9015 (mt) REVERT: J 297 ASN cc_start: 0.9228 (m110) cc_final: 0.8943 (t0) REVERT: J 365 THR cc_start: 0.8756 (m) cc_final: 0.8481 (p) REVERT: J 366 PHE cc_start: 0.8930 (t80) cc_final: 0.8262 (t80) REVERT: J 412 SER cc_start: 0.9230 (m) cc_final: 0.8959 (p) REVERT: J 415 ASN cc_start: 0.8409 (m-40) cc_final: 0.7819 (t0) REVERT: B 14 ASN cc_start: 0.9054 (m-40) cc_final: 0.8792 (m-40) REVERT: B 20 PHE cc_start: 0.8591 (t80) cc_final: 0.8178 (t80) REVERT: B 21 TRP cc_start: 0.9205 (m100) cc_final: 0.8428 (m100) REVERT: B 51 PHE cc_start: 0.9179 (m-80) cc_final: 0.8844 (m-80) REVERT: B 53 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7237 (tm-30) REVERT: B 83 ASN cc_start: 0.8425 (m-40) cc_final: 0.8063 (m110) REVERT: B 84 LEU cc_start: 0.9072 (mt) cc_final: 0.8563 (mt) REVERT: B 85 PHE cc_start: 0.7607 (m-80) cc_final: 0.7374 (m-10) REVERT: B 151 LEU cc_start: 0.9630 (mt) cc_final: 0.9321 (mt) REVERT: B 164 MET cc_start: 0.8068 (mmp) cc_final: 0.6655 (mmp) REVERT: B 174 LYS cc_start: 0.9026 (mppt) cc_final: 0.8715 (mppt) REVERT: B 181 GLU cc_start: 0.8218 (tt0) cc_final: 0.7895 (tt0) REVERT: B 189 MET cc_start: 0.8849 (tpp) cc_final: 0.8466 (tpp) REVERT: B 202 ILE cc_start: 0.8963 (mm) cc_final: 0.8760 (mm) REVERT: B 233 MET cc_start: 0.9271 (mtm) cc_final: 0.8606 (mmm) REVERT: B 343 TRP cc_start: 0.7269 (m100) cc_final: 0.6978 (m100) REVERT: B 395 HIS cc_start: 0.8825 (p-80) cc_final: 0.8221 (p-80) REVERT: C 6 HIS cc_start: 0.9072 (t70) cc_final: 0.7960 (t-170) REVERT: C 20 PHE cc_start: 0.8317 (t80) cc_final: 0.7472 (t80) REVERT: C 35 ILE cc_start: 0.8857 (mp) cc_final: 0.8440 (mm) REVERT: C 53 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7002 (tm-30) REVERT: C 101 TRP cc_start: 0.8409 (t60) cc_final: 0.8199 (t60) REVERT: C 139 LEU cc_start: 0.8772 (mt) cc_final: 0.8451 (mt) REVERT: C 147 MET cc_start: 0.8565 (ppp) cc_final: 0.8080 (ppp) REVERT: C 157 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8602 (tm-30) REVERT: C 182 PRO cc_start: 0.9451 (Cg_endo) cc_final: 0.9164 (Cg_exo) REVERT: C 223 ASP cc_start: 0.8831 (m-30) cc_final: 0.8058 (t70) REVERT: C 252 LYS cc_start: 0.9116 (mptt) cc_final: 0.8629 (mmtp) REVERT: C 394 LEU cc_start: 0.8932 (tp) cc_final: 0.8658 (tt) REVERT: C 423 GLN cc_start: 0.8035 (mt0) cc_final: 0.7640 (mt0) outliers start: 0 outliers final: 0 residues processed: 1000 average time/residue: 0.1867 time to fit residues: 298.6789 Evaluate side-chains 817 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 817 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 341 optimal weight: 20.0000 chunk 213 optimal weight: 30.0000 chunk 286 optimal weight: 10.0000 chunk 318 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 131 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS F 210 ASN ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 HIS ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 297 ASN C 413 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.103531 restraints weight = 59504.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106993 restraints weight = 34815.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.109400 restraints weight = 22331.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.111072 restraints weight = 15360.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.112271 restraints weight = 11183.802| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28752 Z= 0.136 Angle : 0.690 10.493 39006 Z= 0.341 Chirality : 0.048 0.193 4200 Planarity : 0.005 0.070 5117 Dihedral : 9.032 161.841 3979 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.30 (0.14), residues: 3543 helix: -0.43 (0.13), residues: 1540 sheet: 0.40 (0.24), residues: 520 loop : -1.75 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 241 TYR 0.033 0.002 TYR H 107 PHE 0.053 0.002 PHE F 408 TRP 0.039 0.002 TRP A 21 HIS 0.009 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00313 (28752) covalent geometry : angle 0.68981 (39006) hydrogen bonds : bond 0.03585 ( 951) hydrogen bonds : angle 4.77488 ( 2754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1002 time to evaluate : 1.128 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 HIS cc_start: 0.9133 (t-170) cc_final: 0.8846 (t-170) REVERT: A 20 PHE cc_start: 0.8107 (t80) cc_final: 0.7829 (t80) REVERT: A 51 PHE cc_start: 0.8971 (m-80) cc_final: 0.8567 (m-80) REVERT: A 136 THR cc_start: 0.8511 (m) cc_final: 0.8300 (t) REVERT: A 145 SER cc_start: 0.8988 (m) cc_final: 0.8564 (p) REVERT: A 147 MET cc_start: 0.8100 (ppp) cc_final: 0.7611 (ppp) REVERT: A 157 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 181 GLU cc_start: 0.9168 (pp20) cc_final: 0.8666 (pp20) REVERT: A 198 GLU cc_start: 0.8504 (pm20) cc_final: 0.7699 (tp30) REVERT: A 202 ILE cc_start: 0.8761 (mm) cc_final: 0.8522 (mm) REVERT: A 215 LEU cc_start: 0.9198 (mp) cc_final: 0.8957 (mp) REVERT: A 218 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8648 (tmtt) REVERT: A 252 LYS cc_start: 0.9018 (mptt) cc_final: 0.8186 (mppt) REVERT: A 256 ASN cc_start: 0.9401 (m-40) cc_final: 0.9060 (m-40) REVERT: A 265 PHE cc_start: 0.7766 (p90) cc_final: 0.6778 (p90) REVERT: A 288 LEU cc_start: 0.9463 (mt) cc_final: 0.9122 (mt) REVERT: A 330 ARG cc_start: 0.9021 (mtm180) cc_final: 0.8647 (mtp180) REVERT: A 340 PHE cc_start: 0.7381 (m-80) cc_final: 0.7124 (m-10) REVERT: A 355 VAL cc_start: 0.8012 (p) cc_final: 0.7746 (p) REVERT: A 405 MET cc_start: 0.7267 (mmt) cc_final: 0.7040 (mmm) REVERT: A 414 MET cc_start: 0.8208 (ttp) cc_final: 0.7935 (ptt) REVERT: A 423 GLN cc_start: 0.8176 (mt0) cc_final: 0.7846 (mt0) REVERT: D 5 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7400 (ttp80) REVERT: D 32 MET cc_start: 0.7722 (mmm) cc_final: 0.7396 (mmm) REVERT: D 54 ASN cc_start: 0.6816 (m-40) cc_final: 0.6214 (p0) REVERT: E 21 TRP cc_start: 0.8980 (m100) cc_final: 0.8555 (m100) REVERT: E 24 TYR cc_start: 0.8562 (m-10) cc_final: 0.8237 (m-10) REVERT: E 59 GLU cc_start: 0.7544 (mt-10) cc_final: 0.5642 (pt0) REVERT: E 69 SER cc_start: 0.9529 (p) cc_final: 0.9318 (p) REVERT: E 116 LYS cc_start: 0.8957 (tmmt) cc_final: 0.8550 (ttpt) REVERT: E 131 ASP cc_start: 0.7909 (m-30) cc_final: 0.7584 (m-30) REVERT: E 161 LEU cc_start: 0.8900 (pp) cc_final: 0.8639 (pp) REVERT: E 243 THR cc_start: 0.8081 (p) cc_final: 0.7837 (p) REVERT: E 270 HIS cc_start: 0.8112 (p-80) cc_final: 0.7792 (p-80) REVERT: E 356 LYS cc_start: 0.8831 (tptm) cc_final: 0.8202 (tppt) REVERT: E 377 ARG cc_start: 0.8658 (ptt180) cc_final: 0.8328 (ptt180) REVERT: E 381 MET cc_start: 0.8937 (ttt) cc_final: 0.8445 (ttp) REVERT: E 396 ASP cc_start: 0.9309 (t0) cc_final: 0.8892 (t0) REVERT: E 426 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8022 (tpt-90) REVERT: F 1 MET cc_start: 0.7954 (ptp) cc_final: 0.7594 (ptt) REVERT: F 21 TRP cc_start: 0.8376 (m100) cc_final: 0.7637 (m100) REVERT: F 24 TYR cc_start: 0.8739 (m-10) cc_final: 0.8132 (m-10) REVERT: F 30 ILE cc_start: 0.9195 (mt) cc_final: 0.8983 (mm) REVERT: F 55 THR cc_start: 0.8409 (p) cc_final: 0.7964 (p) REVERT: F 59 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6501 (pt0) REVERT: F 69 SER cc_start: 0.9352 (p) cc_final: 0.8945 (p) REVERT: F 131 ASP cc_start: 0.7908 (m-30) cc_final: 0.7595 (m-30) REVERT: F 187 GLU cc_start: 0.9198 (tt0) cc_final: 0.8642 (tp30) REVERT: F 239 VAL cc_start: 0.8930 (t) cc_final: 0.8717 (t) REVERT: F 247 ARG cc_start: 0.6602 (mmt90) cc_final: 0.4599 (mmt90) REVERT: F 270 HIS cc_start: 0.8128 (p-80) cc_final: 0.7648 (p-80) REVERT: F 349 ASP cc_start: 0.6178 (p0) cc_final: 0.5261 (p0) REVERT: F 381 MET cc_start: 0.8970 (tmm) cc_final: 0.8111 (tmm) REVERT: F 415 GLU cc_start: 0.6491 (pt0) cc_final: 0.6210 (pt0) REVERT: F 426 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8641 (mmp80) REVERT: F 441 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8407 (tm-30) REVERT: G 23 LEU cc_start: 0.9109 (tp) cc_final: 0.8437 (tt) REVERT: G 27 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7459 (mt-10) REVERT: G 59 GLU cc_start: 0.7068 (mt-10) cc_final: 0.5658 (pt0) REVERT: G 65 PHE cc_start: 0.7438 (p90) cc_final: 0.5515 (p90) REVERT: G 94 GLU cc_start: 0.7779 (tp30) cc_final: 0.7147 (tp30) REVERT: G 102 ASP cc_start: 0.7889 (t0) cc_final: 0.7207 (p0) REVERT: G 129 MET cc_start: 0.8987 (mmm) cc_final: 0.8726 (mmm) REVERT: G 133 CYS cc_start: 0.8890 (m) cc_final: 0.8656 (m) REVERT: G 143 HIS cc_start: 0.8270 (p90) cc_final: 0.8037 (p90) REVERT: G 145 PHE cc_start: 0.8736 (m-80) cc_final: 0.8342 (m-80) REVERT: G 167 LYS cc_start: 0.7877 (mptt) cc_final: 0.7494 (ptpt) REVERT: G 219 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6758 (ttp-170) REVERT: G 351 CYS cc_start: 0.8157 (t) cc_final: 0.7815 (t) REVERT: G 356 LYS cc_start: 0.8595 (tppt) cc_final: 0.8185 (tppt) REVERT: G 374 LYS cc_start: 0.9060 (tttm) cc_final: 0.8486 (tptp) REVERT: G 377 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7916 (mtm110) REVERT: G 380 CYS cc_start: 0.9086 (t) cc_final: 0.8454 (p) REVERT: G 381 MET cc_start: 0.8865 (tmm) cc_final: 0.8192 (tmm) REVERT: G 441 GLN cc_start: 0.8728 (mm110) cc_final: 0.8347 (tm-30) REVERT: H 20 CYS cc_start: 0.8810 (m) cc_final: 0.8474 (m) REVERT: H 27 GLU cc_start: 0.8524 (tt0) cc_final: 0.8318 (tt0) REVERT: H 57 PHE cc_start: 0.8205 (m-80) cc_final: 0.7066 (m-80) REVERT: H 73 ASP cc_start: 0.8340 (t0) cc_final: 0.7833 (t0) REVERT: H 94 GLU cc_start: 0.7814 (tp30) cc_final: 0.7329 (tp30) REVERT: H 143 HIS cc_start: 0.8774 (p90) cc_final: 0.7973 (p90) REVERT: H 145 PHE cc_start: 0.9016 (m-80) cc_final: 0.8479 (m-80) REVERT: H 187 GLU cc_start: 0.8736 (tt0) cc_final: 0.8130 (tp30) REVERT: H 276 TYR cc_start: 0.8138 (t80) cc_final: 0.7664 (t80) REVERT: H 301 GLU cc_start: 0.8474 (tt0) cc_final: 0.7974 (tm-30) REVERT: H 306 MET cc_start: 0.8876 (mtp) cc_final: 0.8606 (ttt) REVERT: H 308 LYS cc_start: 0.8678 (tptp) cc_final: 0.8311 (mmtt) REVERT: H 343 ARG cc_start: 0.8690 (ptt180) cc_final: 0.8097 (mtt180) REVERT: H 346 GLN cc_start: 0.7944 (mp10) cc_final: 0.7400 (mm-40) REVERT: H 419 GLU cc_start: 0.8831 (pm20) cc_final: 0.8577 (pm20) REVERT: H 426 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8072 (mmm160) REVERT: H 441 GLN cc_start: 0.8749 (mm110) cc_final: 0.8491 (tm-30) REVERT: J 1 MET cc_start: 0.8473 (tpp) cc_final: 0.8079 (tpt) REVERT: J 6 HIS cc_start: 0.9194 (t-170) cc_final: 0.8916 (t-170) REVERT: J 14 ASN cc_start: 0.9334 (m-40) cc_final: 0.8982 (m-40) REVERT: J 21 TRP cc_start: 0.9201 (m100) cc_final: 0.8689 (m100) REVERT: J 53 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7291 (tm-30) REVERT: J 83 ASN cc_start: 0.8517 (m-40) cc_final: 0.8055 (m110) REVERT: J 84 LEU cc_start: 0.8908 (mt) cc_final: 0.8464 (mm) REVERT: J 86 ARG cc_start: 0.6943 (ptp-170) cc_final: 0.6614 (ptp-170) REVERT: J 111 GLU cc_start: 0.8234 (tt0) cc_final: 0.7631 (tp30) REVERT: J 147 MET cc_start: 0.8373 (tmm) cc_final: 0.7637 (tmm) REVERT: J 151 LEU cc_start: 0.9611 (mp) cc_final: 0.9403 (mp) REVERT: J 157 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8238 (tm-30) REVERT: J 164 MET cc_start: 0.8282 (mmp) cc_final: 0.7063 (mmp) REVERT: J 174 LYS cc_start: 0.8924 (mppt) cc_final: 0.8422 (mtmt) REVERT: J 189 MET cc_start: 0.8798 (mmp) cc_final: 0.8237 (mmp) REVERT: J 198 GLU cc_start: 0.8900 (pm20) cc_final: 0.7796 (tp30) REVERT: J 216 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8709 (mmmt) REVERT: J 233 MET cc_start: 0.9012 (mtp) cc_final: 0.8805 (ttp) REVERT: J 252 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8562 (mmtp) REVERT: J 265 PHE cc_start: 0.7879 (p90) cc_final: 0.6681 (p90) REVERT: J 365 THR cc_start: 0.8821 (m) cc_final: 0.8409 (p) REVERT: J 372 SER cc_start: 0.9179 (p) cc_final: 0.8969 (p) REVERT: J 376 ILE cc_start: 0.8798 (pt) cc_final: 0.8541 (pt) REVERT: J 412 SER cc_start: 0.9266 (m) cc_final: 0.9016 (p) REVERT: J 415 ASN cc_start: 0.8324 (m-40) cc_final: 0.7895 (t0) REVERT: B 14 ASN cc_start: 0.8988 (m-40) cc_final: 0.8706 (m-40) REVERT: B 20 PHE cc_start: 0.8644 (t80) cc_final: 0.8315 (t80) REVERT: B 21 TRP cc_start: 0.9182 (m100) cc_final: 0.8296 (m100) REVERT: B 51 PHE cc_start: 0.9127 (m-80) cc_final: 0.8735 (m-80) REVERT: B 53 GLU cc_start: 0.7771 (mt-10) cc_final: 0.6967 (tm-30) REVERT: B 59 TYR cc_start: 0.8484 (m-10) cc_final: 0.8201 (m-80) REVERT: B 101 TRP cc_start: 0.7902 (t60) cc_final: 0.7488 (t60) REVERT: B 147 MET cc_start: 0.8303 (tmm) cc_final: 0.7614 (tmm) REVERT: B 151 LEU cc_start: 0.9631 (mt) cc_final: 0.9301 (mt) REVERT: B 164 MET cc_start: 0.7983 (mmp) cc_final: 0.6665 (mmp) REVERT: B 174 LYS cc_start: 0.9042 (mppt) cc_final: 0.8797 (mppt) REVERT: B 181 GLU cc_start: 0.8002 (tt0) cc_final: 0.7781 (tt0) REVERT: B 189 MET cc_start: 0.8799 (tpp) cc_final: 0.8453 (tpp) REVERT: B 198 GLU cc_start: 0.8700 (pm20) cc_final: 0.7662 (tp30) REVERT: B 233 MET cc_start: 0.9157 (mtm) cc_final: 0.8556 (mmm) REVERT: B 344 ILE cc_start: 0.9089 (mt) cc_final: 0.8881 (mp) REVERT: B 395 HIS cc_start: 0.8779 (p-80) cc_final: 0.8110 (p-80) REVERT: C 6 HIS cc_start: 0.9041 (t70) cc_final: 0.7962 (t-170) REVERT: C 20 PHE cc_start: 0.8237 (t80) cc_final: 0.7494 (t80) REVERT: C 35 ILE cc_start: 0.8821 (mp) cc_final: 0.8392 (mm) REVERT: C 53 GLU cc_start: 0.7713 (mt-10) cc_final: 0.6886 (tm-30) REVERT: C 101 TRP cc_start: 0.8366 (t60) cc_final: 0.8061 (t60) REVERT: C 157 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8641 (tm-30) REVERT: C 174 LYS cc_start: 0.8931 (mppt) cc_final: 0.8726 (mppt) REVERT: C 241 ARG cc_start: 0.8020 (ptp-110) cc_final: 0.7656 (ptp-110) REVERT: C 297 ASN cc_start: 0.9274 (m-40) cc_final: 0.8784 (t0) REVERT: C 394 LEU cc_start: 0.8910 (tp) cc_final: 0.8612 (tt) REVERT: C 423 GLN cc_start: 0.7896 (mt0) cc_final: 0.7547 (mt0) outliers start: 1 outliers final: 0 residues processed: 1002 average time/residue: 0.1873 time to fit residues: 299.9269 Evaluate side-chains 825 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 825 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 119 optimal weight: 10.0000 chunk 331 optimal weight: 0.6980 chunk 322 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 42 optimal weight: 40.0000 chunk 348 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 310 optimal weight: 0.8980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 91 ASN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN F 257 ASN ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104713 restraints weight = 59703.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108182 restraints weight = 34949.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110607 restraints weight = 22450.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.112343 restraints weight = 15426.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.113569 restraints weight = 11138.575| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28752 Z= 0.132 Angle : 0.692 12.525 39006 Z= 0.341 Chirality : 0.048 0.188 4200 Planarity : 0.005 0.104 5117 Dihedral : 8.913 160.942 3979 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.14), residues: 3543 helix: -0.36 (0.14), residues: 1509 sheet: 0.44 (0.24), residues: 496 loop : -1.65 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 241 TYR 0.029 0.002 TYR H 107 PHE 0.037 0.002 PHE E 408 TRP 0.036 0.002 TRP A 21 HIS 0.008 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00305 (28752) covalent geometry : angle 0.69249 (39006) hydrogen bonds : bond 0.03509 ( 951) hydrogen bonds : angle 4.72089 ( 2754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.40 seconds wall clock time: 101 minutes 17.76 seconds (6077.76 seconds total)