Starting phenix.real_space_refine on Mon Jun 23 23:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mjs_3522/06_2025/5mjs_3522.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mjs_3522/06_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_3522/06_2025/5mjs_3522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mjs_3522/06_2025/5mjs_3522.map" model { file = "/net/cci-nas-00/data/ceres_data/5mjs_3522/06_2025/5mjs_3522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mjs_3522/06_2025/5mjs_3522.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.13, per 1000 atoms: 0.61 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: 7.76 Conformation dependent library (CDL) restraints added in 3.6 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: 3.59 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: 9.75 Time building geometry restraints manager: 8.87 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 63.380 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.180 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.004 TRP D 97 HIS 0.013 0.004 HIS H 196 PHE 0.059 0.004 PHE E 57 TYR 0.032 0.004 TYR H 214 ARG 0.014 0.002 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.32377 ( 951) hydrogen bonds : angle 10.84439 ( 2754) covalent geometry : bond 0.00981 (28752) covalent geometry : angle 1.16646 (39006) *********************** 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 : 3.035 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: 0.8696 (t-90) cc_final: 0.8471 (t-170) REVERT: A 35 ILE cc_start: 0.8902 (tt) cc_final: 0.8232 (tp) REVERT: A 53 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6461 (tm-30) REVERT: A 88 ASP cc_start: 0.8598 (m-30) cc_final: 0.8243 (p0) REVERT: A 89 ASN cc_start: 0.8921 (m-40) cc_final: 0.8109 (m110) REVERT: A 134 GLN cc_start: 0.6904 (mt0) cc_final: 0.6623 (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: 0.8311 (mmm160) REVERT: A 204 ASN cc_start: 0.9092 (m-40) cc_final: 0.8724 (p0) REVERT: A 280 PHE cc_start: 0.7593 (m-10) cc_final: 0.7011 (m-10) REVERT: A 292 MET cc_start: 0.7799 (mtm) cc_final: 0.7537 (mtp) REVERT: A 325 VAL cc_start: 0.9019 (t) cc_final: 0.8814 (t) REVERT: A 340 PHE cc_start: 0.7272 (m-80) cc_final: 0.7024 (m-10) REVERT: A 372 SER cc_start: 0.9349 (p) cc_final: 0.8963 (m) REVERT: A 414 MET cc_start: 0.8877 (ttm) cc_final: 0.8547 (ttm) REVERT: D 14 GLN cc_start: 0.7011 (tt0) cc_final: 0.5151 (tp40) REVERT: D 32 MET cc_start: 0.6410 (mmm) cc_final: 0.5537 (mmm) REVERT: D 35 ILE cc_start: 0.8235 (mt) cc_final: 0.8017 (mt) REVERT: D 65 LEU cc_start: 0.9029 (mt) cc_final: 0.8825 (mp) REVERT: D 71 LYS cc_start: 0.7971 (mttt) cc_final: 0.7624 (mmtp) REVERT: D 106 TYR cc_start: 0.5761 (m-10) cc_final: 0.5326 (m-10) REVERT: E 18 ASN cc_start: 0.9208 (m110) cc_final: 0.8875 (m110) REVERT: E 21 TRP cc_start: 0.9254 (m100) cc_final: 0.8966 (m100) REVERT: E 59 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7190 (pt0) REVERT: E 64 LYS cc_start: 0.8772 (pttm) cc_final: 0.7951 (ptpp) REVERT: E 73 ASP cc_start: 0.7785 (t0) cc_final: 0.7373 (t0) REVERT: E 74 LEU cc_start: 0.7883 (mt) cc_final: 0.7632 (mt) REVERT: E 94 GLU cc_start: 0.8312 (tt0) cc_final: 0.8074 (tm-30) REVERT: E 100 LYS cc_start: 0.8673 (mttm) cc_final: 0.8350 (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: 0.9126 (m) REVERT: E 119 ILE cc_start: 0.8680 (mm) cc_final: 0.8430 (mm) REVERT: E 120 ASP cc_start: 0.8681 (m-30) cc_final: 0.8369 (m-30) REVERT: E 131 ASP cc_start: 0.8168 (m-30) cc_final: 0.7933 (m-30) REVERT: E 156 LEU cc_start: 0.9238 (tt) cc_final: 0.8974 (tp) REVERT: E 158 LEU cc_start: 0.9331 (mp) cc_final: 0.9024 (mp) REVERT: E 201 ASN cc_start: 0.8644 (m110) cc_final: 0.7698 (t0) REVERT: E 209 ASP cc_start: 0.8214 (t0) cc_final: 0.7635 (t0) REVERT: E 213 CYS cc_start: 0.8796 (t) cc_final: 0.8335 (t) REVERT: E 252 LEU cc_start: 0.9087 (mt) cc_final: 0.8819 (mt) REVERT: E 255 ASP cc_start: 0.8643 (t70) cc_final: 0.7923 (m-30) REVERT: E 257 ASN cc_start: 0.8759 (t0) cc_final: 0.8082 (t0) REVERT: E 270 HIS cc_start: 0.8338 (p-80) cc_final: 0.8072 (p-80) REVERT: E 295 ILE cc_start: 0.9098 (mt) cc_final: 0.8787 (tp) REVERT: E 308 LYS cc_start: 0.8580 (tptp) cc_final: 0.7826 (mmtp) REVERT: E 309 CYS cc_start: 0.8962 (m) cc_final: 0.8725 (p) REVERT: E 365 GLN cc_start: 0.9266 (tp40) cc_final: 0.9028 (tp40) REVERT: E 374 LYS cc_start: 0.8495 (tttm) cc_final: 0.7944 (tptp) REVERT: E 402 MET cc_start: 0.8946 (mmt) cc_final: 0.8233 (mmt) REVERT: E 415 GLU cc_start: 0.6830 (pt0) cc_final: 0.6464 (pt0) REVERT: F 18 ASN cc_start: 0.9094 (m110) cc_final: 0.8797 (m110) REVERT: F 21 TRP cc_start: 0.8863 (m100) cc_final: 0.8146 (m100) REVERT: F 30 ILE cc_start: 0.9205 (mt) cc_final: 0.8858 (mt) REVERT: F 59 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7618 (pt0) REVERT: F 82 VAL cc_start: 0.8654 (t) cc_final: 0.8399 (p) REVERT: F 131 ASP cc_start: 0.7605 (m-30) cc_final: 0.7198 (m-30) REVERT: F 149 THR cc_start: 0.9213 (m) cc_final: 0.8796 (p) REVERT: F 219 ARG cc_start: 0.7123 (mtm110) cc_final: 0.6787 (tmm-80) REVERT: F 225 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7685 (mtt-85) REVERT: F 255 ASP cc_start: 0.8425 (t70) cc_final: 0.8085 (m-30) REVERT: F 256 LEU cc_start: 0.9378 (mt) cc_final: 0.8938 (mm) REVERT: F 260 GLN cc_start: 0.8492 (pt0) cc_final: 0.8248 (pm20) REVERT: F 268 ARG cc_start: 0.8497 (mmt90) cc_final: 0.7661 (mmm-85) REVERT: F 270 HIS cc_start: 0.8752 (p-80) cc_final: 0.8105 (p-80) REVERT: F 287 HIS cc_start: 0.7968 (m170) cc_final: 0.7516 (m170) REVERT: F 308 LYS cc_start: 0.8275 (tptp) cc_final: 0.8006 (mmtp) REVERT: F 330 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7798 (tpp-160) REVERT: F 344 THR cc_start: 0.9340 (t) cc_final: 0.9135 (p) REVERT: F 382 LEU cc_start: 0.9002 (mt) cc_final: 0.8797 (mp) REVERT: F 415 GLU cc_start: 0.6685 (pt0) cc_final: 0.6209 (pt0) REVERT: F 424 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7841 (mt-10) REVERT: G 59 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6348 (pt0) REVERT: G 64 LYS cc_start: 0.8413 (pttm) cc_final: 0.7804 (ptpp) REVERT: G 67 PRO cc_start: 0.9549 (Cg_endo) cc_final: 0.9235 (Cg_exo) REVERT: G 73 ASP cc_start: 0.8751 (t0) cc_final: 0.8443 (t0) REVERT: G 82 VAL cc_start: 0.8913 (t) cc_final: 0.8689 (p) REVERT: G 90 LEU cc_start: 0.9238 (tp) cc_final: 0.8937 (tp) REVERT: G 116 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8553 (ptmt) REVERT: G 129 MET cc_start: 0.9299 (mmt) cc_final: 0.9025 (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: 0.8670 (tp) REVERT: G 143 HIS cc_start: 0.8513 (p90) cc_final: 0.8171 (p90) REVERT: G 159 GLU cc_start: 0.8452 (pt0) cc_final: 0.7969 (pt0) REVERT: G 209 ASP cc_start: 0.7854 (t0) cc_final: 0.7436 (t0) REVERT: G 237 GLN cc_start: 0.8787 (mt0) cc_final: 0.8545 (mt0) REVERT: G 242 ILE cc_start: 0.9361 (mt) cc_final: 0.9156 (tp) REVERT: G 270 HIS cc_start: 0.8800 (p-80) cc_final: 0.8461 (p-80) REVERT: G 295 ILE cc_start: 0.9332 (mt) cc_final: 0.8961 (tp) REVERT: G 306 MET cc_start: 0.8415 (mmt) cc_final: 0.8204 (mmt) REVERT: G 308 LYS cc_start: 0.8780 (tptp) cc_final: 0.8429 (ttmm) REVERT: G 343 ARG cc_start: 0.8580 (ptm160) cc_final: 0.7977 (mtt180) REVERT: G 365 GLN cc_start: 0.9063 (tp40) cc_final: 0.8611 (tp-100) REVERT: G 374 LYS cc_start: 0.8415 (tttm) cc_final: 0.8086 (tptp) REVERT: G 380 CYS cc_start: 0.9086 (t) cc_final: 0.8654 (t) REVERT: G 382 LEU cc_start: 0.9671 (mt) cc_final: 0.9287 (mp) REVERT: G 390 GLU cc_start: 0.7706 (pt0) cc_final: 0.7423 (pt0) REVERT: G 396 ASP cc_start: 0.9214 (t0) cc_final: 0.8261 (t0) REVERT: G 403 TYR cc_start: 0.8360 (t80) cc_final: 0.8094 (t80) REVERT: G 424 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8005 (mt-10) 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: 0.8340 (mt0) REVERT: H 21 TRP cc_start: 0.8684 (m100) cc_final: 0.8387 (m100) REVERT: H 70 ILE cc_start: 0.8389 (tp) cc_final: 0.7339 (mt) REVERT: H 73 ASP cc_start: 0.8608 (t0) cc_final: 0.8293 (t0) REVERT: H 79 ILE cc_start: 0.9199 (mm) cc_final: 0.8723 (tp) REVERT: H 94 GLU cc_start: 0.8389 (tt0) cc_final: 0.7920 (tm-30) REVERT: H 97 VAL cc_start: 0.9470 (p) cc_final: 0.9072 (m) REVERT: H 116 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8528 (ptpt) REVERT: H 137 GLN cc_start: 0.8546 (mt0) cc_final: 0.8119 (mm-40) REVERT: H 143 HIS cc_start: 0.8503 (p90) cc_final: 0.7890 (p90) REVERT: H 149 THR cc_start: 0.9129 (m) cc_final: 0.8752 (p) REVERT: H 206 PHE cc_start: 0.8876 (m-80) cc_final: 0.8508 (m-80) REVERT: H 243 THR cc_start: 0.9060 (p) cc_final: 0.8070 (p) REVERT: H 247 ARG cc_start: 0.7232 (mmt90) cc_final: 0.4975 (mmt90) REVERT: H 270 HIS cc_start: 0.8806 (p-80) cc_final: 0.7718 (p-80) REVERT: H 275 THR cc_start: 0.7145 (m) cc_final: 0.6159 (m) REVERT: H 287 HIS cc_start: 0.7643 (m170) cc_final: 0.7000 (m170) REVERT: H 308 LYS cc_start: 0.8878 (tptp) cc_final: 0.8435 (mmtp) REVERT: H 344 THR cc_start: 0.9285 (t) cc_final: 0.9079 (m) REVERT: H 353 THR cc_start: 0.9274 (m) cc_final: 0.8986 (p) REVERT: H 374 LYS cc_start: 0.9035 (tttm) cc_final: 0.8600 (ttmm) REVERT: H 382 LEU cc_start: 0.9552 (mt) cc_final: 0.9119 (mp) REVERT: H 396 ASP cc_start: 0.9127 (t0) cc_final: 0.8439 (t0) REVERT: H 415 GLU cc_start: 0.6336 (pt0) cc_final: 0.6038 (pt0) REVERT: H 424 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8006 (mt-10) REVERT: H 441 GLN cc_start: 0.8891 (mm110) cc_final: 0.7749 (tm-30) REVERT: J 6 HIS cc_start: 0.8748 (t-90) cc_final: 0.8516 (t-170) REVERT: J 51 PHE cc_start: 0.9146 (m-80) cc_final: 0.8883 (m-80) REVERT: J 53 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7696 (tm-30) REVERT: J 64 VAL cc_start: 0.9663 (t) cc_final: 0.9450 (t) REVERT: J 130 LEU cc_start: 0.9384 (mt) cc_final: 0.9070 (mp) REVERT: J 134 GLN cc_start: 0.8430 (mt0) cc_final: 0.7777 (mt0) REVERT: J 136 THR cc_start: 0.9065 (m) cc_final: 0.8860 (m) REVERT: J 150 LEU cc_start: 0.9504 (tt) cc_final: 0.9242 (tp) REVERT: J 181 GLU cc_start: 0.7564 (tt0) cc_final: 0.7107 (tt0) REVERT: J 190 HIS cc_start: 0.8695 (t70) cc_final: 0.8462 (t-90) REVERT: J 198 GLU cc_start: 0.8161 (pt0) cc_final: 0.7474 (tp30) REVERT: J 204 ASN cc_start: 0.8917 (m-40) cc_final: 0.8558 (p0) REVERT: J 233 MET cc_start: 0.9227 (mtm) cc_final: 0.8992 (mtm) REVERT: J 265 PHE cc_start: 0.7380 (p90) cc_final: 0.6470 (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 365 THR cc_start: 0.8280 (m) cc_final: 0.7826 (p) REVERT: B 53 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7366 (tm-30) REVERT: B 64 VAL cc_start: 0.9265 (t) cc_final: 0.9053 (t) REVERT: B 65 LEU cc_start: 0.9247 (mp) cc_final: 0.8584 (mt) 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: 0.7829 (m-80) REVERT: B 101 TRP cc_start: 0.9063 (t60) cc_final: 0.8695 (t60) REVERT: B 117 LEU cc_start: 0.9003 (mp) cc_final: 0.8648 (mp) REVERT: B 127 CYS cc_start: 0.8154 (t) cc_final: 0.5689 (t) REVERT: B 130 LEU cc_start: 0.9604 (mt) cc_final: 0.8736 (mp) REVERT: B 154 LYS cc_start: 0.8908 (mttt) cc_final: 0.8629 (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: 0.8845 (p) REVERT: B 221 SER cc_start: 0.9097 (t) cc_final: 0.8743 (p) REVERT: B 233 MET cc_start: 0.9443 (mtm) cc_final: 0.9148 (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: 0.8801 (mt) REVERT: B 319 LYS cc_start: 0.8909 (tppt) cc_final: 0.8620 (tptm) REVERT: B 352 VAL cc_start: 0.9115 (t) cc_final: 0.8019 (t) REVERT: B 358 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7636 (pttm) REVERT: B 372 SER cc_start: 0.9035 (p) cc_final: 0.8493 (m) REVERT: B 405 MET cc_start: 0.7837 (ttm) cc_final: 0.7211 (tmm) REVERT: B 408 THR cc_start: 0.8701 (p) cc_final: 0.8353 (p) REVERT: C 1 MET cc_start: 0.8175 (mmp) cc_final: 0.7741 (mmm) REVERT: C 6 HIS cc_start: 0.8986 (t-90) cc_final: 0.8343 (t70) REVERT: C 30 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7511 (tp) REVERT: C 35 ILE cc_start: 0.8592 (tt) cc_final: 0.8338 (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: 0.8524 (mp) REVERT: C 101 TRP cc_start: 0.8898 (t60) cc_final: 0.8386 (t60) REVERT: C 154 LYS cc_start: 0.8711 (mttt) cc_final: 0.8484 (mtmt) REVERT: C 177 ASP cc_start: 0.7369 (t0) cc_final: 0.7102 (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: 0.8837 (mm) REVERT: C 233 MET cc_start: 0.9379 (mtm) cc_final: 0.8895 (mtm) REVERT: C 315 LEU cc_start: 0.9149 (mt) cc_final: 0.8545 (mt) REVERT: C 339 TYR cc_start: 0.8474 (m-80) cc_final: 0.8116 (m-80) REVERT: C 343 TRP cc_start: 0.6605 (m100) cc_final: 0.6320 (m100) outliers start: 20 outliers final: 3 residues processed: 1459 average time/residue: 0.4122 time to fit residues: 931.6962 Evaluate side-chains 952 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 948 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 6.9990 chunk 266 optimal weight: 20.0000 chunk 148 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 275 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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** ** 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 F 304 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 137 HIS J 195 ASN J 328 GLN J 415 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 6 HIS C 14 ASN C 37 HIS 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 C 347 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106230 restraints weight = 59602.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109759 restraints weight = 34810.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112172 restraints weight = 22379.149| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3954 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= 0.171 Angle : 0.711 8.661 39006 Z= 0.371 Chirality : 0.050 0.211 4200 Planarity : 0.007 0.079 5117 Dihedral : 10.571 156.140 3979 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.53 % Allowed : 3.89 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.12), residues: 3543 helix: -2.30 (0.11), residues: 1450 sheet: -0.54 (0.23), residues: 484 loop : -2.26 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 411 HIS 0.007 0.001 HIS C 263 PHE 0.020 0.002 PHE A 242 TYR 0.021 0.002 TYR F 228 ARG 0.008 0.001 ARG G 426 Details of bonding type rmsd hydrogen bonds : bond 0.05424 ( 951) hydrogen bonds : angle 6.47543 ( 2754) covalent geometry : bond 0.00360 (28752) covalent geometry : angle 0.71063 (39006) *********************** 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 1232 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1216 time to evaluate : 3.054 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: A 6 HIS cc_start: 0.8856 (t-90) cc_final: 0.8204 (t-170) REVERT: A 14 ASN cc_start: 0.9226 (m-40) cc_final: 0.8898 (m-40) REVERT: A 88 ASP cc_start: 0.8586 (m-30) cc_final: 0.8017 (p0) REVERT: A 89 ASN cc_start: 0.8790 (m-40) cc_final: 0.8127 (m-40) REVERT: A 101 TRP cc_start: 0.9130 (t60) cc_final: 0.8575 (t60) REVERT: A 136 THR cc_start: 0.8694 (m) cc_final: 0.8344 (t) REVERT: A 162 ARG cc_start: 0.8360 (mmt-90) cc_final: 0.7675 (mmt180) REVERT: A 164 MET cc_start: 0.8181 (mmp) cc_final: 0.6986 (mmp) REVERT: A 169 VAL cc_start: 0.9146 (m) cc_final: 0.8835 (p) REVERT: A 280 PHE cc_start: 0.7657 (m-10) cc_final: 0.7399 (m-10) REVERT: A 330 ARG cc_start: 0.9127 (mtm180) cc_final: 0.8827 (mtp85) REVERT: A 340 PHE cc_start: 0.7487 (m-80) cc_final: 0.7141 (m-80) REVERT: A 352 VAL cc_start: 0.8664 (m) cc_final: 0.8251 (m) REVERT: A 372 SER cc_start: 0.9324 (p) cc_final: 0.9062 (m) REVERT: A 387 MET cc_start: 0.8064 (mtp) cc_final: 0.7852 (mtt) REVERT: D 32 MET cc_start: 0.7982 (mmm) cc_final: 0.7609 (mmm) REVERT: D 71 LYS cc_start: 0.7813 (mttt) cc_final: 0.7537 (mmtp) REVERT: D 106 TYR cc_start: 0.6432 (m-10) cc_final: 0.6200 (m-10) REVERT: E 21 TRP cc_start: 0.9037 (m100) cc_final: 0.8628 (m100) REVERT: E 23 LEU cc_start: 0.9117 (tt) cc_final: 0.8400 (tt) REVERT: E 59 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6578 (pt0) REVERT: E 65 PHE cc_start: 0.7216 (p90) cc_final: 0.6167 (p90) REVERT: E 131 ASP cc_start: 0.8020 (m-30) cc_final: 0.7817 (m-30) REVERT: E 156 LEU cc_start: 0.9636 (tt) cc_final: 0.9343 (tp) REVERT: E 162 ASN cc_start: 0.8626 (t0) cc_final: 0.8424 (t0) REVERT: E 192 VAL cc_start: 0.8971 (p) cc_final: 0.8690 (m) REVERT: E 201 ASN cc_start: 0.7993 (m-40) cc_final: 0.7353 (m-40) REVERT: E 213 CYS cc_start: 0.8228 (t) cc_final: 0.7953 (t) REVERT: E 243 THR cc_start: 0.8703 (p) cc_final: 0.8459 (p) REVERT: E 260 GLN cc_start: 0.8461 (pt0) cc_final: 0.8055 (pt0) REVERT: E 270 HIS cc_start: 0.8567 (p-80) cc_final: 0.8335 (p-80) REVERT: E 308 LYS cc_start: 0.8398 (tptp) cc_final: 0.7817 (mmtp) REVERT: E 343 ARG cc_start: 0.7930 (ptt180) cc_final: 0.7678 (mmt180) REVERT: E 344 THR cc_start: 0.8819 (t) cc_final: 0.8504 (p) REVERT: E 381 MET cc_start: 0.8767 (ttt) cc_final: 0.8335 (ttp) REVERT: E 402 MET cc_start: 0.9288 (mmt) cc_final: 0.8552 (mmt) REVERT: E 415 GLU cc_start: 0.6804 (pt0) cc_final: 0.6539 (pt0) REVERT: F 18 ASN cc_start: 0.9021 (m110) cc_final: 0.8790 (m110) REVERT: F 21 TRP cc_start: 0.8723 (m100) cc_final: 0.7976 (m100) REVERT: F 24 TYR cc_start: 0.8903 (m-10) cc_final: 0.8186 (m-10) REVERT: F 30 ILE cc_start: 0.9289 (mt) cc_final: 0.8946 (mt) REVERT: F 59 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7176 (pt0) REVERT: F 65 PHE cc_start: 0.7459 (p90) cc_final: 0.6159 (p90) REVERT: F 131 ASP cc_start: 0.7645 (m-30) cc_final: 0.7358 (m-30) REVERT: F 136 LEU cc_start: 0.8724 (tp) cc_final: 0.8432 (tp) REVERT: F 153 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8459 (tt) REVERT: F 204 CYS cc_start: 0.8592 (t) cc_final: 0.8351 (t) REVERT: F 219 ARG cc_start: 0.7142 (mtm110) cc_final: 0.6794 (ttp-170) REVERT: F 225 ARG cc_start: 0.7886 (ptp90) cc_final: 0.7204 (mtt-85) REVERT: F 231 LEU cc_start: 0.9498 (mp) cc_final: 0.9253 (mp) REVERT: F 243 THR cc_start: 0.8883 (p) cc_final: 0.8558 (p) REVERT: F 256 LEU cc_start: 0.9469 (mt) cc_final: 0.9106 (mm) REVERT: F 270 HIS cc_start: 0.8783 (p-80) cc_final: 0.8056 (p-80) REVERT: F 304 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8431 (t0) REVERT: F 441 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8043 (tm-30) REVERT: G 59 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5345 (pt0) REVERT: G 64 LYS cc_start: 0.8394 (pttm) cc_final: 0.7918 (ptpp) REVERT: G 65 PHE cc_start: 0.7329 (p90) cc_final: 0.6109 (p90) REVERT: G 94 GLU cc_start: 0.8151 (tt0) cc_final: 0.7609 (tp30) REVERT: G 97 VAL cc_start: 0.9473 (p) cc_final: 0.9267 (m) REVERT: G 124 GLU cc_start: 0.8324 (tt0) cc_final: 0.8097 (tt0) REVERT: G 133 CYS cc_start: 0.8956 (m) cc_final: 0.8571 (m) REVERT: G 159 GLU cc_start: 0.8226 (pt0) cc_final: 0.7826 (pt0) REVERT: G 206 PHE cc_start: 0.9363 (m-80) cc_final: 0.8535 (m-80) REVERT: G 215 ASP cc_start: 0.7993 (m-30) cc_final: 0.7676 (m-30) REVERT: G 270 HIS cc_start: 0.8714 (p-80) cc_final: 0.8371 (p-80) REVERT: G 301 GLU cc_start: 0.8979 (tt0) cc_final: 0.8135 (tt0) REVERT: G 306 MET cc_start: 0.8410 (mmt) cc_final: 0.8090 (mmm) REVERT: G 308 LYS cc_start: 0.8536 (tptp) cc_final: 0.8072 (tptt) REVERT: G 343 ARG cc_start: 0.8582 (ptm160) cc_final: 0.8211 (mtt180) REVERT: G 351 CYS cc_start: 0.8452 (t) cc_final: 0.7964 (t) REVERT: G 374 LYS cc_start: 0.8545 (tttm) cc_final: 0.8208 (tmtt) REVERT: G 381 MET cc_start: 0.9146 (tmm) cc_final: 0.8671 (tmm) REVERT: G 408 PHE cc_start: 0.6800 (m-10) cc_final: 0.6074 (m-10) REVERT: G 424 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8412 (pt0) REVERT: G 441 GLN cc_start: 0.9038 (mm110) cc_final: 0.8318 (tm-30) REVERT: H 77 ASN cc_start: 0.8174 (t0) cc_final: 0.7845 (t0) REVERT: H 80 ASP cc_start: 0.8748 (m-30) cc_final: 0.8517 (p0) REVERT: H 94 GLU cc_start: 0.8081 (tt0) cc_final: 0.7733 (tm-30) REVERT: H 109 ARG cc_start: 0.5840 (ptp90) cc_final: 0.5464 (ptp-110) REVERT: H 125 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7147 (mtt90) REVERT: H 137 GLN cc_start: 0.8452 (mt0) cc_final: 0.7934 (mm-40) REVERT: H 167 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8493 (mmtp) REVERT: H 206 PHE cc_start: 0.8664 (m-80) cc_final: 0.8418 (m-80) REVERT: H 209 ASP cc_start: 0.8296 (t0) cc_final: 0.8019 (t0) REVERT: H 237 GLN cc_start: 0.8958 (mt0) cc_final: 0.8413 (mt0) REVERT: H 247 ARG cc_start: 0.7227 (mmt90) cc_final: 0.5037 (mmt90) REVERT: H 268 ARG cc_start: 0.8733 (mmt90) cc_final: 0.8346 (mmm-85) REVERT: H 270 HIS cc_start: 0.8701 (p-80) cc_final: 0.7648 (p-80) REVERT: H 287 HIS cc_start: 0.7652 (m170) cc_final: 0.7378 (m170) REVERT: H 304 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8525 (t0) REVERT: H 317 MET cc_start: 0.7148 (mmm) cc_final: 0.6600 (tpt) REVERT: H 343 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7780 (mtt180) REVERT: H 374 LYS cc_start: 0.9028 (tttm) cc_final: 0.8567 (tmtt) REVERT: H 402 MET cc_start: 0.8529 (mmp) cc_final: 0.8319 (mmp) REVERT: H 415 GLU cc_start: 0.6662 (pt0) cc_final: 0.5777 (pt0) REVERT: H 424 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8301 (mt-10) REVERT: H 429 LEU cc_start: 0.9334 (tp) cc_final: 0.9083 (tp) REVERT: H 441 GLN cc_start: 0.8814 (mm110) cc_final: 0.7836 (tm-30) REVERT: J 6 HIS cc_start: 0.8813 (t-90) cc_final: 0.8445 (t-170) REVERT: J 14 ASN cc_start: 0.9141 (m-40) cc_final: 0.8713 (m-40) REVERT: J 21 TRP cc_start: 0.9090 (m100) cc_final: 0.8540 (m100) REVERT: J 50 TYR cc_start: 0.8043 (m-10) cc_final: 0.7735 (m-10) REVERT: J 51 PHE cc_start: 0.8918 (m-80) cc_final: 0.8691 (m-80) REVERT: J 53 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7664 (tm-30) REVERT: J 67 ASP cc_start: 0.8248 (t0) cc_final: 0.7807 (p0) REVERT: J 68 LEU cc_start: 0.8799 (mm) cc_final: 0.8587 (mm) REVERT: J 84 LEU cc_start: 0.8882 (mt) cc_final: 0.8494 (mt) REVERT: J 89 ASN cc_start: 0.9183 (m110) cc_final: 0.8930 (m110) REVERT: J 134 GLN cc_start: 0.8460 (mt0) cc_final: 0.8038 (mt0) REVERT: J 164 MET cc_start: 0.8191 (mmp) cc_final: 0.7905 (mmm) REVERT: J 174 LYS cc_start: 0.9025 (mppt) cc_final: 0.8611 (mttp) REVERT: J 189 MET cc_start: 0.8476 (mmt) cc_final: 0.8017 (mmp) REVERT: J 204 ASN cc_start: 0.8405 (m-40) cc_final: 0.8151 (m-40) REVERT: J 222 TYR cc_start: 0.8876 (m-10) cc_final: 0.8546 (m-80) REVERT: J 225 LEU cc_start: 0.9466 (mp) cc_final: 0.9180 (mp) REVERT: J 257 MET cc_start: 0.8328 (mmp) cc_final: 0.8016 (mmp) REVERT: J 297 ASN cc_start: 0.9036 (m110) cc_final: 0.8815 (t0) REVERT: J 330 ARG cc_start: 0.9015 (mtp85) cc_final: 0.8794 (mmm160) REVERT: J 343 TRP cc_start: 0.8087 (m100) cc_final: 0.7773 (m100) REVERT: J 394 LEU cc_start: 0.8841 (tp) cc_final: 0.8546 (tt) REVERT: J 405 MET cc_start: 0.8478 (tpp) cc_final: 0.8265 (tpp) REVERT: J 406 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8420 (mt-10) REVERT: J 415 ASN cc_start: 0.8720 (m-40) cc_final: 0.8396 (t0) REVERT: B 6 HIS cc_start: 0.8943 (t70) cc_final: 0.8646 (t-170) REVERT: B 20 PHE cc_start: 0.8390 (t80) cc_final: 0.8016 (t80) REVERT: B 53 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7156 (tm-30) REVERT: B 85 PHE cc_start: 0.7749 (m-80) cc_final: 0.7312 (m-10) REVERT: B 101 TRP cc_start: 0.8638 (t60) cc_final: 0.8394 (t60) REVERT: B 103 LYS cc_start: 0.8628 (tttp) cc_final: 0.8240 (tttp) REVERT: B 164 MET cc_start: 0.7802 (mmp) cc_final: 0.6706 (mmp) REVERT: B 181 GLU cc_start: 0.7714 (tt0) cc_final: 0.7457 (tt0) REVERT: B 192 LEU cc_start: 0.9196 (mt) cc_final: 0.8948 (mt) REVERT: B 221 SER cc_start: 0.9169 (t) cc_final: 0.8506 (p) REVERT: B 325 VAL cc_start: 0.7554 (t) cc_final: 0.7197 (t) REVERT: B 336 ASN cc_start: 0.8329 (m110) cc_final: 0.8039 (m110) REVERT: B 358 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7762 (pttm) REVERT: B 372 SER cc_start: 0.8830 (p) cc_final: 0.8438 (m) REVERT: B 376 ILE cc_start: 0.8791 (mm) cc_final: 0.8537 (mm) REVERT: B 394 LEU cc_start: 0.8540 (tt) cc_final: 0.8272 (tp) REVERT: B 414 MET cc_start: 0.7989 (ttt) cc_final: 0.7160 (tpp) REVERT: C 6 HIS cc_start: 0.8752 (t70) cc_final: 0.8137 (t-170) REVERT: C 101 TRP cc_start: 0.8966 (t60) cc_final: 0.8039 (t60) REVERT: C 202 ILE cc_start: 0.9139 (mm) cc_final: 0.8934 (mm) REVERT: C 233 MET cc_start: 0.9315 (mtm) cc_final: 0.9005 (ttp) REVERT: C 335 LYS cc_start: 0.7926 (mttp) cc_final: 0.7451 (ptpp) REVERT: C 339 TYR cc_start: 0.8494 (m-80) cc_final: 0.8229 (m-80) REVERT: C 352 VAL cc_start: 0.8849 (m) cc_final: 0.8307 (m) REVERT: C 405 MET cc_start: 0.8251 (tpp) cc_final: 0.7498 (tpt) REVERT: C 406 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8342 (mt-10) REVERT: C 412 SER cc_start: 0.9247 (m) cc_final: 0.8857 (p) REVERT: C 414 MET cc_start: 0.8539 (ttt) cc_final: 0.8152 (tmm) outliers start: 16 outliers final: 3 residues processed: 1222 average time/residue: 0.3990 time to fit residues: 761.3655 Evaluate side-chains 933 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 927 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 199 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 324 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 131 optimal weight: 0.0770 overall best weight: 7.0148 ------------------------------------------------------------------------------- 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 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 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN J 422 GLN B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** 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 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 = 0.3767 r_free = 0.3767 target = 0.118759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103047 restraints weight = 60647.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106434 restraints weight = 35811.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.108782 restraints weight = 23219.213| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28752 Z= 0.183 Angle : 0.700 8.287 39006 Z= 0.359 Chirality : 0.050 0.238 4200 Planarity : 0.006 0.085 5117 Dihedral : 10.071 158.272 3979 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.23 % Allowed : 3.99 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 3543 helix: -1.44 (0.13), residues: 1412 sheet: -0.48 (0.22), residues: 516 loop : -2.07 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 350 HIS 0.006 0.001 HIS E 410 PHE 0.020 0.002 PHE F 57 TYR 0.016 0.002 TYR J 36 ARG 0.006 0.001 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 951) hydrogen bonds : angle 5.81857 ( 2754) covalent geometry : bond 0.00402 (28752) covalent geometry : angle 0.69972 (39006) *********************** 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 1113 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1106 time to evaluate : 3.214 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: A 1 MET cc_start: 0.7857 (mmm) cc_final: 0.7633 (mmm) REVERT: A 6 HIS cc_start: 0.8721 (t-90) cc_final: 0.8216 (t-170) REVERT: A 14 ASN cc_start: 0.9329 (m-40) cc_final: 0.8970 (m-40) REVERT: A 53 GLU cc_start: 0.7999 (mt-10) cc_final: 0.6583 (tm-30) REVERT: A 58 LYS cc_start: 0.4506 (tttt) cc_final: 0.4151 (ttpt) REVERT: A 88 ASP cc_start: 0.8655 (m-30) cc_final: 0.8387 (p0) REVERT: A 89 ASN cc_start: 0.8830 (m-40) cc_final: 0.8247 (m110) REVERT: A 134 GLN cc_start: 0.7863 (mt0) cc_final: 0.7174 (mt0) REVERT: A 136 THR cc_start: 0.8730 (m) cc_final: 0.8500 (t) REVERT: A 162 ARG cc_start: 0.8551 (mmt-90) cc_final: 0.8007 (mmt-90) REVERT: A 164 MET cc_start: 0.8148 (mmp) cc_final: 0.6988 (mmp) REVERT: A 166 THR cc_start: 0.8741 (t) cc_final: 0.8444 (p) REVERT: A 196 SER cc_start: 0.9548 (t) cc_final: 0.9052 (p) REVERT: A 197 ASP cc_start: 0.8600 (t70) cc_final: 0.8122 (t0) REVERT: A 252 LYS cc_start: 0.8982 (mptt) cc_final: 0.8567 (mmtp) REVERT: A 293 PHE cc_start: 0.6717 (t80) cc_final: 0.6031 (t80) REVERT: A 330 ARG cc_start: 0.9090 (mtm180) cc_final: 0.8770 (mtp85) REVERT: A 340 PHE cc_start: 0.7442 (m-80) cc_final: 0.7148 (m-10) REVERT: A 380 LEU cc_start: 0.9294 (mm) cc_final: 0.8902 (tt) REVERT: A 396 TRP cc_start: 0.8531 (m100) cc_final: 0.8326 (m100) REVERT: A 414 MET cc_start: 0.8520 (ttt) cc_final: 0.7958 (tpp) REVERT: D 5 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7728 (ttp80) REVERT: D 47 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8372 (mtpt) REVERT: D 71 LYS cc_start: 0.7753 (mttt) cc_final: 0.7511 (mmtp) REVERT: D 106 TYR cc_start: 0.6686 (m-10) cc_final: 0.5905 (m-10) REVERT: E 18 ASN cc_start: 0.9295 (m110) cc_final: 0.9089 (m110) REVERT: E 21 TRP cc_start: 0.8860 (m100) cc_final: 0.8583 (m100) REVERT: E 59 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6332 (pt0) REVERT: E 65 PHE cc_start: 0.7621 (p90) cc_final: 0.5951 (p90) REVERT: E 94 GLU cc_start: 0.7818 (pp20) cc_final: 0.7346 (pp20) REVERT: E 131 ASP cc_start: 0.8108 (m-30) cc_final: 0.7730 (m-30) REVERT: E 201 ASN cc_start: 0.7954 (m-40) cc_final: 0.7556 (m-40) REVERT: E 243 THR cc_start: 0.8767 (p) cc_final: 0.8537 (p) REVERT: E 270 HIS cc_start: 0.8724 (p-80) cc_final: 0.8330 (p-80) REVERT: E 303 TYR cc_start: 0.9005 (m-10) cc_final: 0.8730 (m-10) REVERT: E 343 ARG cc_start: 0.8105 (ptt180) cc_final: 0.7647 (mpt180) REVERT: E 344 THR cc_start: 0.8907 (t) cc_final: 0.8590 (p) REVERT: E 381 MET cc_start: 0.8930 (ttt) cc_final: 0.8422 (tmm) REVERT: E 399 PHE cc_start: 0.8138 (t80) cc_final: 0.7915 (t80) REVERT: E 402 MET cc_start: 0.9252 (mmt) cc_final: 0.8742 (mmt) REVERT: E 415 GLU cc_start: 0.7071 (pt0) cc_final: 0.6342 (pt0) REVERT: E 441 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8124 (tm-30) REVERT: F 3 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6146 (mm-30) REVERT: F 21 TRP cc_start: 0.8813 (m100) cc_final: 0.7875 (m100) REVERT: F 24 TYR cc_start: 0.8987 (m-10) cc_final: 0.8230 (m-10) REVERT: F 30 ILE cc_start: 0.9301 (mt) cc_final: 0.8997 (mt) REVERT: F 56 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.6588 (m-10) REVERT: F 59 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6943 (pt0) REVERT: F 65 PHE cc_start: 0.7987 (p90) cc_final: 0.6197 (p90) REVERT: F 79 ILE cc_start: 0.9295 (mm) cc_final: 0.9066 (tp) REVERT: F 81 GLN cc_start: 0.8028 (mt0) cc_final: 0.7615 (mt0) REVERT: F 94 GLU cc_start: 0.8635 (pp20) cc_final: 0.6945 (tm-30) REVERT: F 125 ARG cc_start: 0.7908 (mtt90) cc_final: 0.6604 (mtt90) REVERT: F 131 ASP cc_start: 0.7927 (m-30) cc_final: 0.7667 (m-30) REVERT: F 136 LEU cc_start: 0.8424 (tp) cc_final: 0.7945 (tt) REVERT: F 196 HIS cc_start: 0.7937 (m-70) cc_final: 0.6558 (t70) REVERT: F 225 ARG cc_start: 0.8073 (ptp90) cc_final: 0.7812 (mtt-85) REVERT: F 237 GLN cc_start: 0.8902 (mt0) cc_final: 0.8206 (tt0) REVERT: F 247 ARG cc_start: 0.6947 (mmt90) cc_final: 0.5293 (mmt90) REVERT: F 270 HIS cc_start: 0.8691 (p-80) cc_final: 0.7933 (p-80) REVERT: F 276 TYR cc_start: 0.8425 (t80) cc_final: 0.7525 (t80) REVERT: F 356 LYS cc_start: 0.8601 (tptt) cc_final: 0.8002 (tppt) REVERT: F 415 GLU cc_start: 0.6692 (pt0) cc_final: 0.6201 (pt0) REVERT: G 23 LEU cc_start: 0.9172 (tp) cc_final: 0.8545 (tt) REVERT: G 27 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7584 (mt-10) REVERT: G 59 GLU cc_start: 0.6567 (mt-10) cc_final: 0.5817 (pt0) REVERT: G 97 VAL cc_start: 0.9478 (p) cc_final: 0.9254 (m) REVERT: G 124 GLU cc_start: 0.8477 (tt0) cc_final: 0.8268 (tt0) REVERT: G 125 ARG cc_start: 0.8520 (mtt90) cc_final: 0.7681 (mtt90) REVERT: G 204 CYS cc_start: 0.9148 (p) cc_final: 0.8873 (p) REVERT: G 206 PHE cc_start: 0.9164 (m-80) cc_final: 0.8633 (m-10) REVERT: G 215 ASP cc_start: 0.8023 (m-30) cc_final: 0.7603 (m-30) REVERT: G 241 SER cc_start: 0.9484 (m) cc_final: 0.8991 (p) REVERT: G 305 GLN cc_start: 0.8994 (mp-120) cc_final: 0.8732 (mm-40) REVERT: G 308 LYS cc_start: 0.8641 (tptp) cc_final: 0.8397 (mttp) REVERT: G 343 ARG cc_start: 0.8521 (ptm160) cc_final: 0.8277 (mtt180) REVERT: G 351 CYS cc_start: 0.8442 (t) cc_final: 0.7877 (t) REVERT: G 374 LYS cc_start: 0.8770 (tttm) cc_final: 0.8335 (tmtt) REVERT: G 380 CYS cc_start: 0.8968 (t) cc_final: 0.7939 (p) REVERT: G 381 MET cc_start: 0.9025 (tmm) cc_final: 0.8376 (tmm) REVERT: G 424 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8473 (pt0) REVERT: G 441 GLN cc_start: 0.8798 (mm110) cc_final: 0.8383 (tm-30) REVERT: H 15 GLN cc_start: 0.8694 (mt0) cc_final: 0.8431 (mt0) REVERT: H 20 CYS cc_start: 0.8963 (m) cc_final: 0.8659 (m) REVERT: H 80 ASP cc_start: 0.8794 (m-30) cc_final: 0.8578 (p0) REVERT: H 94 GLU cc_start: 0.8129 (tt0) cc_final: 0.7783 (tp30) REVERT: H 131 ASP cc_start: 0.8324 (m-30) cc_final: 0.8113 (m-30) REVERT: H 137 GLN cc_start: 0.8415 (mt0) cc_final: 0.7870 (mm-40) REVERT: H 143 HIS cc_start: 0.8963 (p90) cc_final: 0.8481 (p90) REVERT: H 171 LEU cc_start: 0.7350 (mt) cc_final: 0.5602 (mt) REVERT: H 206 PHE cc_start: 0.8710 (m-80) cc_final: 0.8275 (m-80) REVERT: H 209 ASP cc_start: 0.8372 (t0) cc_final: 0.8171 (t0) REVERT: H 237 GLN cc_start: 0.8855 (mt0) cc_final: 0.8398 (tt0) REVERT: H 276 TYR cc_start: 0.8264 (t80) cc_final: 0.6011 (t80) REVERT: H 287 HIS cc_start: 0.7539 (m170) cc_final: 0.7177 (m170) REVERT: H 305 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8813 (mm-40) REVERT: H 306 MET cc_start: 0.8760 (mmm) cc_final: 0.8467 (mmm) REVERT: H 343 ARG cc_start: 0.8442 (ptt180) cc_final: 0.8079 (mtt180) REVERT: H 374 LYS cc_start: 0.8981 (tttm) cc_final: 0.8642 (tmtt) REVERT: H 402 MET cc_start: 0.8976 (mmp) cc_final: 0.8606 (mmp) REVERT: H 415 GLU cc_start: 0.6745 (pt0) cc_final: 0.6341 (pt0) REVERT: H 424 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8414 (pt0) REVERT: H 434 ARG cc_start: 0.9165 (mtt90) cc_final: 0.8889 (mtt90) REVERT: H 441 GLN cc_start: 0.8692 (mm110) cc_final: 0.7981 (tm-30) REVERT: J 6 HIS cc_start: 0.8978 (t-90) cc_final: 0.8532 (t-170) REVERT: J 14 ASN cc_start: 0.9170 (m-40) cc_final: 0.8784 (m-40) REVERT: J 21 TRP cc_start: 0.9136 (m100) cc_final: 0.8430 (m100) REVERT: J 50 TYR cc_start: 0.8083 (m-10) cc_final: 0.7444 (m-10) REVERT: J 51 PHE cc_start: 0.8912 (m-80) cc_final: 0.7980 (m-80) REVERT: J 53 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7684 (tm-30) REVERT: J 62 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8395 (mtt90) REVERT: J 84 LEU cc_start: 0.8924 (mt) cc_final: 0.8498 (mm) REVERT: J 89 ASN cc_start: 0.9171 (m110) cc_final: 0.8822 (m110) REVERT: J 130 LEU cc_start: 0.9216 (mt) cc_final: 0.8846 (mp) REVERT: J 134 GLN cc_start: 0.8485 (mt0) cc_final: 0.7837 (mt0) REVERT: J 162 ARG cc_start: 0.8218 (mpt90) cc_final: 0.7995 (mmt180) REVERT: J 198 GLU cc_start: 0.8806 (pm20) cc_final: 0.8540 (pm20) REVERT: J 216 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8810 (mmtp) REVERT: J 257 MET cc_start: 0.8670 (mmp) cc_final: 0.8283 (mmp) REVERT: J 297 ASN cc_start: 0.8999 (m110) cc_final: 0.8782 (t0) REVERT: J 365 THR cc_start: 0.8460 (m) cc_final: 0.8064 (p) REVERT: J 405 MET cc_start: 0.8558 (tpp) cc_final: 0.7928 (tpp) REVERT: J 408 THR cc_start: 0.9203 (p) cc_final: 0.8993 (p) REVERT: J 415 ASN cc_start: 0.8760 (m-40) cc_final: 0.8294 (t0) REVERT: B 14 ASN cc_start: 0.8926 (m-40) cc_final: 0.8627 (m-40) REVERT: B 20 PHE cc_start: 0.8302 (t80) cc_final: 0.7708 (t80) REVERT: B 53 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7258 (tm-30) REVERT: B 65 LEU cc_start: 0.9145 (mt) cc_final: 0.8755 (mt) REVERT: B 85 PHE cc_start: 0.7966 (m-80) cc_final: 0.7581 (m-80) REVERT: B 135 LEU cc_start: 0.9290 (mp) cc_final: 0.8816 (mp) REVERT: B 164 MET cc_start: 0.7486 (mmp) cc_final: 0.6290 (mmp) REVERT: B 166 THR cc_start: 0.8965 (t) cc_final: 0.8590 (p) REVERT: B 174 LYS cc_start: 0.8735 (mppt) cc_final: 0.8408 (mppt) REVERT: B 181 GLU cc_start: 0.8076 (tt0) cc_final: 0.7747 (tt0) REVERT: B 189 MET cc_start: 0.8327 (tpt) cc_final: 0.8103 (tpt) REVERT: B 193 VAL cc_start: 0.8996 (t) cc_final: 0.7336 (t) REVERT: B 247 ASN cc_start: 0.5380 (m110) cc_final: 0.4676 (m110) REVERT: B 257 MET cc_start: 0.7901 (mmt) cc_final: 0.7509 (mmm) REVERT: B 344 ILE cc_start: 0.8688 (mt) cc_final: 0.8452 (mt) REVERT: B 372 SER cc_start: 0.8962 (p) cc_final: 0.8547 (m) REVERT: B 394 LEU cc_start: 0.8729 (tt) cc_final: 0.8525 (tt) REVERT: B 412 SER cc_start: 0.9418 (m) cc_final: 0.9209 (p) REVERT: C 6 HIS cc_start: 0.8931 (t70) cc_final: 0.7537 (t-170) REVERT: C 8 GLN cc_start: 0.7751 (mt0) cc_final: 0.7141 (mt0) REVERT: C 30 LEU cc_start: 0.8676 (tp) cc_final: 0.8361 (tp) REVERT: C 53 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6605 (tm-30) REVERT: C 134 GLN cc_start: 0.8444 (mt0) cc_final: 0.8077 (mt0) REVERT: C 147 MET cc_start: 0.8542 (ppp) cc_final: 0.8208 (ppp) REVERT: C 174 LYS cc_start: 0.8934 (mppt) cc_final: 0.8688 (mppt) REVERT: C 233 MET cc_start: 0.9354 (mtm) cc_final: 0.9074 (ttp) REVERT: C 252 LYS cc_start: 0.9005 (mmtp) cc_final: 0.8549 (mmtp) REVERT: C 297 ASN cc_start: 0.9238 (m-40) cc_final: 0.8841 (t0) REVERT: C 352 VAL cc_start: 0.8611 (m) cc_final: 0.8246 (m) REVERT: C 359 ASP cc_start: 0.9064 (m-30) cc_final: 0.8825 (m-30) REVERT: C 372 SER cc_start: 0.9234 (p) cc_final: 0.8830 (m) outliers start: 7 outliers final: 0 residues processed: 1109 average time/residue: 0.3924 time to fit residues: 689.0635 Evaluate side-chains 877 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 876 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 194 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 170 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 222 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 347 optimal weight: 5.9990 chunk 236 optimal weight: 40.0000 chunk 305 optimal weight: 5.9990 chunk 346 optimal weight: 40.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 83 ASN A 204 ASN A 226 ASN A 297 ASN A 328 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN E 260 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 170 ASN H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 422 GLN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.102451 restraints weight = 60526.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106002 restraints weight = 34872.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108438 restraints weight = 22056.752| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5526 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= 0.152 Angle : 0.669 12.005 39006 Z= 0.338 Chirality : 0.049 0.258 4200 Planarity : 0.005 0.087 5117 Dihedral : 9.742 158.051 3979 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3543 helix: -1.09 (0.13), residues: 1452 sheet: -0.05 (0.23), residues: 488 loop : -1.90 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 21 HIS 0.005 0.001 HIS B 263 PHE 0.022 0.002 PHE G 65 TYR 0.021 0.001 TYR G 176 ARG 0.007 0.001 ARG G 426 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 951) hydrogen bonds : angle 5.45071 ( 2754) covalent geometry : bond 0.00338 (28752) covalent geometry : angle 0.66932 (39006) *********************** 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 1062 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1058 time to evaluate : 3.306 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: 0.8820 (t-90) cc_final: 0.8146 (t-170) REVERT: A 14 ASN cc_start: 0.9299 (m-40) cc_final: 0.8991 (m-40) REVERT: A 53 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7008 (tm-30) REVERT: A 58 LYS cc_start: 0.4302 (tttt) cc_final: 0.4054 (ttpt) REVERT: A 89 ASN cc_start: 0.8810 (m-40) cc_final: 0.8521 (m110) REVERT: A 101 TRP cc_start: 0.8996 (t60) cc_final: 0.8789 (t60) REVERT: A 130 LEU cc_start: 0.9298 (mt) cc_final: 0.9021 (tt) REVERT: A 134 GLN cc_start: 0.8305 (mt0) cc_final: 0.7676 (mt0) REVERT: A 136 THR cc_start: 0.8670 (m) cc_final: 0.8395 (t) REVERT: A 147 MET cc_start: 0.8160 (ppp) cc_final: 0.7493 (ppp) REVERT: A 157 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 166 THR cc_start: 0.8613 (t) cc_final: 0.8275 (p) REVERT: A 181 GLU cc_start: 0.9460 (pp20) cc_final: 0.9016 (pp20) REVERT: A 196 SER cc_start: 0.9492 (t) cc_final: 0.9103 (p) REVERT: A 197 ASP cc_start: 0.8622 (t70) cc_final: 0.8296 (t0) REVERT: A 293 PHE cc_start: 0.6667 (t80) cc_final: 0.6384 (t80) REVERT: A 297 ASN cc_start: 0.9306 (m-40) cc_final: 0.8800 (t0) REVERT: A 315 LEU cc_start: 0.8961 (mt) cc_final: 0.8649 (mt) REVERT: A 330 ARG cc_start: 0.9083 (mtm180) cc_final: 0.8883 (mtp180) REVERT: A 340 PHE cc_start: 0.7471 (m-80) cc_final: 0.7221 (m-10) REVERT: A 350 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7288 (mttt) REVERT: A 365 THR cc_start: 0.8792 (m) cc_final: 0.8524 (p) REVERT: A 380 LEU cc_start: 0.9405 (mm) cc_final: 0.8872 (tt) REVERT: D 5 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7649 (ttp80) REVERT: D 32 MET cc_start: 0.8032 (mmm) cc_final: 0.7419 (mmm) REVERT: D 35 ILE cc_start: 0.8833 (mt) cc_final: 0.8598 (mt) REVERT: D 71 LYS cc_start: 0.7657 (mttt) cc_final: 0.7431 (mmtp) REVERT: D 106 TYR cc_start: 0.6826 (m-10) cc_final: 0.5857 (m-10) REVERT: E 18 ASN cc_start: 0.9267 (m110) cc_final: 0.9033 (m-40) REVERT: E 21 TRP cc_start: 0.8868 (m100) cc_final: 0.8474 (m100) REVERT: E 27 GLU cc_start: 0.8701 (tt0) cc_final: 0.8268 (tt0) REVERT: E 59 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6493 (pt0) REVERT: E 65 PHE cc_start: 0.7777 (p90) cc_final: 0.6013 (p90) REVERT: E 94 GLU cc_start: 0.7536 (pp20) cc_final: 0.6998 (tm-30) REVERT: E 118 MET cc_start: 0.9082 (mtp) cc_final: 0.8874 (mtt) REVERT: E 131 ASP cc_start: 0.7900 (m-30) cc_final: 0.7508 (m-30) REVERT: E 192 VAL cc_start: 0.9270 (p) cc_final: 0.8824 (m) REVERT: E 237 GLN cc_start: 0.8874 (mm110) cc_final: 0.8107 (mm-40) REVERT: E 255 ASP cc_start: 0.8685 (t70) cc_final: 0.8122 (m-30) REVERT: E 270 HIS cc_start: 0.8651 (p-80) cc_final: 0.8306 (p-80) REVERT: E 294 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7925 (mm-30) REVERT: E 303 TYR cc_start: 0.9022 (m-10) cc_final: 0.8805 (m-10) REVERT: E 343 ARG cc_start: 0.8229 (ptt180) cc_final: 0.7602 (mpt180) REVERT: E 350 TRP cc_start: 0.6943 (m-10) cc_final: 0.6431 (m-10) REVERT: E 381 MET cc_start: 0.8899 (ttt) cc_final: 0.8294 (tmm) REVERT: E 399 PHE cc_start: 0.8411 (t80) cc_final: 0.8198 (t80) REVERT: E 402 MET cc_start: 0.9124 (mmt) cc_final: 0.8851 (mmt) REVERT: E 415 GLU cc_start: 0.6848 (pt0) cc_final: 0.6545 (pt0) REVERT: E 439 VAL cc_start: 0.8146 (t) cc_final: 0.7814 (t) REVERT: E 441 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8093 (tm-30) REVERT: F 3 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6825 (mt-10) REVERT: F 21 TRP cc_start: 0.8711 (m100) cc_final: 0.7905 (m100) REVERT: F 24 TYR cc_start: 0.8827 (m-10) cc_final: 0.8012 (m-10) REVERT: F 30 ILE cc_start: 0.9281 (mt) cc_final: 0.9029 (mm) REVERT: F 59 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6913 (pt0) REVERT: F 81 GLN cc_start: 0.7912 (mt0) cc_final: 0.7607 (mt0) REVERT: F 94 GLU cc_start: 0.8407 (pp20) cc_final: 0.7708 (tm-30) REVERT: F 131 ASP cc_start: 0.7792 (m-30) cc_final: 0.7470 (m-30) REVERT: F 136 LEU cc_start: 0.8484 (tp) cc_final: 0.8069 (tt) REVERT: F 173 PHE cc_start: 0.8607 (m-80) cc_final: 0.8246 (m-80) REVERT: F 207 MET cc_start: 0.7762 (ptm) cc_final: 0.7546 (ttm) REVERT: F 225 ARG cc_start: 0.7983 (ptp90) cc_final: 0.7773 (ptp-170) REVERT: F 237 GLN cc_start: 0.8798 (mt0) cc_final: 0.8167 (tt0) REVERT: F 239 VAL cc_start: 0.8946 (t) cc_final: 0.8705 (t) REVERT: F 247 ARG cc_start: 0.6721 (mmt90) cc_final: 0.4586 (mmt90) REVERT: F 260 GLN cc_start: 0.8874 (pm20) cc_final: 0.8366 (pm20) REVERT: F 270 HIS cc_start: 0.8543 (p-80) cc_final: 0.7898 (p-80) REVERT: F 301 GLU cc_start: 0.8621 (mt-10) cc_final: 0.7732 (pp20) REVERT: F 328 ILE cc_start: 0.9159 (mm) cc_final: 0.8749 (pt) REVERT: F 356 LYS cc_start: 0.8909 (tptt) cc_final: 0.8121 (tppt) REVERT: F 441 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8096 (tm-30) REVERT: G 23 LEU cc_start: 0.9213 (tp) cc_final: 0.8578 (tt) REVERT: G 27 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7648 (mt-10) REVERT: G 59 GLU cc_start: 0.6501 (mt-10) cc_final: 0.5331 (pt0) REVERT: G 65 PHE cc_start: 0.7492 (p90) cc_final: 0.6324 (p90) REVERT: G 80 ASP cc_start: 0.8589 (m-30) cc_final: 0.8380 (m-30) REVERT: G 94 GLU cc_start: 0.7935 (pp20) cc_final: 0.7523 (pp20) REVERT: G 109 ARG cc_start: 0.6496 (ptp-110) cc_final: 0.6228 (ptp-110) REVERT: G 124 GLU cc_start: 0.8457 (tt0) cc_final: 0.8132 (tt0) REVERT: G 129 MET cc_start: 0.9145 (mmm) cc_final: 0.8770 (mmm) REVERT: G 206 PHE cc_start: 0.9166 (m-80) cc_final: 0.8662 (m-80) REVERT: G 260 GLN cc_start: 0.7201 (pm20) cc_final: 0.6597 (tm-30) REVERT: G 343 ARG cc_start: 0.8585 (ptm160) cc_final: 0.8173 (mtt180) REVERT: G 351 CYS cc_start: 0.8274 (t) cc_final: 0.7817 (t) REVERT: G 356 LYS cc_start: 0.7751 (tppt) cc_final: 0.7510 (tppt) REVERT: G 374 LYS cc_start: 0.8854 (tttm) cc_final: 0.8350 (tmtt) REVERT: G 380 CYS cc_start: 0.9036 (t) cc_final: 0.8519 (p) REVERT: G 381 MET cc_start: 0.9128 (tmm) cc_final: 0.8529 (tmm) REVERT: G 434 ARG cc_start: 0.9108 (mpt-90) cc_final: 0.8699 (mtt90) REVERT: G 441 GLN cc_start: 0.8797 (mm110) cc_final: 0.8336 (tm-30) REVERT: H 15 GLN cc_start: 0.8571 (mt0) cc_final: 0.8241 (mt0) REVERT: H 20 CYS cc_start: 0.8766 (m) cc_final: 0.8534 (m) REVERT: H 80 ASP cc_start: 0.8804 (m-30) cc_final: 0.8442 (p0) REVERT: H 94 GLU cc_start: 0.8013 (tt0) cc_final: 0.7673 (tp30) REVERT: H 109 ARG cc_start: 0.6167 (ptp90) cc_final: 0.5523 (ptp-110) REVERT: H 137 GLN cc_start: 0.8466 (mt0) cc_final: 0.8230 (mp10) REVERT: H 140 LEU cc_start: 0.8575 (tp) cc_final: 0.7990 (mm) REVERT: H 142 PHE cc_start: 0.8222 (m-10) cc_final: 0.7911 (m-10) REVERT: H 143 HIS cc_start: 0.8901 (p90) cc_final: 0.8415 (p90) REVERT: H 187 GLU cc_start: 0.8432 (tt0) cc_final: 0.8076 (tp30) REVERT: H 209 ASP cc_start: 0.8434 (t0) cc_final: 0.8177 (t0) REVERT: H 247 ARG cc_start: 0.7037 (mmt90) cc_final: 0.4956 (mmt90) REVERT: H 276 TYR cc_start: 0.8340 (t80) cc_final: 0.7643 (t80) REVERT: H 305 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8673 (mm-40) REVERT: H 306 MET cc_start: 0.8709 (mmm) cc_final: 0.8442 (mmm) REVERT: H 308 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8535 (mmtp) REVERT: H 317 MET cc_start: 0.7202 (mmm) cc_final: 0.6467 (tpt) REVERT: H 343 ARG cc_start: 0.8470 (ptt180) cc_final: 0.8189 (mtt180) REVERT: H 374 LYS cc_start: 0.9056 (tttm) cc_final: 0.8644 (tmtt) REVERT: H 381 MET cc_start: 0.9039 (tmm) cc_final: 0.8504 (tmm) REVERT: H 415 GLU cc_start: 0.6629 (pt0) cc_final: 0.5237 (pt0) REVERT: H 441 GLN cc_start: 0.8732 (mm110) cc_final: 0.8098 (tm-30) REVERT: J 1 MET cc_start: 0.8655 (tpt) cc_final: 0.8414 (tpp) REVERT: J 4 ILE cc_start: 0.9306 (mm) cc_final: 0.8921 (mm) REVERT: J 14 ASN cc_start: 0.9102 (m-40) cc_final: 0.8651 (m-40) REVERT: J 21 TRP cc_start: 0.9102 (m100) cc_final: 0.8516 (m100) REVERT: J 31 ASP cc_start: 0.7964 (p0) cc_final: 0.7725 (p0) REVERT: J 51 PHE cc_start: 0.8953 (m-80) cc_final: 0.8719 (m-80) REVERT: J 53 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7449 (tm-30) REVERT: J 83 ASN cc_start: 0.8906 (m-40) cc_final: 0.8670 (m110) REVERT: J 84 LEU cc_start: 0.8972 (mt) cc_final: 0.8613 (mm) REVERT: J 89 ASN cc_start: 0.9067 (m110) cc_final: 0.8795 (m110) REVERT: J 127 CYS cc_start: 0.8309 (t) cc_final: 0.8030 (t) REVERT: J 130 LEU cc_start: 0.9155 (mt) cc_final: 0.8937 (mp) REVERT: J 134 GLN cc_start: 0.8508 (mt0) cc_final: 0.7864 (mt0) REVERT: J 149 THR cc_start: 0.9191 (p) cc_final: 0.8885 (p) REVERT: J 174 LYS cc_start: 0.9069 (mppt) cc_final: 0.8559 (mtmm) REVERT: J 190 HIS cc_start: 0.8571 (t-90) cc_final: 0.8231 (t-90) REVERT: J 196 SER cc_start: 0.9538 (t) cc_final: 0.8998 (p) REVERT: J 198 GLU cc_start: 0.8746 (pm20) cc_final: 0.8516 (pm20) REVERT: J 216 LYS cc_start: 0.9088 (mmtp) cc_final: 0.8709 (mmmt) REVERT: J 222 TYR cc_start: 0.8705 (m-10) cc_final: 0.8422 (m-10) REVERT: J 297 ASN cc_start: 0.9068 (m110) cc_final: 0.8796 (t0) REVERT: J 365 THR cc_start: 0.8587 (m) cc_final: 0.8162 (p) REVERT: J 405 MET cc_start: 0.8296 (tpp) cc_final: 0.7647 (mmm) REVERT: J 408 THR cc_start: 0.9219 (p) cc_final: 0.8896 (p) REVERT: J 415 ASN cc_start: 0.8617 (m-40) cc_final: 0.8216 (t0) REVERT: B 14 ASN cc_start: 0.9016 (m-40) cc_final: 0.8620 (m-40) REVERT: B 20 PHE cc_start: 0.8230 (t80) cc_final: 0.7719 (t80) REVERT: B 21 TRP cc_start: 0.9274 (m100) cc_final: 0.8914 (m100) REVERT: B 53 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7225 (tm-30) REVERT: B 83 ASN cc_start: 0.8457 (m-40) cc_final: 0.8214 (m110) REVERT: B 84 LEU cc_start: 0.8969 (mt) cc_final: 0.8592 (mt) REVERT: B 85 PHE cc_start: 0.7841 (m-80) cc_final: 0.7543 (m-10) REVERT: B 135 LEU cc_start: 0.9276 (mp) cc_final: 0.8728 (mp) REVERT: B 164 MET cc_start: 0.7658 (mmp) cc_final: 0.6636 (mmp) REVERT: B 166 THR cc_start: 0.8800 (t) cc_final: 0.8463 (p) REVERT: B 225 LEU cc_start: 0.9557 (mp) cc_final: 0.9286 (mp) REVERT: B 247 ASN cc_start: 0.5723 (m110) cc_final: 0.5331 (m110) REVERT: B 256 ASN cc_start: 0.7966 (p0) cc_final: 0.7728 (p0) REVERT: B 257 MET cc_start: 0.7973 (mmt) cc_final: 0.7718 (mmm) REVERT: B 344 ILE cc_start: 0.9050 (mt) cc_final: 0.8793 (mt) REVERT: B 352 VAL cc_start: 0.8904 (t) cc_final: 0.8124 (t) REVERT: C 6 HIS cc_start: 0.9017 (t70) cc_final: 0.7817 (t-170) REVERT: C 8 GLN cc_start: 0.7770 (mt0) cc_final: 0.6904 (mt0) REVERT: C 53 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7025 (tm-30) REVERT: C 101 TRP cc_start: 0.8843 (t60) cc_final: 0.8136 (t60) REVERT: C 134 GLN cc_start: 0.8473 (mt0) cc_final: 0.8133 (mt0) REVERT: C 174 LYS cc_start: 0.8923 (mppt) cc_final: 0.8723 (mppt) REVERT: C 233 MET cc_start: 0.9275 (mtm) cc_final: 0.9018 (ttp) REVERT: C 247 ASN cc_start: 0.5725 (m110) cc_final: 0.5413 (m110) REVERT: C 359 ASP cc_start: 0.9035 (m-30) cc_final: 0.8771 (m-30) REVERT: C 372 SER cc_start: 0.9299 (p) cc_final: 0.8923 (m) REVERT: C 397 TYR cc_start: 0.8746 (m-80) cc_final: 0.8386 (m-80) REVERT: C 405 MET cc_start: 0.8147 (tpp) cc_final: 0.7881 (tpp) REVERT: C 406 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8774 (mt-10) REVERT: C 408 THR cc_start: 0.8718 (p) cc_final: 0.8484 (p) outliers start: 4 outliers final: 1 residues processed: 1060 average time/residue: 0.3884 time to fit residues: 655.2652 Evaluate side-chains 863 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 862 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 4 optimal weight: 0.0970 chunk 296 optimal weight: 0.0870 chunk 227 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 348 optimal weight: 30.0000 chunk 333 optimal weight: 0.2980 chunk 204 optimal weight: 20.0000 chunk 239 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 overall best weight: 2.6960 ------------------------------------------------------------------------------- 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 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 162 ASN E 210 ASN F 28 HIS ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** 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 305 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN ** G 346 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** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 190 HIS B 6 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3809 r_free = 0.3809 target = 0.121815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105775 restraints weight = 60211.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.109280 restraints weight = 35202.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.111719 restraints weight = 22667.794| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5971 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= 0.121 Angle : 0.638 16.711 39006 Z= 0.316 Chirality : 0.047 0.205 4200 Planarity : 0.005 0.059 5117 Dihedral : 9.345 158.163 3979 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3543 helix: -0.76 (0.13), residues: 1494 sheet: -0.11 (0.23), residues: 500 loop : -1.89 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 396 HIS 0.007 0.001 HIS B 263 PHE 0.024 0.001 PHE F 408 TYR 0.019 0.001 TYR G 176 ARG 0.009 0.001 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 951) hydrogen bonds : angle 5.14511 ( 2754) covalent geometry : bond 0.00272 (28752) covalent geometry : angle 0.63808 (39006) *********************** 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 1060 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1059 time to evaluate : 3.320 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 14 ASN cc_start: 0.9274 (m-40) cc_final: 0.8922 (m-40) REVERT: A 35 ILE cc_start: 0.8566 (mp) cc_final: 0.8127 (mm) REVERT: A 58 LYS cc_start: 0.4517 (tttt) cc_final: 0.4051 (ttpt) REVERT: A 88 ASP cc_start: 0.7710 (p0) cc_final: 0.7117 (p0) REVERT: A 101 TRP cc_start: 0.8904 (t60) cc_final: 0.8680 (t60) REVERT: A 136 THR cc_start: 0.8624 (m) cc_final: 0.8180 (t) REVERT: A 139 LEU cc_start: 0.8782 (mt) cc_final: 0.8578 (mt) REVERT: A 147 MET cc_start: 0.8301 (ppp) cc_final: 0.7742 (ppp) REVERT: A 151 LEU cc_start: 0.9487 (mt) cc_final: 0.9254 (mt) REVERT: A 166 THR cc_start: 0.8425 (t) cc_final: 0.8081 (p) REVERT: A 181 GLU cc_start: 0.9359 (pp20) cc_final: 0.8912 (pp20) REVERT: A 196 SER cc_start: 0.9500 (t) cc_final: 0.9143 (p) REVERT: A 293 PHE cc_start: 0.6758 (t80) cc_final: 0.6363 (t80) REVERT: A 297 ASN cc_start: 0.9216 (m-40) cc_final: 0.8710 (t0) REVERT: A 330 ARG cc_start: 0.9056 (mtm180) cc_final: 0.8784 (mtp180) REVERT: A 340 PHE cc_start: 0.7519 (m-80) cc_final: 0.7231 (m-10) REVERT: A 350 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7109 (mttt) REVERT: A 380 LEU cc_start: 0.9324 (mm) cc_final: 0.8886 (tt) REVERT: A 405 MET cc_start: 0.7718 (mmt) cc_final: 0.7224 (mmm) REVERT: A 408 THR cc_start: 0.8660 (p) cc_final: 0.8170 (p) REVERT: A 412 SER cc_start: 0.9078 (m) cc_final: 0.8771 (p) REVERT: D 5 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7694 (ttp80) REVERT: D 32 MET cc_start: 0.8036 (mmm) cc_final: 0.7530 (mmm) REVERT: D 71 LYS cc_start: 0.7498 (mttt) cc_final: 0.7252 (mmtp) REVERT: E 18 ASN cc_start: 0.9228 (m110) cc_final: 0.9011 (m110) REVERT: E 21 TRP cc_start: 0.8872 (m100) cc_final: 0.8399 (m100) REVERT: E 27 GLU cc_start: 0.8653 (tt0) cc_final: 0.8286 (tt0) REVERT: E 55 THR cc_start: 0.9073 (p) cc_final: 0.8777 (p) REVERT: E 59 GLU cc_start: 0.7413 (mt-10) cc_final: 0.5927 (pt0) REVERT: E 65 PHE cc_start: 0.7709 (p90) cc_final: 0.6828 (p90) REVERT: E 94 GLU cc_start: 0.7394 (pp20) cc_final: 0.6848 (tm-30) REVERT: E 116 LYS cc_start: 0.8998 (tmmt) cc_final: 0.8416 (ttpt) REVERT: E 118 MET cc_start: 0.8888 (mtp) cc_final: 0.8647 (mtt) REVERT: E 131 ASP cc_start: 0.7752 (m-30) cc_final: 0.7528 (m-30) REVERT: E 161 LEU cc_start: 0.8516 (pp) cc_final: 0.8288 (pp) REVERT: E 162 ASN cc_start: 0.9175 (t160) cc_final: 0.8903 (t0) REVERT: E 167 LYS cc_start: 0.8062 (pttp) cc_final: 0.7771 (ptmt) REVERT: E 237 GLN cc_start: 0.8973 (mm110) cc_final: 0.8696 (mm110) REVERT: E 255 ASP cc_start: 0.8677 (t70) cc_final: 0.8059 (m-30) REVERT: E 260 GLN cc_start: 0.8040 (pt0) cc_final: 0.7761 (pt0) REVERT: E 270 HIS cc_start: 0.8619 (p-80) cc_final: 0.8149 (p-80) REVERT: E 333 GLN cc_start: 0.7309 (pp30) cc_final: 0.6961 (pp30) REVERT: E 343 ARG cc_start: 0.8099 (ptt180) cc_final: 0.7636 (mpt180) REVERT: E 350 TRP cc_start: 0.6657 (m-10) cc_final: 0.6449 (m-10) REVERT: E 381 MET cc_start: 0.9059 (ttt) cc_final: 0.8594 (ttp) REVERT: E 402 MET cc_start: 0.9280 (mmt) cc_final: 0.8710 (mmt) REVERT: E 441 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8227 (tm-30) REVERT: F 1 MET cc_start: 0.7982 (ptp) cc_final: 0.7662 (ptp) REVERT: F 14 VAL cc_start: 0.9371 (t) cc_final: 0.9123 (t) REVERT: F 18 ASN cc_start: 0.9153 (m110) cc_final: 0.8427 (t0) REVERT: F 21 TRP cc_start: 0.8420 (m100) cc_final: 0.7700 (m100) REVERT: F 24 TYR cc_start: 0.8657 (m-10) cc_final: 0.7897 (m-10) REVERT: F 30 ILE cc_start: 0.9234 (mt) cc_final: 0.8918 (mm) REVERT: F 59 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6825 (pt0) REVERT: F 81 GLN cc_start: 0.7760 (mt0) cc_final: 0.7493 (mt0) REVERT: F 94 GLU cc_start: 0.8437 (pp20) cc_final: 0.7804 (tm-30) REVERT: F 131 ASP cc_start: 0.7803 (m-30) cc_final: 0.7439 (m-30) REVERT: F 136 LEU cc_start: 0.8389 (tp) cc_final: 0.7891 (tt) REVERT: F 149 THR cc_start: 0.8408 (m) cc_final: 0.8200 (p) REVERT: F 173 PHE cc_start: 0.8674 (m-80) cc_final: 0.8368 (m-80) REVERT: F 187 GLU cc_start: 0.9215 (tt0) cc_final: 0.8492 (tp30) REVERT: F 219 ARG cc_start: 0.7590 (mtm110) cc_final: 0.6936 (mtm110) REVERT: F 225 ARG cc_start: 0.8324 (ptp90) cc_final: 0.7812 (mtt-85) REVERT: F 239 VAL cc_start: 0.8814 (t) cc_final: 0.8577 (t) REVERT: F 247 ARG cc_start: 0.6836 (mmt90) cc_final: 0.5078 (mmt90) REVERT: F 255 ASP cc_start: 0.8643 (t70) cc_final: 0.8348 (m-30) REVERT: F 270 HIS cc_start: 0.8545 (p-80) cc_final: 0.7703 (p-80) REVERT: F 295 ILE cc_start: 0.9484 (mt) cc_final: 0.9156 (tt) REVERT: F 317 MET cc_start: 0.7347 (tpt) cc_final: 0.6830 (tpt) REVERT: F 349 ASP cc_start: 0.6065 (p0) cc_final: 0.4739 (p0) REVERT: F 356 LYS cc_start: 0.8857 (tptt) cc_final: 0.8288 (tppt) REVERT: F 441 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8293 (tm-30) REVERT: G 23 LEU cc_start: 0.9167 (tp) cc_final: 0.8519 (tt) REVERT: G 27 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7729 (mt-10) REVERT: G 59 GLU cc_start: 0.6758 (mt-10) cc_final: 0.5310 (pt0) REVERT: G 65 PHE cc_start: 0.7541 (p90) cc_final: 0.6230 (p90) REVERT: G 70 ILE cc_start: 0.8787 (tp) cc_final: 0.8423 (pt) REVERT: G 124 GLU cc_start: 0.8403 (tt0) cc_final: 0.7572 (tt0) REVERT: G 209 ASP cc_start: 0.7874 (t0) cc_final: 0.7361 (t0) REVERT: G 215 ASP cc_start: 0.7874 (m-30) cc_final: 0.7612 (m-30) REVERT: G 260 GLN cc_start: 0.7311 (pm20) cc_final: 0.6914 (tm-30) REVERT: G 343 ARG cc_start: 0.8560 (ptm160) cc_final: 0.8165 (mtt180) REVERT: G 351 CYS cc_start: 0.8309 (t) cc_final: 0.7857 (t) REVERT: G 356 LYS cc_start: 0.7808 (tppt) cc_final: 0.7551 (tppt) REVERT: G 374 LYS cc_start: 0.8878 (tttm) cc_final: 0.8356 (tmtt) REVERT: G 380 CYS cc_start: 0.9029 (t) cc_final: 0.8733 (t) REVERT: G 381 MET cc_start: 0.9067 (tmm) cc_final: 0.8803 (tmm) REVERT: G 419 GLU cc_start: 0.8775 (pm20) cc_final: 0.8542 (mp0) REVERT: G 441 GLN cc_start: 0.8854 (mm110) cc_final: 0.8411 (tm-30) REVERT: H 15 GLN cc_start: 0.8399 (mt0) cc_final: 0.8109 (mt0) REVERT: H 20 CYS cc_start: 0.8814 (m) cc_final: 0.8500 (m) REVERT: H 80 ASP cc_start: 0.8559 (m-30) cc_final: 0.8309 (p0) REVERT: H 102 ASP cc_start: 0.8884 (t70) cc_final: 0.8615 (t70) REVERT: H 109 ARG cc_start: 0.6145 (ptp90) cc_final: 0.5804 (ptp-110) REVERT: H 131 ASP cc_start: 0.8294 (m-30) cc_final: 0.8075 (m-30) REVERT: H 137 GLN cc_start: 0.8470 (mt0) cc_final: 0.8262 (mp10) REVERT: H 143 HIS cc_start: 0.8707 (p90) cc_final: 0.8375 (p90) REVERT: H 187 GLU cc_start: 0.8575 (tt0) cc_final: 0.8073 (tp30) REVERT: H 237 GLN cc_start: 0.8520 (mt0) cc_final: 0.7600 (tt0) REVERT: H 276 TYR cc_start: 0.7904 (t80) cc_final: 0.6880 (t80) REVERT: H 317 MET cc_start: 0.7195 (mmm) cc_final: 0.6492 (tpt) REVERT: H 343 ARG cc_start: 0.8484 (ptt180) cc_final: 0.8138 (mtt180) REVERT: H 374 LYS cc_start: 0.9007 (tttm) cc_final: 0.8586 (tmtt) REVERT: H 415 GLU cc_start: 0.6631 (pt0) cc_final: 0.5629 (pt0) REVERT: H 435 ASP cc_start: 0.8792 (t0) cc_final: 0.8525 (t0) REVERT: H 441 GLN cc_start: 0.8721 (mm110) cc_final: 0.8189 (tm-30) REVERT: J 6 HIS cc_start: 0.9095 (t-170) cc_final: 0.8864 (t-170) REVERT: J 14 ASN cc_start: 0.9159 (m-40) cc_final: 0.8385 (m-40) REVERT: J 31 ASP cc_start: 0.7962 (p0) cc_final: 0.7718 (p0) REVERT: J 53 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7047 (tm-30) REVERT: J 67 ASP cc_start: 0.8141 (t0) cc_final: 0.7650 (p0) REVERT: J 83 ASN cc_start: 0.8876 (m-40) cc_final: 0.8658 (m110) REVERT: J 84 LEU cc_start: 0.8976 (mt) cc_final: 0.8684 (mm) REVERT: J 89 ASN cc_start: 0.9042 (m110) cc_final: 0.8796 (m110) REVERT: J 101 TRP cc_start: 0.9152 (t60) cc_final: 0.8764 (t60) REVERT: J 174 LYS cc_start: 0.9078 (mppt) cc_final: 0.8839 (mmtt) REVERT: J 190 HIS cc_start: 0.8347 (t70) cc_final: 0.8095 (t-90) REVERT: J 191 GLN cc_start: 0.8742 (mp10) cc_final: 0.8141 (mp10) REVERT: J 196 SER cc_start: 0.9532 (t) cc_final: 0.9049 (p) REVERT: J 198 GLU cc_start: 0.8606 (pm20) cc_final: 0.7983 (tp30) REVERT: J 216 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8740 (mmmt) REVERT: J 257 MET cc_start: 0.8656 (mmp) cc_final: 0.8385 (mmp) REVERT: J 297 ASN cc_start: 0.9081 (m110) cc_final: 0.8816 (t0) REVERT: J 405 MET cc_start: 0.8579 (tpp) cc_final: 0.8231 (tpp) REVERT: J 412 SER cc_start: 0.9155 (m) cc_final: 0.8869 (p) REVERT: J 415 ASN cc_start: 0.8513 (m-40) cc_final: 0.8087 (t0) REVERT: B 14 ASN cc_start: 0.8753 (m-40) cc_final: 0.8369 (m-40) REVERT: B 20 PHE cc_start: 0.8290 (t80) cc_final: 0.8036 (t80) REVERT: B 21 TRP cc_start: 0.9262 (m100) cc_final: 0.8460 (m100) REVERT: B 35 ILE cc_start: 0.8778 (mp) cc_final: 0.8435 (mm) REVERT: B 49 VAL cc_start: 0.9104 (m) cc_final: 0.8889 (m) REVERT: B 51 PHE cc_start: 0.9024 (m-80) cc_final: 0.8769 (m-80) REVERT: B 84 LEU cc_start: 0.8986 (mt) cc_final: 0.8589 (mt) REVERT: B 85 PHE cc_start: 0.7677 (m-80) cc_final: 0.7151 (m-80) REVERT: B 147 MET cc_start: 0.8217 (tmm) cc_final: 0.7627 (tmm) REVERT: B 151 LEU cc_start: 0.9637 (mt) cc_final: 0.9240 (mt) REVERT: B 164 MET cc_start: 0.7558 (mmp) cc_final: 0.6608 (mmt) REVERT: B 166 THR cc_start: 0.8958 (t) cc_final: 0.8709 (p) REVERT: B 225 LEU cc_start: 0.9567 (mp) cc_final: 0.9354 (mp) REVERT: B 247 ASN cc_start: 0.5832 (m110) cc_final: 0.5248 (m110) REVERT: B 322 MET cc_start: 0.8857 (mmm) cc_final: 0.8510 (mmp) REVERT: B 406 GLU cc_start: 0.8653 (tp30) cc_final: 0.8324 (tp30) REVERT: B 408 THR cc_start: 0.9038 (p) cc_final: 0.8218 (p) REVERT: B 414 MET cc_start: 0.8633 (mmm) cc_final: 0.8296 (tpp) REVERT: B 417 LEU cc_start: 0.9144 (mt) cc_final: 0.8879 (mt) REVERT: C 6 HIS cc_start: 0.8908 (t70) cc_final: 0.7777 (t-170) REVERT: C 8 GLN cc_start: 0.7408 (mt0) cc_final: 0.6692 (mt0) REVERT: C 134 GLN cc_start: 0.8359 (mt0) cc_final: 0.7943 (mt0) REVERT: C 157 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8674 (tm-30) REVERT: C 225 LEU cc_start: 0.9322 (mp) cc_final: 0.9056 (mp) REVERT: C 233 MET cc_start: 0.9225 (mtm) cc_final: 0.8900 (ttp) REVERT: C 247 ASN cc_start: 0.5603 (m110) cc_final: 0.5220 (m110) REVERT: C 257 MET cc_start: 0.8131 (mmm) cc_final: 0.7863 (mmp) REVERT: C 297 ASN cc_start: 0.9229 (m-40) cc_final: 0.8767 (t0) REVERT: C 359 ASP cc_start: 0.9057 (m-30) cc_final: 0.8814 (m-30) REVERT: C 394 LEU cc_start: 0.8854 (tp) cc_final: 0.8472 (tt) REVERT: C 397 TYR cc_start: 0.8667 (m-80) cc_final: 0.8433 (m-80) REVERT: C 406 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8743 (mt-10) outliers start: 1 outliers final: 0 residues processed: 1060 average time/residue: 0.3905 time to fit residues: 655.8031 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 : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 150 optimal weight: 0.6980 chunk 256 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 211 optimal weight: 0.9990 chunk 302 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 chunk 298 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 334 optimal weight: 0.0270 chunk 35 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 overall best weight: 1.9444 ------------------------------------------------------------------------------- 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 204 ASN D 91 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 162 ASN E 230 ASN E 262 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN ** 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 8 HIS ** 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 210 ASN ** 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 6 HIS J 14 ASN J 99 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107257 restraints weight = 58731.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110856 restraints weight = 33954.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.113321 restraints weight = 21645.564| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28752 Z= 0.115 Angle : 0.636 13.414 39006 Z= 0.313 Chirality : 0.046 0.173 4200 Planarity : 0.005 0.061 5117 Dihedral : 9.148 159.396 3979 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3543 helix: -0.59 (0.13), residues: 1503 sheet: 0.11 (0.24), residues: 488 loop : -1.77 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 396 HIS 0.010 0.001 HIS A 395 PHE 0.030 0.001 PHE E 408 TYR 0.021 0.001 TYR H 107 ARG 0.012 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 951) hydrogen bonds : angle 4.93021 ( 2754) covalent geometry : bond 0.00261 (28752) covalent geometry : angle 0.63571 (39006) *********************** 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 1077 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1076 time to evaluate : 3.358 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: A 21 TRP cc_start: 0.8978 (m100) cc_final: 0.8708 (m100) REVERT: A 35 ILE cc_start: 0.8501 (mp) cc_final: 0.8107 (mm) REVERT: A 88 ASP cc_start: 0.7700 (p0) cc_final: 0.7147 (p0) REVERT: A 101 TRP cc_start: 0.8758 (t60) cc_final: 0.8490 (t60) REVERT: A 136 THR cc_start: 0.8632 (m) cc_final: 0.8128 (t) REVERT: A 145 SER cc_start: 0.8985 (m) cc_final: 0.8683 (p) REVERT: A 147 MET cc_start: 0.8311 (ppp) cc_final: 0.7703 (ppp) REVERT: A 166 THR cc_start: 0.8349 (t) cc_final: 0.7827 (p) REVERT: A 181 GLU cc_start: 0.9351 (pp20) cc_final: 0.8859 (pp20) REVERT: A 198 GLU cc_start: 0.8364 (pm20) cc_final: 0.8028 (tp30) REVERT: A 265 PHE cc_start: 0.7941 (p90) cc_final: 0.7329 (p90) REVERT: A 293 PHE cc_start: 0.6776 (t80) cc_final: 0.6461 (t80) REVERT: A 297 ASN cc_start: 0.9121 (m-40) cc_final: 0.8673 (t0) REVERT: A 380 LEU cc_start: 0.9348 (mm) cc_final: 0.8813 (tp) REVERT: A 423 GLN cc_start: 0.8132 (mt0) cc_final: 0.7333 (mp10) REVERT: D 5 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7449 (ttp80) REVERT: D 32 MET cc_start: 0.7846 (mmm) cc_final: 0.7480 (mmm) REVERT: D 54 ASN cc_start: 0.7049 (m-40) cc_final: 0.6146 (p0) REVERT: D 65 LEU cc_start: 0.8590 (mm) cc_final: 0.8299 (mm) REVERT: D 71 LYS cc_start: 0.7560 (mttt) cc_final: 0.7346 (mmtp) REVERT: D 92 LEU cc_start: 0.8052 (mt) cc_final: 0.7493 (pp) REVERT: E 14 VAL cc_start: 0.9599 (t) cc_final: 0.9399 (t) REVERT: E 18 ASN cc_start: 0.9192 (m110) cc_final: 0.8989 (m110) REVERT: E 24 TYR cc_start: 0.8611 (m-10) cc_final: 0.8092 (m-10) REVERT: E 27 GLU cc_start: 0.8628 (tt0) cc_final: 0.8240 (tt0) REVERT: E 55 THR cc_start: 0.8927 (p) cc_final: 0.8559 (p) REVERT: E 59 GLU cc_start: 0.7359 (mt-10) cc_final: 0.5584 (pt0) REVERT: E 65 PHE cc_start: 0.7661 (p90) cc_final: 0.6597 (p90) REVERT: E 69 SER cc_start: 0.9354 (p) cc_final: 0.9102 (p) REVERT: E 94 GLU cc_start: 0.7404 (pp20) cc_final: 0.6778 (tm-30) REVERT: E 116 LYS cc_start: 0.9122 (tmmt) cc_final: 0.8685 (ttmt) REVERT: E 162 ASN cc_start: 0.9122 (t160) cc_final: 0.8411 (t0) REVERT: E 163 MET cc_start: 0.8962 (mmp) cc_final: 0.8374 (mmm) REVERT: E 167 LYS cc_start: 0.7859 (pttp) cc_final: 0.7617 (ptmt) REVERT: E 184 SER cc_start: 0.7956 (p) cc_final: 0.7629 (m) REVERT: E 201 ASN cc_start: 0.8288 (m-40) cc_final: 0.7522 (t0) REVERT: E 237 GLN cc_start: 0.8909 (mm110) cc_final: 0.8320 (mm-40) REVERT: E 255 ASP cc_start: 0.8661 (t70) cc_final: 0.7935 (m-30) REVERT: E 256 LEU cc_start: 0.9253 (mt) cc_final: 0.8940 (mm) REVERT: E 270 HIS cc_start: 0.8343 (p-80) cc_final: 0.7877 (p-80) REVERT: E 333 GLN cc_start: 0.7300 (pp30) cc_final: 0.6946 (pp30) REVERT: E 343 ARG cc_start: 0.8097 (ptt180) cc_final: 0.7697 (mtt180) REVERT: E 381 MET cc_start: 0.8993 (ttt) cc_final: 0.8547 (ttp) REVERT: E 396 ASP cc_start: 0.9404 (t0) cc_final: 0.9002 (t0) REVERT: E 402 MET cc_start: 0.9071 (mmt) cc_final: 0.8618 (mmt) REVERT: F 16 ILE cc_start: 0.9229 (mm) cc_final: 0.8856 (mm) REVERT: F 21 TRP cc_start: 0.8361 (m100) cc_final: 0.7743 (m100) REVERT: F 24 TYR cc_start: 0.8692 (m-10) cc_final: 0.7983 (m-10) REVERT: F 30 ILE cc_start: 0.9294 (mt) cc_final: 0.8957 (mt) REVERT: F 59 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6419 (pt0) REVERT: F 81 GLN cc_start: 0.7794 (mt0) cc_final: 0.7513 (mt0) REVERT: F 94 GLU cc_start: 0.8698 (pp20) cc_final: 0.8192 (tm-30) REVERT: F 118 MET cc_start: 0.8432 (mmm) cc_final: 0.8132 (mmm) REVERT: F 131 ASP cc_start: 0.7938 (m-30) cc_final: 0.7578 (m-30) REVERT: F 171 LEU cc_start: 0.6939 (mt) cc_final: 0.6426 (mt) REVERT: F 201 ASN cc_start: 0.7928 (m-40) cc_final: 0.7233 (m-40) REVERT: F 204 CYS cc_start: 0.8696 (t) cc_final: 0.8036 (t) REVERT: F 206 PHE cc_start: 0.8776 (m-80) cc_final: 0.8521 (m-80) REVERT: F 237 GLN cc_start: 0.9279 (mm110) cc_final: 0.8274 (mm-40) REVERT: F 239 VAL cc_start: 0.8750 (t) cc_final: 0.8506 (t) REVERT: F 247 ARG cc_start: 0.6562 (mmt90) cc_final: 0.5228 (mmt90) REVERT: F 255 ASP cc_start: 0.8662 (t70) cc_final: 0.8387 (m-30) REVERT: F 270 HIS cc_start: 0.8445 (p-80) cc_final: 0.7612 (p-80) REVERT: F 279 ILE cc_start: 0.8923 (mm) cc_final: 0.8655 (mm) REVERT: F 295 ILE cc_start: 0.9463 (mt) cc_final: 0.9143 (tt) REVERT: F 317 MET cc_start: 0.7181 (tpt) cc_final: 0.6611 (tpt) REVERT: F 346 GLN cc_start: 0.7576 (pp30) cc_final: 0.7302 (pp30) REVERT: F 349 ASP cc_start: 0.6331 (p0) cc_final: 0.5146 (p0) REVERT: F 361 TYR cc_start: 0.8231 (m-80) cc_final: 0.7965 (m-80) REVERT: F 441 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8301 (tm-30) REVERT: G 23 LEU cc_start: 0.9120 (tp) cc_final: 0.8302 (tp) REVERT: G 27 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7719 (mt-10) REVERT: G 65 PHE cc_start: 0.7447 (p90) cc_final: 0.6432 (p90) REVERT: G 209 ASP cc_start: 0.7517 (t0) cc_final: 0.7164 (t0) REVERT: G 308 LYS cc_start: 0.8498 (tptp) cc_final: 0.8113 (mmtt) REVERT: G 317 MET cc_start: 0.7366 (mmm) cc_final: 0.7110 (mtp) REVERT: G 343 ARG cc_start: 0.8537 (ptm160) cc_final: 0.8152 (mtt180) REVERT: G 351 CYS cc_start: 0.8249 (t) cc_final: 0.7120 (p) REVERT: G 374 LYS cc_start: 0.8970 (tttm) cc_final: 0.8385 (tptp) REVERT: G 380 CYS cc_start: 0.8929 (t) cc_final: 0.8583 (t) REVERT: G 381 MET cc_start: 0.8902 (tmm) cc_final: 0.8685 (tmm) REVERT: G 441 GLN cc_start: 0.8764 (mm110) cc_final: 0.8500 (tm-30) REVERT: H 18 ASN cc_start: 0.8911 (m110) cc_final: 0.8702 (m110) REVERT: H 20 CYS cc_start: 0.8751 (m) cc_final: 0.8446 (m) REVERT: H 73 ASP cc_start: 0.8089 (t0) cc_final: 0.7789 (t0) REVERT: H 80 ASP cc_start: 0.8551 (m-30) cc_final: 0.8329 (p0) REVERT: H 94 GLU cc_start: 0.8306 (tp30) cc_final: 0.7732 (tp30) REVERT: H 102 ASP cc_start: 0.8850 (t70) cc_final: 0.8476 (t70) REVERT: H 131 ASP cc_start: 0.8293 (m-30) cc_final: 0.8082 (m-30) REVERT: H 145 PHE cc_start: 0.8917 (m-80) cc_final: 0.8496 (m-80) REVERT: H 187 GLU cc_start: 0.8443 (tt0) cc_final: 0.8094 (tp30) REVERT: H 211 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8692 (mt-10) REVERT: H 237 GLN cc_start: 0.8448 (mt0) cc_final: 0.7755 (tt0) REVERT: H 276 TYR cc_start: 0.7858 (t80) cc_final: 0.6812 (t80) REVERT: H 308 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8725 (mmtt) REVERT: H 330 ARG cc_start: 0.5246 (mtm180) cc_final: 0.4395 (mtt180) REVERT: H 343 ARG cc_start: 0.8490 (ptt180) cc_final: 0.8169 (mtt180) REVERT: H 374 LYS cc_start: 0.8941 (tttm) cc_final: 0.8607 (tmtt) REVERT: H 379 VAL cc_start: 0.8857 (t) cc_final: 0.8619 (t) REVERT: H 381 MET cc_start: 0.8810 (tmm) cc_final: 0.8466 (tmm) REVERT: H 415 GLU cc_start: 0.6326 (pt0) cc_final: 0.5958 (pt0) REVERT: H 418 GLU cc_start: 0.8190 (pt0) cc_final: 0.7676 (mp0) REVERT: H 441 GLN cc_start: 0.8769 (mm110) cc_final: 0.8261 (tm-30) REVERT: J 6 HIS cc_start: 0.9090 (t-90) cc_final: 0.8848 (t-170) REVERT: J 14 ASN cc_start: 0.9122 (m110) cc_final: 0.8727 (m-40) REVERT: J 21 TRP cc_start: 0.8695 (m100) cc_final: 0.8297 (m100) REVERT: J 31 ASP cc_start: 0.7927 (p0) cc_final: 0.7614 (p0) REVERT: J 53 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7099 (tm-30) REVERT: J 67 ASP cc_start: 0.8201 (t0) cc_final: 0.7645 (p0) REVERT: J 83 ASN cc_start: 0.8872 (m-40) cc_final: 0.8507 (m110) REVERT: J 89 ASN cc_start: 0.9011 (m110) cc_final: 0.8572 (m110) REVERT: J 101 TRP cc_start: 0.8995 (t60) cc_final: 0.8506 (t60) REVERT: J 162 ARG cc_start: 0.7641 (mmt180) cc_final: 0.7109 (mpt180) REVERT: J 174 LYS cc_start: 0.9104 (mppt) cc_final: 0.8843 (mmtt) REVERT: J 189 MET cc_start: 0.8735 (mmt) cc_final: 0.8352 (mmp) REVERT: J 191 GLN cc_start: 0.8706 (mp10) cc_final: 0.8196 (mp10) REVERT: J 198 GLU cc_start: 0.8753 (pm20) cc_final: 0.7858 (tp30) REVERT: J 216 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8592 (mmmt) REVERT: J 257 MET cc_start: 0.8625 (mmp) cc_final: 0.8349 (mmp) REVERT: J 297 ASN cc_start: 0.9138 (m110) cc_final: 0.8718 (t0) REVERT: J 375 GLU cc_start: 0.8487 (tp30) cc_final: 0.7868 (tm-30) REVERT: J 376 ILE cc_start: 0.9054 (pt) cc_final: 0.8336 (pt) REVERT: J 405 MET cc_start: 0.8448 (tpp) cc_final: 0.8024 (tpp) REVERT: J 412 SER cc_start: 0.9139 (m) cc_final: 0.8887 (p) REVERT: J 415 ASN cc_start: 0.8498 (m-40) cc_final: 0.8140 (t0) REVERT: B 6 HIS cc_start: 0.8816 (t-90) cc_final: 0.8282 (t-170) REVERT: B 14 ASN cc_start: 0.8633 (m-40) cc_final: 0.8256 (m-40) REVERT: B 21 TRP cc_start: 0.9102 (m100) cc_final: 0.8547 (m100) REVERT: B 31 ASP cc_start: 0.7867 (p0) cc_final: 0.7624 (p0) REVERT: B 50 TYR cc_start: 0.7678 (m-10) cc_final: 0.7342 (m-10) REVERT: B 51 PHE cc_start: 0.8990 (m-80) cc_final: 0.8615 (m-80) REVERT: B 83 ASN cc_start: 0.8521 (m-40) cc_final: 0.8260 (m110) REVERT: B 85 PHE cc_start: 0.7540 (m-80) cc_final: 0.7084 (m-80) REVERT: B 86 ARG cc_start: 0.7239 (ptp-170) cc_final: 0.6980 (ptp-170) REVERT: B 101 TRP cc_start: 0.7512 (t60) cc_final: 0.7303 (t60) REVERT: B 130 LEU cc_start: 0.9162 (tp) cc_final: 0.8916 (tp) REVERT: B 134 GLN cc_start: 0.8506 (mt0) cc_final: 0.8202 (mt0) REVERT: B 147 MET cc_start: 0.7978 (tmm) cc_final: 0.7446 (tmm) REVERT: B 151 LEU cc_start: 0.9639 (mt) cc_final: 0.9248 (mt) REVERT: B 163 MET cc_start: 0.6805 (pmm) cc_final: 0.6587 (pmm) REVERT: B 164 MET cc_start: 0.7602 (mmp) cc_final: 0.6566 (mmp) REVERT: B 166 THR cc_start: 0.8893 (t) cc_final: 0.8466 (p) REVERT: B 217 ILE cc_start: 0.8745 (mp) cc_final: 0.8529 (pt) REVERT: B 247 ASN cc_start: 0.5692 (m110) cc_final: 0.5017 (m110) REVERT: B 299 MET cc_start: 0.9194 (mmp) cc_final: 0.8897 (mmt) REVERT: B 358 LYS cc_start: 0.7817 (pttm) cc_final: 0.7511 (pttm) REVERT: B 359 ASP cc_start: 0.9295 (m-30) cc_final: 0.9068 (m-30) REVERT: B 405 MET cc_start: 0.8382 (tpt) cc_final: 0.7948 (tpt) REVERT: B 408 THR cc_start: 0.9020 (p) cc_final: 0.8446 (p) REVERT: C 6 HIS cc_start: 0.9002 (t70) cc_final: 0.7980 (t-170) REVERT: C 8 GLN cc_start: 0.7357 (mt0) cc_final: 0.6468 (mt0) REVERT: C 20 PHE cc_start: 0.8203 (t80) cc_final: 0.7407 (t80) REVERT: C 134 GLN cc_start: 0.8357 (mt0) cc_final: 0.7791 (mt0) REVERT: C 157 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8641 (tm-30) REVERT: C 297 ASN cc_start: 0.9165 (m-40) cc_final: 0.8774 (t0) REVERT: C 359 ASP cc_start: 0.8945 (m-30) cc_final: 0.8656 (m-30) REVERT: C 394 LEU cc_start: 0.8851 (tp) cc_final: 0.8488 (tt) REVERT: C 397 TYR cc_start: 0.8610 (m-80) cc_final: 0.8399 (m-80) REVERT: C 405 MET cc_start: 0.8161 (tpp) cc_final: 0.7670 (tpp) REVERT: C 406 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8809 (mt-10) outliers start: 1 outliers final: 0 residues processed: 1077 average time/residue: 0.3857 time to fit residues: 660.3758 Evaluate side-chains 872 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 872 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 259 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 306 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 chunk 236 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 294 optimal weight: 0.0870 chunk 223 optimal weight: 6.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 131 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 111 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** 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 384 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN J 328 GLN B 6 HIS B 44 HIS B 89 ASN B 131 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.119444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.104147 restraints weight = 59479.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107625 restraints weight = 34198.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110017 restraints weight = 21692.143| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28752 Z= 0.147 Angle : 0.670 11.955 39006 Z= 0.333 Chirality : 0.048 0.316 4200 Planarity : 0.005 0.086 5117 Dihedral : 9.119 160.818 3979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.10 % Allowed : 2.16 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3543 helix: -0.50 (0.13), residues: 1510 sheet: 0.27 (0.24), residues: 488 loop : -1.56 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 350 HIS 0.008 0.001 HIS B 263 PHE 0.024 0.002 PHE F 408 TYR 0.025 0.001 TYR G 107 ARG 0.014 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 951) hydrogen bonds : angle 4.98726 ( 2754) covalent geometry : bond 0.00334 (28752) covalent geometry : angle 0.67011 (39006) *********************** 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 1057 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1054 time to evaluate : 3.007 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: A 6 HIS cc_start: 0.8963 (t-170) cc_final: 0.8453 (t-170) REVERT: A 35 ILE cc_start: 0.8690 (mp) cc_final: 0.8275 (mm) REVERT: A 53 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7030 (tm-30) REVERT: A 88 ASP cc_start: 0.7883 (p0) cc_final: 0.7586 (p0) REVERT: A 89 ASN cc_start: 0.8560 (m110) cc_final: 0.8283 (m110) REVERT: A 136 THR cc_start: 0.8609 (m) cc_final: 0.8150 (t) REVERT: A 145 SER cc_start: 0.8942 (m) cc_final: 0.8438 (p) REVERT: A 166 THR cc_start: 0.8615 (t) cc_final: 0.8004 (p) REVERT: A 181 GLU cc_start: 0.9331 (pp20) cc_final: 0.8813 (pp20) REVERT: A 198 GLU cc_start: 0.8473 (pm20) cc_final: 0.7736 (tp30) REVERT: A 202 ILE cc_start: 0.8884 (mm) cc_final: 0.8657 (mm) REVERT: A 213 ASN cc_start: 0.8848 (m-40) cc_final: 0.8347 (t0) REVERT: A 233 MET cc_start: 0.9306 (ptm) cc_final: 0.8929 (ptm) REVERT: A 265 PHE cc_start: 0.7998 (p90) cc_final: 0.7315 (p90) REVERT: A 293 PHE cc_start: 0.6888 (t80) cc_final: 0.6641 (t80) REVERT: A 297 ASN cc_start: 0.9196 (m-40) cc_final: 0.8819 (t0) REVERT: A 330 ARG cc_start: 0.8844 (mtp180) cc_final: 0.8528 (mtp85) REVERT: A 340 PHE cc_start: 0.7410 (m-80) cc_final: 0.7098 (m-10) REVERT: A 380 LEU cc_start: 0.9380 (mm) cc_final: 0.8787 (tt) REVERT: A 423 GLN cc_start: 0.8199 (mt0) cc_final: 0.7476 (mp10) REVERT: D 5 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7478 (ttp80) REVERT: D 32 MET cc_start: 0.7957 (mmm) cc_final: 0.7715 (mmm) REVERT: D 71 LYS cc_start: 0.7617 (mttt) cc_final: 0.7394 (mmtp) REVERT: D 92 LEU cc_start: 0.8146 (mt) cc_final: 0.7531 (pp) REVERT: E 14 VAL cc_start: 0.9602 (t) cc_final: 0.9334 (t) REVERT: E 21 TRP cc_start: 0.8887 (m100) cc_final: 0.8461 (m100) REVERT: E 24 TYR cc_start: 0.8661 (m-10) cc_final: 0.8152 (m-10) REVERT: E 27 GLU cc_start: 0.8590 (tt0) cc_final: 0.8304 (tt0) REVERT: E 55 THR cc_start: 0.8971 (p) cc_final: 0.8715 (p) REVERT: E 59 GLU cc_start: 0.7512 (mt-10) cc_final: 0.5805 (pt0) REVERT: E 65 PHE cc_start: 0.7777 (p90) cc_final: 0.6146 (p90) REVERT: E 68 ARG cc_start: 0.8685 (mtt180) cc_final: 0.8302 (mtp85) REVERT: E 94 GLU cc_start: 0.8325 (pp20) cc_final: 0.7968 (tm-30) REVERT: E 116 LYS cc_start: 0.9084 (tmmt) cc_final: 0.8489 (ttpt) REVERT: E 131 ASP cc_start: 0.7665 (m-30) cc_final: 0.7343 (m-30) REVERT: E 161 LEU cc_start: 0.8625 (pp) cc_final: 0.8384 (pp) REVERT: E 162 ASN cc_start: 0.9185 (t0) cc_final: 0.8620 (t0) REVERT: E 163 MET cc_start: 0.8862 (mmp) cc_final: 0.8230 (mmm) REVERT: E 167 LYS cc_start: 0.8015 (pttp) cc_final: 0.7656 (ptmt) REVERT: E 201 ASN cc_start: 0.8243 (m-40) cc_final: 0.7756 (t0) REVERT: E 237 GLN cc_start: 0.9091 (mm110) cc_final: 0.8767 (mm110) REVERT: E 255 ASP cc_start: 0.8600 (t70) cc_final: 0.7736 (m-30) REVERT: E 270 HIS cc_start: 0.8477 (p-80) cc_final: 0.8046 (p-80) REVERT: E 317 MET cc_start: 0.6539 (tpt) cc_final: 0.5487 (tpt) REVERT: E 333 GLN cc_start: 0.7458 (pp30) cc_final: 0.7045 (pp30) REVERT: E 343 ARG cc_start: 0.8328 (ptt180) cc_final: 0.7978 (mpt180) REVERT: E 350 TRP cc_start: 0.7145 (m-90) cc_final: 0.6547 (m-90) REVERT: E 351 CYS cc_start: 0.8804 (t) cc_final: 0.8356 (t) REVERT: E 381 MET cc_start: 0.8968 (ttt) cc_final: 0.8534 (ttp) REVERT: E 396 ASP cc_start: 0.9238 (t0) cc_final: 0.8742 (t0) REVERT: E 402 MET cc_start: 0.9119 (mmt) cc_final: 0.8574 (mmt) REVERT: F 1 MET cc_start: 0.8107 (ptp) cc_final: 0.7739 (ptp) REVERT: F 16 ILE cc_start: 0.9220 (mm) cc_final: 0.8867 (mm) REVERT: F 21 TRP cc_start: 0.8414 (m100) cc_final: 0.7757 (m100) REVERT: F 24 TYR cc_start: 0.8854 (m-10) cc_final: 0.8207 (m-10) REVERT: F 30 ILE cc_start: 0.9292 (mt) cc_final: 0.8933 (mm) REVERT: F 59 GLU cc_start: 0.7739 (mt-10) cc_final: 0.6567 (pt0) REVERT: F 94 GLU cc_start: 0.8416 (pp20) cc_final: 0.7944 (tm-30) REVERT: F 102 ASP cc_start: 0.9135 (t70) cc_final: 0.8777 (t70) REVERT: F 131 ASP cc_start: 0.7891 (m-30) cc_final: 0.7522 (m-30) REVERT: F 201 ASN cc_start: 0.7873 (m-40) cc_final: 0.7297 (m-40) REVERT: F 204 CYS cc_start: 0.8819 (t) cc_final: 0.8592 (t) REVERT: F 239 VAL cc_start: 0.8807 (t) cc_final: 0.8566 (t) REVERT: F 247 ARG cc_start: 0.6961 (mmt90) cc_final: 0.5225 (mmt90) REVERT: F 270 HIS cc_start: 0.8642 (p-80) cc_final: 0.7918 (p-80) REVERT: F 276 TYR cc_start: 0.8152 (t80) cc_final: 0.7924 (t80) REVERT: F 279 ILE cc_start: 0.9007 (mm) cc_final: 0.8734 (mm) REVERT: F 308 LYS cc_start: 0.8529 (tptp) cc_final: 0.8211 (mmtt) REVERT: F 361 TYR cc_start: 0.8260 (m-80) cc_final: 0.8044 (m-80) REVERT: F 381 MET cc_start: 0.7890 (ttt) cc_final: 0.7352 (ttp) REVERT: F 441 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8304 (tm-30) REVERT: G 23 LEU cc_start: 0.9102 (tp) cc_final: 0.8289 (tp) REVERT: G 27 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7356 (mt-10) REVERT: G 59 GLU cc_start: 0.6782 (mt-10) cc_final: 0.5163 (pt0) REVERT: G 65 PHE cc_start: 0.7644 (p90) cc_final: 0.6341 (p90) REVERT: G 124 GLU cc_start: 0.8921 (pt0) cc_final: 0.8589 (tt0) REVERT: G 161 LEU cc_start: 0.9068 (pp) cc_final: 0.8833 (pp) REVERT: G 257 ASN cc_start: 0.8570 (t0) cc_final: 0.8231 (p0) REVERT: G 295 ILE cc_start: 0.9474 (mt) cc_final: 0.9260 (tt) REVERT: G 305 GLN cc_start: 0.8603 (mp-120) cc_final: 0.8238 (mp10) REVERT: G 317 MET cc_start: 0.7431 (mmm) cc_final: 0.7106 (mtp) REVERT: G 343 ARG cc_start: 0.8586 (ptm160) cc_final: 0.8110 (mtt180) REVERT: G 351 CYS cc_start: 0.8255 (t) cc_final: 0.7177 (p) REVERT: G 374 LYS cc_start: 0.9034 (tttm) cc_final: 0.8457 (tptp) REVERT: G 380 CYS cc_start: 0.9028 (t) cc_final: 0.8344 (p) REVERT: G 381 MET cc_start: 0.8977 (tmm) cc_final: 0.8382 (tmm) REVERT: G 441 GLN cc_start: 0.8766 (mm110) cc_final: 0.8489 (tm-30) REVERT: H 20 CYS cc_start: 0.8746 (m) cc_final: 0.8432 (m) REVERT: H 27 GLU cc_start: 0.8570 (tt0) cc_final: 0.8319 (tt0) REVERT: H 73 ASP cc_start: 0.8171 (t0) cc_final: 0.7812 (t0) REVERT: H 94 GLU cc_start: 0.8185 (tp30) cc_final: 0.7609 (tp30) REVERT: H 102 ASP cc_start: 0.8822 (t70) cc_final: 0.7754 (t70) REVERT: H 131 ASP cc_start: 0.8263 (m-30) cc_final: 0.8049 (m-30) REVERT: H 143 HIS cc_start: 0.8837 (p90) cc_final: 0.8344 (p90) REVERT: H 187 GLU cc_start: 0.8405 (tt0) cc_final: 0.7968 (tp30) REVERT: H 204 CYS cc_start: 0.8966 (p) cc_final: 0.8748 (p) REVERT: H 211 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8758 (mt-10) REVERT: H 237 GLN cc_start: 0.8506 (mt0) cc_final: 0.7629 (tt0) REVERT: H 276 TYR cc_start: 0.8301 (t80) cc_final: 0.7414 (t80) REVERT: H 343 ARG cc_start: 0.8451 (ptt180) cc_final: 0.7861 (mtt180) REVERT: H 374 LYS cc_start: 0.9025 (tttm) cc_final: 0.8645 (tmtt) REVERT: H 415 GLU cc_start: 0.6651 (pt0) cc_final: 0.6426 (pt0) REVERT: H 441 GLN cc_start: 0.8911 (mm110) cc_final: 0.8473 (tm-30) REVERT: J 14 ASN cc_start: 0.9034 (m110) cc_final: 0.8785 (m-40) REVERT: J 21 TRP cc_start: 0.8784 (m100) cc_final: 0.8183 (m100) REVERT: J 31 ASP cc_start: 0.7910 (p0) cc_final: 0.7636 (p0) REVERT: J 50 TYR cc_start: 0.7836 (m-10) cc_final: 0.7518 (m-10) REVERT: J 53 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7064 (tm-30) REVERT: J 67 ASP cc_start: 0.8183 (t0) cc_final: 0.7562 (p0) REVERT: J 101 TRP cc_start: 0.8971 (t60) cc_final: 0.8557 (t60) REVERT: J 189 MET cc_start: 0.8832 (mmt) cc_final: 0.8466 (mmp) REVERT: J 191 GLN cc_start: 0.8749 (mp10) cc_final: 0.8339 (mp10) REVERT: J 198 GLU cc_start: 0.8782 (pm20) cc_final: 0.7922 (tp30) REVERT: J 253 LEU cc_start: 0.9445 (tt) cc_final: 0.9180 (tt) REVERT: J 257 MET cc_start: 0.8649 (mmp) cc_final: 0.8247 (mmp) REVERT: J 297 ASN cc_start: 0.9161 (m110) cc_final: 0.8660 (t0) REVERT: J 315 LEU cc_start: 0.9028 (mt) cc_final: 0.8792 (mt) REVERT: J 365 THR cc_start: 0.8723 (m) cc_final: 0.8491 (p) REVERT: J 376 ILE cc_start: 0.9090 (pt) cc_final: 0.8297 (pt) REVERT: J 405 MET cc_start: 0.8509 (tpp) cc_final: 0.8083 (tpp) REVERT: J 412 SER cc_start: 0.9180 (m) cc_final: 0.8908 (p) REVERT: J 415 ASN cc_start: 0.8624 (m-40) cc_final: 0.8253 (t0) REVERT: B 6 HIS cc_start: 0.9201 (t70) cc_final: 0.8654 (t-170) REVERT: B 21 TRP cc_start: 0.9058 (m100) cc_final: 0.8484 (m100) REVERT: B 51 PHE cc_start: 0.9109 (m-80) cc_final: 0.8769 (m-80) REVERT: B 53 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7094 (tm-30) REVERT: B 83 ASN cc_start: 0.8610 (m-40) cc_final: 0.8228 (m110) REVERT: B 85 PHE cc_start: 0.7826 (m-80) cc_final: 0.7368 (m-80) REVERT: B 86 ARG cc_start: 0.7289 (ptp-170) cc_final: 0.6991 (ptp-170) REVERT: B 101 TRP cc_start: 0.7778 (t60) cc_final: 0.7367 (t60) REVERT: B 147 MET cc_start: 0.8038 (tmm) cc_final: 0.7460 (tmm) REVERT: B 151 LEU cc_start: 0.9646 (mt) cc_final: 0.9250 (mt) REVERT: B 163 MET cc_start: 0.7327 (pmm) cc_final: 0.7067 (pmm) REVERT: B 164 MET cc_start: 0.7959 (mmp) cc_final: 0.6758 (mmp) REVERT: B 217 ILE cc_start: 0.8875 (mp) cc_final: 0.8568 (pt) REVERT: B 241 ARG cc_start: 0.7768 (ptp-110) cc_final: 0.7504 (ptp-110) REVERT: B 344 ILE cc_start: 0.9219 (mt) cc_final: 0.8935 (mt) REVERT: B 408 THR cc_start: 0.9090 (p) cc_final: 0.8434 (p) REVERT: C 3 GLU cc_start: 0.5630 (mm-30) cc_final: 0.5231 (mp0) REVERT: C 6 HIS cc_start: 0.9109 (t70) cc_final: 0.8120 (t-170) REVERT: C 20 PHE cc_start: 0.8238 (t80) cc_final: 0.7460 (t80) REVERT: C 134 GLN cc_start: 0.8413 (mt0) cc_final: 0.7843 (mt0) REVERT: C 157 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 164 MET cc_start: 0.7583 (mmm) cc_final: 0.7082 (mmm) REVERT: C 297 ASN cc_start: 0.9165 (m-40) cc_final: 0.8754 (t0) REVERT: C 359 ASP cc_start: 0.9024 (m-30) cc_final: 0.8723 (m-30) REVERT: C 372 SER cc_start: 0.9321 (p) cc_final: 0.9081 (p) REVERT: C 375 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8335 (tm-30) REVERT: C 394 LEU cc_start: 0.8877 (tp) cc_final: 0.8491 (tt) REVERT: C 397 TYR cc_start: 0.8562 (m-80) cc_final: 0.8345 (m-80) REVERT: C 405 MET cc_start: 0.8292 (tpp) cc_final: 0.7786 (tpt) REVERT: C 406 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8736 (mt-10) outliers start: 3 outliers final: 0 residues processed: 1056 average time/residue: 0.3957 time to fit residues: 664.6541 Evaluate side-chains 854 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 854 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 228 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 27 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 332 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS 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** E 210 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN ** 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 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 83 ASN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 ASN C 204 ASN C 328 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100985 restraints weight = 60946.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104376 restraints weight = 35212.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106680 restraints weight = 22450.352| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28752 Z= 0.178 Angle : 0.703 11.192 39006 Z= 0.354 Chirality : 0.050 0.275 4200 Planarity : 0.005 0.079 5117 Dihedral : 9.181 160.746 3979 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.03 % Allowed : 1.06 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3543 helix: -0.61 (0.13), residues: 1508 sheet: 0.14 (0.24), residues: 520 loop : -1.55 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 21 HIS 0.007 0.001 HIS A 395 PHE 0.053 0.002 PHE E 408 TYR 0.029 0.002 TYR J 222 ARG 0.014 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 951) hydrogen bonds : angle 5.06494 ( 2754) covalent geometry : bond 0.00400 (28752) covalent geometry : angle 0.70278 (39006) *********************** 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 1028 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1027 time to evaluate : 3.360 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 14 ASN cc_start: 0.9033 (m-40) cc_final: 0.8759 (m-40) REVERT: A 20 PHE cc_start: 0.8014 (t80) cc_final: 0.7035 (t80) REVERT: A 35 ILE cc_start: 0.8712 (mp) cc_final: 0.8297 (mm) REVERT: A 53 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7120 (tm-30) REVERT: A 88 ASP cc_start: 0.7888 (p0) cc_final: 0.7512 (p0) REVERT: A 136 THR cc_start: 0.8657 (m) cc_final: 0.8396 (p) REVERT: A 139 LEU cc_start: 0.9030 (mt) cc_final: 0.8753 (mt) REVERT: A 157 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 181 GLU cc_start: 0.9297 (pp20) cc_final: 0.8809 (pp20) REVERT: A 198 GLU cc_start: 0.8535 (pm20) cc_final: 0.7750 (tp30) REVERT: A 202 ILE cc_start: 0.8831 (mm) cc_final: 0.8596 (mm) REVERT: A 265 PHE cc_start: 0.8193 (p90) cc_final: 0.7489 (p90) REVERT: A 293 PHE cc_start: 0.7097 (t80) cc_final: 0.6798 (t80) REVERT: A 297 ASN cc_start: 0.9205 (m-40) cc_final: 0.8836 (t0) REVERT: A 315 LEU cc_start: 0.9096 (mt) cc_final: 0.8850 (mt) REVERT: A 330 ARG cc_start: 0.8859 (mtp180) cc_final: 0.8533 (mtp85) REVERT: A 340 PHE cc_start: 0.7482 (m-80) cc_final: 0.7106 (m-10) REVERT: A 365 THR cc_start: 0.8804 (m) cc_final: 0.8372 (p) REVERT: A 375 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 423 GLN cc_start: 0.8188 (mt0) cc_final: 0.7814 (mt0) REVERT: D 5 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7680 (tmm-80) REVERT: D 32 MET cc_start: 0.7925 (mmm) cc_final: 0.7628 (mmm) REVERT: D 71 LYS cc_start: 0.7628 (mttt) cc_final: 0.7325 (mmtp) REVERT: D 92 LEU cc_start: 0.8189 (mt) cc_final: 0.7558 (pp) REVERT: E 18 ASN cc_start: 0.9230 (m110) cc_final: 0.9025 (m110) REVERT: E 21 TRP cc_start: 0.8820 (m100) cc_final: 0.8428 (m100) REVERT: E 24 TYR cc_start: 0.8640 (m-10) cc_final: 0.8181 (m-10) REVERT: E 27 GLU cc_start: 0.8603 (tt0) cc_final: 0.8374 (tt0) REVERT: E 59 GLU cc_start: 0.7580 (mt-10) cc_final: 0.5864 (pt0) REVERT: E 65 PHE cc_start: 0.8029 (p90) cc_final: 0.6209 (p90) REVERT: E 68 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8164 (mtt90) REVERT: E 69 SER cc_start: 0.8708 (p) cc_final: 0.8472 (p) REVERT: E 80 ASP cc_start: 0.8210 (m-30) cc_final: 0.7984 (m-30) REVERT: E 94 GLU cc_start: 0.8406 (pp20) cc_final: 0.8072 (tm-30) REVERT: E 162 ASN cc_start: 0.9287 (t0) cc_final: 0.8868 (t0) REVERT: E 163 MET cc_start: 0.8774 (mmp) cc_final: 0.8545 (mmp) REVERT: E 167 LYS cc_start: 0.8172 (pttp) cc_final: 0.7852 (ptmt) REVERT: E 201 ASN cc_start: 0.8251 (m-40) cc_final: 0.7790 (t0) REVERT: E 219 ARG cc_start: 0.7375 (mtm110) cc_final: 0.6642 (ptm160) REVERT: E 243 THR cc_start: 0.8320 (p) cc_final: 0.8029 (p) REVERT: E 255 ASP cc_start: 0.8323 (t70) cc_final: 0.7845 (m-30) REVERT: E 270 HIS cc_start: 0.8447 (p-80) cc_final: 0.7970 (p-80) REVERT: E 303 TYR cc_start: 0.8543 (m-10) cc_final: 0.8284 (m-10) REVERT: E 308 LYS cc_start: 0.8377 (tptp) cc_final: 0.7777 (mtpp) REVERT: E 333 GLN cc_start: 0.7319 (pp30) cc_final: 0.7042 (pp30) REVERT: E 381 MET cc_start: 0.8900 (ttt) cc_final: 0.8278 (ttp) REVERT: E 402 MET cc_start: 0.9088 (mmt) cc_final: 0.8778 (mmt) REVERT: F 1 MET cc_start: 0.8063 (ptp) cc_final: 0.7686 (ptp) REVERT: F 21 TRP cc_start: 0.8399 (m100) cc_final: 0.7868 (m100) REVERT: F 24 TYR cc_start: 0.8906 (m-10) cc_final: 0.8208 (m-10) REVERT: F 30 ILE cc_start: 0.9277 (mt) cc_final: 0.8981 (mt) REVERT: F 59 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6289 (pt0) REVERT: F 77 ASN cc_start: 0.9167 (t0) cc_final: 0.8756 (t0) REVERT: F 80 ASP cc_start: 0.8493 (m-30) cc_final: 0.8197 (p0) REVERT: F 102 ASP cc_start: 0.9119 (t70) cc_final: 0.8748 (t70) REVERT: F 131 ASP cc_start: 0.7899 (m-30) cc_final: 0.7571 (m-30) REVERT: F 158 LEU cc_start: 0.9048 (mp) cc_final: 0.8815 (mp) REVERT: F 201 ASN cc_start: 0.8103 (m-40) cc_final: 0.7560 (m-40) REVERT: F 247 ARG cc_start: 0.6607 (mmt90) cc_final: 0.4812 (mmt90) REVERT: F 270 HIS cc_start: 0.8604 (p-80) cc_final: 0.7896 (p-80) REVERT: F 276 TYR cc_start: 0.8116 (t80) cc_final: 0.7828 (t80) REVERT: F 304 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8545 (t0) REVERT: F 308 LYS cc_start: 0.8617 (tptp) cc_final: 0.8374 (mmtt) REVERT: F 361 TYR cc_start: 0.8309 (m-80) cc_final: 0.8103 (m-80) REVERT: F 426 ARG cc_start: 0.8795 (mmp-170) cc_final: 0.8461 (tpp-160) REVERT: F 441 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8394 (tm-30) REVERT: G 23 LEU cc_start: 0.9167 (tp) cc_final: 0.8488 (tt) REVERT: G 24 TYR cc_start: 0.8605 (m-10) cc_final: 0.8324 (m-80) REVERT: G 27 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7536 (mt-10) REVERT: G 59 GLU cc_start: 0.6807 (mt-10) cc_final: 0.5684 (pt0) REVERT: G 143 HIS cc_start: 0.8724 (p90) cc_final: 0.8462 (p90) REVERT: G 161 LEU cc_start: 0.9123 (pp) cc_final: 0.8907 (pp) REVERT: G 206 PHE cc_start: 0.8595 (m-10) cc_final: 0.8293 (m-10) REVERT: G 215 ASP cc_start: 0.7963 (m-30) cc_final: 0.7494 (m-30) REVERT: G 257 ASN cc_start: 0.8525 (t0) cc_final: 0.8187 (p0) REVERT: G 308 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8056 (mttt) REVERT: G 317 MET cc_start: 0.7382 (mmm) cc_final: 0.7063 (mtp) REVERT: G 343 ARG cc_start: 0.8786 (ptm160) cc_final: 0.8137 (mtt180) REVERT: G 351 CYS cc_start: 0.8156 (t) cc_final: 0.7146 (p) REVERT: G 356 LYS cc_start: 0.8287 (tppt) cc_final: 0.7702 (tppt) REVERT: G 374 LYS cc_start: 0.9082 (tttm) cc_final: 0.8511 (tptp) REVERT: G 380 CYS cc_start: 0.9071 (t) cc_final: 0.8680 (t) REVERT: G 381 MET cc_start: 0.8954 (tmm) cc_final: 0.8734 (tmm) REVERT: G 426 ARG cc_start: 0.8909 (mmm160) cc_final: 0.8469 (mmm160) REVERT: G 434 ARG cc_start: 0.9256 (mtt90) cc_final: 0.9022 (ptp-110) REVERT: G 441 GLN cc_start: 0.8772 (mm110) cc_final: 0.8346 (tm-30) REVERT: H 20 CYS cc_start: 0.8823 (m) cc_final: 0.8581 (m) REVERT: H 27 GLU cc_start: 0.8522 (tt0) cc_final: 0.8278 (tt0) REVERT: H 94 GLU cc_start: 0.8134 (tp30) cc_final: 0.7669 (tp30) REVERT: H 102 ASP cc_start: 0.8801 (t70) cc_final: 0.7565 (t70) REVERT: H 131 ASP cc_start: 0.8288 (m-30) cc_final: 0.8062 (m-30) REVERT: H 140 LEU cc_start: 0.8536 (tp) cc_final: 0.8152 (mm) REVERT: H 143 HIS cc_start: 0.8843 (p90) cc_final: 0.8218 (p90) REVERT: H 187 GLU cc_start: 0.8697 (tt0) cc_final: 0.8104 (tp30) REVERT: H 211 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8722 (mt-10) REVERT: H 237 GLN cc_start: 0.8469 (mt0) cc_final: 0.7543 (tt0) REVERT: H 276 TYR cc_start: 0.8355 (t80) cc_final: 0.7465 (t80) REVERT: H 344 THR cc_start: 0.9469 (t) cc_final: 0.9190 (t) REVERT: H 346 GLN cc_start: 0.8320 (mp10) cc_final: 0.7629 (tp40) REVERT: H 374 LYS cc_start: 0.8998 (tttm) cc_final: 0.8593 (tmtt) REVERT: H 415 GLU cc_start: 0.6880 (pt0) cc_final: 0.6629 (pt0) REVERT: H 441 GLN cc_start: 0.8837 (mm110) cc_final: 0.8526 (tm-30) REVERT: J 6 HIS cc_start: 0.9063 (t70) cc_final: 0.8720 (t-170) REVERT: J 21 TRP cc_start: 0.8948 (m100) cc_final: 0.8291 (m100) REVERT: J 31 ASP cc_start: 0.8005 (p0) cc_final: 0.7663 (p0) REVERT: J 50 TYR cc_start: 0.8005 (m-10) cc_final: 0.7481 (m-10) REVERT: J 53 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7129 (tm-30) REVERT: J 111 GLU cc_start: 0.8345 (tt0) cc_final: 0.7813 (tp30) REVERT: J 162 ARG cc_start: 0.7593 (mmt180) cc_final: 0.7335 (mmt180) REVERT: J 189 MET cc_start: 0.8856 (mmt) cc_final: 0.8467 (mmp) REVERT: J 198 GLU cc_start: 0.8732 (pm20) cc_final: 0.7918 (tp30) REVERT: J 215 LEU cc_start: 0.9347 (mp) cc_final: 0.9138 (mt) REVERT: J 216 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8733 (mmmt) REVERT: J 297 ASN cc_start: 0.9222 (m110) cc_final: 0.8845 (t0) REVERT: J 376 ILE cc_start: 0.9006 (pt) cc_final: 0.8793 (pt) REVERT: J 405 MET cc_start: 0.8584 (tpp) cc_final: 0.8124 (tpp) REVERT: J 415 ASN cc_start: 0.8633 (m-40) cc_final: 0.8165 (t0) REVERT: B 6 HIS cc_start: 0.9111 (t70) cc_final: 0.8715 (t-90) REVERT: B 14 ASN cc_start: 0.8904 (m-40) cc_final: 0.8510 (m-40) REVERT: B 20 PHE cc_start: 0.8436 (t80) cc_final: 0.7324 (t80) REVERT: B 51 PHE cc_start: 0.9173 (m-80) cc_final: 0.8854 (m-80) REVERT: B 53 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7226 (tm-30) REVERT: B 83 ASN cc_start: 0.8473 (m-40) cc_final: 0.8146 (m110) REVERT: B 85 PHE cc_start: 0.7730 (m-80) cc_final: 0.7108 (m-80) REVERT: B 86 ARG cc_start: 0.7267 (ptp-170) cc_final: 0.6934 (ptp-170) REVERT: B 101 TRP cc_start: 0.8137 (t60) cc_final: 0.7549 (t60) REVERT: B 147 MET cc_start: 0.8080 (tmm) cc_final: 0.7677 (tmm) REVERT: B 164 MET cc_start: 0.7880 (mmp) cc_final: 0.6661 (mmp) REVERT: B 189 MET cc_start: 0.8866 (tpp) cc_final: 0.8599 (tpp) REVERT: B 202 ILE cc_start: 0.8829 (mm) cc_final: 0.8620 (mm) REVERT: B 223 ASP cc_start: 0.8960 (m-30) cc_final: 0.8259 (t70) REVERT: B 288 LEU cc_start: 0.9069 (mt) cc_final: 0.8709 (mt) REVERT: B 407 PHE cc_start: 0.8501 (m-80) cc_final: 0.8000 (m-80) REVERT: C 6 HIS cc_start: 0.9019 (t70) cc_final: 0.7997 (t-170) REVERT: C 20 PHE cc_start: 0.8274 (t80) cc_final: 0.7471 (t80) REVERT: C 35 ILE cc_start: 0.8717 (mm) cc_final: 0.8505 (mp) REVERT: C 53 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6798 (tm-30) REVERT: C 134 GLN cc_start: 0.8505 (mt0) cc_final: 0.8055 (mt0) REVERT: C 157 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 174 LYS cc_start: 0.8882 (mppt) cc_final: 0.8651 (mppt) REVERT: C 202 ILE cc_start: 0.9043 (mm) cc_final: 0.8818 (mt) REVERT: C 297 ASN cc_start: 0.9228 (m-40) cc_final: 0.8880 (t0) REVERT: C 359 ASP cc_start: 0.9032 (m-30) cc_final: 0.8782 (m-30) REVERT: C 372 SER cc_start: 0.9339 (p) cc_final: 0.9106 (p) REVERT: C 375 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8296 (tm-30) REVERT: C 397 TYR cc_start: 0.8350 (m-80) cc_final: 0.8084 (m-80) REVERT: C 405 MET cc_start: 0.8482 (tpp) cc_final: 0.7855 (mmm) REVERT: C 406 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8776 (mt-10) REVERT: C 408 THR cc_start: 0.8613 (p) cc_final: 0.7790 (p) outliers start: 1 outliers final: 0 residues processed: 1028 average time/residue: 0.4122 time to fit residues: 680.9005 Evaluate side-chains 842 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 841 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 222 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 321 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 83 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN G 106 ASN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** 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 83 ASN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS C 256 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.119139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103696 restraints weight = 60081.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.107155 restraints weight = 34447.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.109565 restraints weight = 21833.070| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.7080 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= 0.133 Angle : 0.680 13.262 39006 Z= 0.336 Chirality : 0.048 0.207 4200 Planarity : 0.005 0.066 5117 Dihedral : 8.984 159.627 3979 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.03 % Allowed : 0.80 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3543 helix: -0.43 (0.13), residues: 1514 sheet: 0.25 (0.24), residues: 500 loop : -1.51 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 21 HIS 0.006 0.001 HIS C 263 PHE 0.043 0.002 PHE F 408 TYR 0.030 0.002 TYR H 24 ARG 0.016 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 951) hydrogen bonds : angle 4.88768 ( 2754) covalent geometry : bond 0.00306 (28752) covalent geometry : angle 0.68029 (39006) *********************** 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 1031 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1030 time to evaluate : 3.908 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 20 PHE cc_start: 0.7954 (t80) cc_final: 0.7066 (t80) REVERT: A 21 TRP cc_start: 0.9132 (m100) cc_final: 0.8741 (m100) REVERT: A 35 ILE cc_start: 0.8628 (mp) cc_final: 0.8162 (mm) REVERT: A 53 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7072 (tm-30) REVERT: A 136 THR cc_start: 0.8643 (m) cc_final: 0.8154 (t) REVERT: A 139 LEU cc_start: 0.9007 (mt) cc_final: 0.8669 (mt) REVERT: A 157 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 166 THR cc_start: 0.8679 (t) cc_final: 0.8122 (p) REVERT: A 181 GLU cc_start: 0.9193 (pp20) cc_final: 0.8744 (pp20) REVERT: A 198 GLU cc_start: 0.8539 (pm20) cc_final: 0.7712 (tp30) REVERT: A 202 ILE cc_start: 0.8957 (mm) cc_final: 0.8709 (mm) REVERT: A 265 PHE cc_start: 0.7989 (p90) cc_final: 0.7227 (p90) REVERT: A 293 PHE cc_start: 0.7134 (t80) cc_final: 0.6858 (t80) REVERT: A 297 ASN cc_start: 0.9145 (m-40) cc_final: 0.8841 (t0) REVERT: A 315 LEU cc_start: 0.9093 (mt) cc_final: 0.8833 (mt) REVERT: A 330 ARG cc_start: 0.8859 (mtp180) cc_final: 0.8540 (mtp85) REVERT: A 340 PHE cc_start: 0.7410 (m-80) cc_final: 0.7048 (m-10) REVERT: A 365 THR cc_start: 0.8873 (m) cc_final: 0.8543 (p) REVERT: A 375 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 423 GLN cc_start: 0.8288 (mt0) cc_final: 0.7948 (mt0) REVERT: D 5 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7671 (tmm-80) REVERT: D 32 MET cc_start: 0.7829 (mmm) cc_final: 0.7603 (mmm) REVERT: D 71 LYS cc_start: 0.7577 (mttt) cc_final: 0.7294 (mmtp) REVERT: D 92 LEU cc_start: 0.8129 (mt) cc_final: 0.7517 (pp) REVERT: E 18 ASN cc_start: 0.9203 (m110) cc_final: 0.8398 (t0) REVERT: E 21 TRP cc_start: 0.8776 (m100) cc_final: 0.8320 (m100) REVERT: E 24 TYR cc_start: 0.8553 (m-10) cc_final: 0.8181 (m-10) REVERT: E 27 GLU cc_start: 0.8651 (tt0) cc_final: 0.8417 (tt0) REVERT: E 59 GLU cc_start: 0.7589 (mt-10) cc_final: 0.5809 (pt0) REVERT: E 65 PHE cc_start: 0.7919 (p90) cc_final: 0.6021 (p90) REVERT: E 68 ARG cc_start: 0.8753 (mtt180) cc_final: 0.8543 (mtp85) REVERT: E 69 SER cc_start: 0.8959 (p) cc_final: 0.8718 (p) REVERT: E 94 GLU cc_start: 0.8478 (pp20) cc_final: 0.8229 (tm-30) REVERT: E 161 LEU cc_start: 0.8729 (pp) cc_final: 0.8509 (pp) REVERT: E 162 ASN cc_start: 0.9217 (t0) cc_final: 0.8781 (t0) REVERT: E 167 LYS cc_start: 0.8169 (pttp) cc_final: 0.7870 (ptmt) REVERT: E 201 ASN cc_start: 0.7961 (m-40) cc_final: 0.7749 (t0) REVERT: E 219 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6708 (ptm160) REVERT: E 255 ASP cc_start: 0.8278 (t70) cc_final: 0.7858 (m-30) REVERT: E 270 HIS cc_start: 0.8266 (p-80) cc_final: 0.7878 (p-80) REVERT: E 306 MET cc_start: 0.8172 (tpp) cc_final: 0.7970 (tpp) REVERT: E 333 GLN cc_start: 0.7300 (pp30) cc_final: 0.6990 (pp30) REVERT: E 381 MET cc_start: 0.8922 (ttt) cc_final: 0.8305 (ttp) REVERT: F 1 MET cc_start: 0.8096 (ptp) cc_final: 0.7108 (ptt) REVERT: F 21 TRP cc_start: 0.8426 (m100) cc_final: 0.7725 (m100) REVERT: F 24 TYR cc_start: 0.8805 (m-10) cc_final: 0.8174 (m-10) REVERT: F 30 ILE cc_start: 0.9329 (mt) cc_final: 0.8991 (mm) REVERT: F 59 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6465 (pt0) REVERT: F 77 ASN cc_start: 0.8979 (t0) cc_final: 0.8634 (t0) REVERT: F 80 ASP cc_start: 0.8436 (m-30) cc_final: 0.8102 (p0) REVERT: F 94 GLU cc_start: 0.8273 (pp20) cc_final: 0.7815 (tm-30) REVERT: F 102 ASP cc_start: 0.9165 (t70) cc_final: 0.8607 (t70) REVERT: F 131 ASP cc_start: 0.7942 (m-30) cc_final: 0.7644 (m-30) REVERT: F 158 LEU cc_start: 0.9124 (mp) cc_final: 0.8863 (mp) REVERT: F 201 ASN cc_start: 0.7856 (m-40) cc_final: 0.7288 (m-40) REVERT: F 247 ARG cc_start: 0.6611 (mmt90) cc_final: 0.5144 (mmt90) REVERT: F 270 HIS cc_start: 0.8472 (p-80) cc_final: 0.7823 (p-80) REVERT: F 306 MET cc_start: 0.8703 (mtp) cc_final: 0.8453 (mmm) REVERT: F 308 LYS cc_start: 0.8585 (tptp) cc_final: 0.8282 (mmtt) REVERT: F 320 CYS cc_start: 0.8703 (t) cc_final: 0.7935 (t) REVERT: F 361 TYR cc_start: 0.8319 (m-80) cc_final: 0.8107 (m-80) REVERT: F 379 VAL cc_start: 0.8700 (t) cc_final: 0.8469 (t) REVERT: F 426 ARG cc_start: 0.8702 (mmp-170) cc_final: 0.8040 (tpp80) REVERT: F 441 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8511 (tm-30) REVERT: G 23 LEU cc_start: 0.9172 (tp) cc_final: 0.8321 (tp) REVERT: G 27 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7434 (mt-10) REVERT: G 59 GLU cc_start: 0.6834 (mt-10) cc_final: 0.5699 (pt0) REVERT: G 209 ASP cc_start: 0.7802 (t0) cc_final: 0.7316 (t0) REVERT: G 257 ASN cc_start: 0.8388 (t0) cc_final: 0.7979 (p0) REVERT: G 308 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8071 (mmtt) REVERT: G 343 ARG cc_start: 0.8753 (ptm160) cc_final: 0.8085 (mtt180) REVERT: G 351 CYS cc_start: 0.8035 (t) cc_final: 0.7159 (p) REVERT: G 356 LYS cc_start: 0.8271 (tppt) cc_final: 0.7759 (tppt) REVERT: G 360 CYS cc_start: 0.9361 (t) cc_final: 0.8316 (p) REVERT: G 374 LYS cc_start: 0.9079 (tttm) cc_final: 0.8501 (tptp) REVERT: G 380 CYS cc_start: 0.9030 (t) cc_final: 0.8475 (p) REVERT: G 381 MET cc_start: 0.9012 (tmm) cc_final: 0.8369 (tmm) REVERT: G 402 MET cc_start: 0.9016 (mmm) cc_final: 0.8549 (mmt) REVERT: G 426 ARG cc_start: 0.8612 (mmm160) cc_final: 0.8253 (mmm160) REVERT: G 434 ARG cc_start: 0.9074 (mtt90) cc_final: 0.8865 (mtm-85) REVERT: G 441 GLN cc_start: 0.8732 (mm110) cc_final: 0.8332 (tm-30) REVERT: H 3 GLU cc_start: 0.6735 (mt-10) cc_final: 0.5759 (mt-10) REVERT: H 20 CYS cc_start: 0.8791 (m) cc_final: 0.8416 (m) REVERT: H 73 ASP cc_start: 0.8249 (t0) cc_final: 0.8018 (t0) REVERT: H 94 GLU cc_start: 0.8105 (tp30) cc_final: 0.7651 (tp30) REVERT: H 102 ASP cc_start: 0.8819 (t70) cc_final: 0.7585 (t0) REVERT: H 131 ASP cc_start: 0.8257 (m-30) cc_final: 0.7983 (m-30) REVERT: H 143 HIS cc_start: 0.8788 (p90) cc_final: 0.8032 (p90) REVERT: H 145 PHE cc_start: 0.8988 (m-80) cc_final: 0.8568 (m-80) REVERT: H 187 GLU cc_start: 0.8611 (tt0) cc_final: 0.8076 (tp30) REVERT: H 211 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8802 (mt-10) REVERT: H 237 GLN cc_start: 0.8604 (mt0) cc_final: 0.8058 (tt0) REVERT: H 276 TYR cc_start: 0.8282 (t80) cc_final: 0.7674 (t80) REVERT: H 304 ASN cc_start: 0.8977 (t0) cc_final: 0.8505 (t0) REVERT: H 344 THR cc_start: 0.9344 (t) cc_final: 0.9051 (t) REVERT: H 346 GLN cc_start: 0.8319 (mp10) cc_final: 0.7686 (mm-40) REVERT: H 374 LYS cc_start: 0.8996 (tttm) cc_final: 0.8576 (tmtt) REVERT: H 415 GLU cc_start: 0.6816 (pt0) cc_final: 0.6518 (pt0) REVERT: H 441 GLN cc_start: 0.8853 (mm110) cc_final: 0.8617 (tm-30) REVERT: J 6 HIS cc_start: 0.8969 (t70) cc_final: 0.8754 (t-170) REVERT: J 31 ASP cc_start: 0.8029 (p0) cc_final: 0.7655 (p0) REVERT: J 53 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7136 (tm-30) REVERT: J 65 LEU cc_start: 0.8835 (mp) cc_final: 0.8605 (mp) REVERT: J 101 TRP cc_start: 0.8896 (t60) cc_final: 0.8317 (t60) REVERT: J 111 GLU cc_start: 0.8239 (tt0) cc_final: 0.7936 (tp30) REVERT: J 157 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8207 (tm-30) REVERT: J 189 MET cc_start: 0.8843 (mmt) cc_final: 0.8461 (mmp) REVERT: J 191 GLN cc_start: 0.8741 (mp10) cc_final: 0.8358 (mp10) REVERT: J 198 GLU cc_start: 0.8551 (pm20) cc_final: 0.7894 (tp30) REVERT: J 215 LEU cc_start: 0.9249 (mp) cc_final: 0.9014 (mp) REVERT: J 216 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8720 (mmmt) REVERT: J 266 MET cc_start: 0.8874 (mtm) cc_final: 0.8560 (mtp) REVERT: J 324 GLU cc_start: 0.8363 (mp0) cc_final: 0.7881 (pm20) REVERT: J 405 MET cc_start: 0.8367 (tpp) cc_final: 0.7980 (tpp) REVERT: J 415 ASN cc_start: 0.8579 (m-40) cc_final: 0.8269 (t0) REVERT: B 6 HIS cc_start: 0.9086 (t70) cc_final: 0.8388 (t-170) REVERT: B 14 ASN cc_start: 0.9069 (m-40) cc_final: 0.8814 (m-40) REVERT: B 51 PHE cc_start: 0.9093 (m-80) cc_final: 0.8718 (m-80) REVERT: B 53 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7188 (tm-30) REVERT: B 83 ASN cc_start: 0.8436 (m-40) cc_final: 0.8037 (m110) REVERT: B 85 PHE cc_start: 0.7781 (m-80) cc_final: 0.7247 (m-80) REVERT: B 86 ARG cc_start: 0.7180 (ptp-170) cc_final: 0.6969 (ptp-170) REVERT: B 135 LEU cc_start: 0.9255 (mp) cc_final: 0.9008 (mp) REVERT: B 147 MET cc_start: 0.8186 (tmm) cc_final: 0.7368 (tmm) REVERT: B 151 LEU cc_start: 0.9686 (mt) cc_final: 0.9254 (mt) REVERT: B 164 MET cc_start: 0.7851 (mmp) cc_final: 0.6509 (mmp) REVERT: B 189 MET cc_start: 0.8833 (tpp) cc_final: 0.8510 (tpp) REVERT: B 198 GLU cc_start: 0.8752 (pm20) cc_final: 0.7519 (tp30) REVERT: B 223 ASP cc_start: 0.8872 (m-30) cc_final: 0.8200 (t70) REVERT: B 292 MET cc_start: 0.7844 (ppp) cc_final: 0.7538 (ppp) REVERT: B 395 HIS cc_start: 0.8920 (p-80) cc_final: 0.8477 (p-80) REVERT: C 6 HIS cc_start: 0.9076 (t70) cc_final: 0.8130 (t-170) REVERT: C 20 PHE cc_start: 0.8275 (t80) cc_final: 0.7475 (t80) REVERT: C 35 ILE cc_start: 0.8673 (mm) cc_final: 0.8465 (mp) REVERT: C 134 GLN cc_start: 0.8482 (mt0) cc_final: 0.7890 (mt0) REVERT: C 157 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8588 (tm-30) REVERT: C 163 MET cc_start: 0.5864 (ptp) cc_final: 0.5558 (ptm) REVERT: C 164 MET cc_start: 0.8212 (mmm) cc_final: 0.7674 (mmm) REVERT: C 297 ASN cc_start: 0.9204 (m-40) cc_final: 0.8980 (t0) REVERT: C 359 ASP cc_start: 0.9018 (m-30) cc_final: 0.8774 (m-30) REVERT: C 372 SER cc_start: 0.9292 (p) cc_final: 0.9040 (p) REVERT: C 375 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8237 (tm-30) REVERT: C 394 LEU cc_start: 0.8927 (tp) cc_final: 0.8583 (tt) REVERT: C 397 TYR cc_start: 0.8340 (m-80) cc_final: 0.8050 (m-10) REVERT: C 405 MET cc_start: 0.8622 (tpp) cc_final: 0.7775 (mmm) REVERT: C 408 THR cc_start: 0.8739 (p) cc_final: 0.8039 (p) outliers start: 1 outliers final: 0 residues processed: 1031 average time/residue: 0.3951 time to fit residues: 650.7664 Evaluate side-chains 844 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 844 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 326 optimal weight: 30.0000 chunk 191 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 HIS F 62 GLN G 8 HIS G 143 HIS ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN H 15 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 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 83 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 291 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN C 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.117842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102749 restraints weight = 60082.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106205 restraints weight = 34344.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108546 restraints weight = 21720.282| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.7219 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= 0.145 Angle : 0.693 10.490 39006 Z= 0.344 Chirality : 0.049 0.198 4200 Planarity : 0.005 0.069 5117 Dihedral : 8.958 160.991 3979 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.07 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3543 helix: -0.55 (0.13), residues: 1552 sheet: 0.25 (0.24), residues: 500 loop : -1.59 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 21 HIS 0.007 0.001 HIS G 8 PHE 0.034 0.002 PHE E 408 TYR 0.029 0.002 TYR H 24 ARG 0.015 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 951) hydrogen bonds : angle 4.92550 ( 2754) covalent geometry : bond 0.00332 (28752) covalent geometry : angle 0.69344 (39006) ********************** 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 990 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 988 time to evaluate : 3.059 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: A 20 PHE cc_start: 0.7982 (t80) cc_final: 0.7132 (t80) REVERT: A 21 TRP cc_start: 0.9185 (m100) cc_final: 0.8758 (m100) REVERT: A 53 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7106 (tm-30) REVERT: A 136 THR cc_start: 0.8650 (m) cc_final: 0.8375 (p) REVERT: A 157 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8300 (tm-30) REVERT: A 181 GLU cc_start: 0.9148 (pp20) cc_final: 0.8644 (pp20) REVERT: A 190 HIS cc_start: 0.8799 (t-90) cc_final: 0.8446 (t-90) REVERT: A 192 LEU cc_start: 0.9371 (mt) cc_final: 0.9072 (mt) REVERT: A 196 SER cc_start: 0.9471 (t) cc_final: 0.9231 (p) REVERT: A 198 GLU cc_start: 0.8568 (pm20) cc_final: 0.7676 (tp30) REVERT: A 202 ILE cc_start: 0.8999 (mm) cc_final: 0.8693 (mm) REVERT: A 218 LYS cc_start: 0.8886 (pptt) cc_final: 0.8683 (pptt) REVERT: A 265 PHE cc_start: 0.7872 (p90) cc_final: 0.7008 (p90) REVERT: A 293 PHE cc_start: 0.7288 (t80) cc_final: 0.6973 (t80) REVERT: A 297 ASN cc_start: 0.9168 (m-40) cc_final: 0.8839 (t0) REVERT: A 315 LEU cc_start: 0.9221 (mt) cc_final: 0.8957 (mt) REVERT: A 330 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8528 (mtp85) REVERT: A 340 PHE cc_start: 0.7404 (m-80) cc_final: 0.7067 (m-10) REVERT: A 365 THR cc_start: 0.8850 (m) cc_final: 0.8534 (p) REVERT: A 375 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 394 LEU cc_start: 0.8750 (tp) cc_final: 0.8549 (tp) REVERT: A 414 MET cc_start: 0.8338 (ttp) cc_final: 0.8002 (ptt) REVERT: A 423 GLN cc_start: 0.8194 (mt0) cc_final: 0.7873 (mt0) REVERT: D 5 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7675 (tmm-80) REVERT: D 32 MET cc_start: 0.7835 (mmm) cc_final: 0.7629 (mmm) REVERT: D 71 LYS cc_start: 0.7509 (mttt) cc_final: 0.7167 (mmtp) REVERT: D 92 LEU cc_start: 0.8074 (mt) cc_final: 0.7442 (pp) REVERT: E 18 ASN cc_start: 0.9198 (m110) cc_final: 0.8460 (t0) REVERT: E 21 TRP cc_start: 0.8742 (m100) cc_final: 0.8196 (m100) REVERT: E 24 TYR cc_start: 0.8532 (m-10) cc_final: 0.8183 (m-10) REVERT: E 27 GLU cc_start: 0.8610 (tt0) cc_final: 0.8357 (tt0) REVERT: E 59 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6128 (pt0) REVERT: E 65 PHE cc_start: 0.7886 (p90) cc_final: 0.5872 (p90) REVERT: E 69 SER cc_start: 0.8848 (p) cc_final: 0.8374 (p) REVERT: E 94 GLU cc_start: 0.8541 (pp20) cc_final: 0.8046 (tm-30) REVERT: E 162 ASN cc_start: 0.9252 (t0) cc_final: 0.8801 (t0) REVERT: E 167 LYS cc_start: 0.8151 (pttp) cc_final: 0.7870 (ptmt) REVERT: E 201 ASN cc_start: 0.7980 (m-40) cc_final: 0.7615 (t0) REVERT: E 219 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6808 (ttp-170) REVERT: E 237 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8719 (mm110) REVERT: E 243 THR cc_start: 0.8179 (p) cc_final: 0.7961 (p) REVERT: E 255 ASP cc_start: 0.8300 (t70) cc_final: 0.8018 (m-30) REVERT: E 270 HIS cc_start: 0.8178 (p-80) cc_final: 0.7806 (p-80) REVERT: E 308 LYS cc_start: 0.8497 (tptp) cc_final: 0.8125 (mtpp) REVERT: E 377 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7267 (mtm110) REVERT: E 381 MET cc_start: 0.8910 (ttt) cc_final: 0.8368 (ttp) REVERT: E 402 MET cc_start: 0.9183 (tpp) cc_final: 0.8880 (tpp) REVERT: F 21 TRP cc_start: 0.8433 (m100) cc_final: 0.7759 (m100) REVERT: F 24 TYR cc_start: 0.8790 (m-10) cc_final: 0.8230 (m-10) REVERT: F 30 ILE cc_start: 0.9312 (mt) cc_final: 0.8993 (mm) REVERT: F 59 GLU cc_start: 0.7776 (mt-10) cc_final: 0.6455 (pt0) REVERT: F 77 ASN cc_start: 0.9080 (t0) cc_final: 0.8647 (t0) REVERT: F 102 ASP cc_start: 0.9124 (t70) cc_final: 0.8628 (t70) REVERT: F 131 ASP cc_start: 0.8016 (m-30) cc_final: 0.7671 (m-30) REVERT: F 158 LEU cc_start: 0.9136 (mp) cc_final: 0.8878 (mp) REVERT: F 201 ASN cc_start: 0.7869 (m-40) cc_final: 0.7351 (m-40) REVERT: F 247 ARG cc_start: 0.6765 (mmt90) cc_final: 0.4739 (mmt90) REVERT: F 270 HIS cc_start: 0.8461 (p-80) cc_final: 0.7779 (p-80) REVERT: F 305 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8082 (mm-40) REVERT: F 308 LYS cc_start: 0.8595 (tptp) cc_final: 0.8292 (mmtt) REVERT: F 320 CYS cc_start: 0.8778 (t) cc_final: 0.8349 (t) REVERT: F 426 ARG cc_start: 0.8756 (mmp-170) cc_final: 0.8034 (tpp80) REVERT: F 441 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8509 (tm-30) REVERT: G 23 LEU cc_start: 0.9176 (tp) cc_final: 0.8474 (tt) REVERT: G 27 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7520 (mt-10) REVERT: G 59 GLU cc_start: 0.6782 (mt-10) cc_final: 0.5733 (pt0) REVERT: G 161 LEU cc_start: 0.9057 (pp) cc_final: 0.8841 (pp) REVERT: G 204 CYS cc_start: 0.8822 (p) cc_final: 0.8599 (p) REVERT: G 257 ASN cc_start: 0.8239 (t0) cc_final: 0.7772 (p0) REVERT: G 275 THR cc_start: 0.7811 (m) cc_final: 0.7179 (p) REVERT: G 343 ARG cc_start: 0.8783 (ptm160) cc_final: 0.8089 (mtt180) REVERT: G 351 CYS cc_start: 0.8125 (t) cc_final: 0.7159 (p) REVERT: G 356 LYS cc_start: 0.8345 (tppt) cc_final: 0.7774 (tppt) REVERT: G 374 LYS cc_start: 0.9191 (tttm) cc_final: 0.8583 (tptp) REVERT: G 380 CYS cc_start: 0.9055 (t) cc_final: 0.8378 (p) REVERT: G 381 MET cc_start: 0.9065 (tmm) cc_final: 0.8017 (tmm) REVERT: G 426 ARG cc_start: 0.8623 (mmm160) cc_final: 0.8140 (mmm160) REVERT: G 434 ARG cc_start: 0.9085 (mtt90) cc_final: 0.8822 (mtm-85) REVERT: G 441 GLN cc_start: 0.8775 (mm110) cc_final: 0.8272 (tm-30) REVERT: H 15 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: H 18 ASN cc_start: 0.8841 (m110) cc_final: 0.8573 (m110) REVERT: H 20 CYS cc_start: 0.8715 (m) cc_final: 0.8446 (m) REVERT: H 73 ASP cc_start: 0.8284 (t0) cc_final: 0.8017 (t0) REVERT: H 94 GLU cc_start: 0.8060 (tp30) cc_final: 0.7688 (tp30) REVERT: H 102 ASP cc_start: 0.8821 (t70) cc_final: 0.7584 (t0) REVERT: H 131 ASP cc_start: 0.8234 (m-30) cc_final: 0.7996 (m-30) REVERT: H 143 HIS cc_start: 0.8781 (p90) cc_final: 0.8127 (p90) REVERT: H 145 PHE cc_start: 0.8967 (m-80) cc_final: 0.8722 (m-80) REVERT: H 187 GLU cc_start: 0.8764 (tt0) cc_final: 0.8234 (tp30) REVERT: H 211 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8809 (mt-10) REVERT: H 276 TYR cc_start: 0.8409 (t80) cc_final: 0.7983 (t80) REVERT: H 304 ASN cc_start: 0.9037 (t0) cc_final: 0.8601 (t0) REVERT: H 344 THR cc_start: 0.9321 (t) cc_final: 0.9003 (t) REVERT: H 346 GLN cc_start: 0.8351 (mp10) cc_final: 0.7597 (mm-40) REVERT: H 374 LYS cc_start: 0.8912 (tttm) cc_final: 0.8596 (tmtt) REVERT: H 381 MET cc_start: 0.8657 (tmm) cc_final: 0.8212 (tmm) REVERT: J 6 HIS cc_start: 0.8937 (t70) cc_final: 0.8648 (t70) REVERT: J 21 TRP cc_start: 0.8952 (m100) cc_final: 0.8709 (m100) REVERT: J 31 ASP cc_start: 0.8009 (p0) cc_final: 0.7515 (p0) REVERT: J 53 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7282 (tm-30) REVERT: J 111 GLU cc_start: 0.8268 (tt0) cc_final: 0.8012 (tp30) REVERT: J 189 MET cc_start: 0.8862 (mmt) cc_final: 0.8450 (mmp) REVERT: J 191 GLN cc_start: 0.8764 (mp10) cc_final: 0.8284 (mp10) REVERT: J 198 GLU cc_start: 0.8433 (pm20) cc_final: 0.7883 (tp30) REVERT: J 215 LEU cc_start: 0.9259 (mp) cc_final: 0.9023 (mp) REVERT: J 216 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8718 (mmmt) REVERT: J 228 LEU cc_start: 0.9409 (tp) cc_final: 0.9174 (tp) REVERT: J 266 MET cc_start: 0.8818 (mtm) cc_final: 0.8609 (mtp) REVERT: J 324 GLU cc_start: 0.8342 (mp0) cc_final: 0.7741 (pm20) REVERT: J 405 MET cc_start: 0.8378 (tpp) cc_final: 0.7987 (tpp) REVERT: J 415 ASN cc_start: 0.8606 (m-40) cc_final: 0.8269 (t0) REVERT: B 6 HIS cc_start: 0.9041 (t70) cc_final: 0.8478 (t70) REVERT: B 14 ASN cc_start: 0.9126 (m-40) cc_final: 0.8855 (m-40) REVERT: B 51 PHE cc_start: 0.9130 (m-80) cc_final: 0.8867 (m-80) REVERT: B 53 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7120 (tm-30) REVERT: B 85 PHE cc_start: 0.7840 (m-80) cc_final: 0.7612 (m-80) REVERT: B 147 MET cc_start: 0.8089 (tmm) cc_final: 0.7273 (tmm) REVERT: B 151 LEU cc_start: 0.9713 (mt) cc_final: 0.9246 (mt) REVERT: B 164 MET cc_start: 0.7931 (mmp) cc_final: 0.6636 (mmp) REVERT: B 189 MET cc_start: 0.8780 (tpp) cc_final: 0.8462 (mpp) REVERT: B 198 GLU cc_start: 0.8784 (pm20) cc_final: 0.7526 (tp30) REVERT: B 215 LEU cc_start: 0.9115 (mm) cc_final: 0.8473 (mm) REVERT: B 223 ASP cc_start: 0.8933 (m-30) cc_final: 0.8150 (t70) REVERT: B 267 VAL cc_start: 0.8075 (t) cc_final: 0.7675 (t) REVERT: B 366 PHE cc_start: 0.8862 (t80) cc_final: 0.8531 (t80) REVERT: B 395 HIS cc_start: 0.8889 (p-80) cc_final: 0.8454 (p-80) REVERT: C 6 HIS cc_start: 0.9066 (t70) cc_final: 0.8143 (t-170) REVERT: C 20 PHE cc_start: 0.8271 (t80) cc_final: 0.7422 (t80) REVERT: C 134 GLN cc_start: 0.8507 (mt0) cc_final: 0.7958 (mt0) REVERT: C 157 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8571 (tm-30) REVERT: C 163 MET cc_start: 0.5766 (ptp) cc_final: 0.5481 (ptp) REVERT: C 164 MET cc_start: 0.8267 (mmm) cc_final: 0.7753 (mmm) REVERT: C 174 LYS cc_start: 0.8942 (mppt) cc_final: 0.8709 (mppt) REVERT: C 202 ILE cc_start: 0.8968 (mm) cc_final: 0.8714 (tp) REVERT: C 297 ASN cc_start: 0.9186 (m-40) cc_final: 0.8887 (t0) REVERT: C 372 SER cc_start: 0.9340 (p) cc_final: 0.9110 (p) REVERT: C 375 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8237 (tm-30) REVERT: C 394 LEU cc_start: 0.8947 (tp) cc_final: 0.8624 (tt) REVERT: C 405 MET cc_start: 0.7571 (tpp) cc_final: 0.7370 (tpp) REVERT: C 408 THR cc_start: 0.8945 (p) cc_final: 0.8642 (p) outliers start: 2 outliers final: 0 residues processed: 990 average time/residue: 0.4039 time to fit residues: 636.5001 Evaluate side-chains 826 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 825 time to evaluate : 6.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 200 optimal weight: 0.3980 chunk 99 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** 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 196 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 83 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 297 ASN C 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104414 restraints weight = 59855.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107943 restraints weight = 34154.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110319 restraints weight = 21602.317| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.7433 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= 0.127 Angle : 0.677 11.080 39006 Z= 0.335 Chirality : 0.048 0.175 4200 Planarity : 0.005 0.063 5117 Dihedral : 8.836 160.221 3979 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3543 helix: -0.44 (0.13), residues: 1526 sheet: 0.27 (0.24), residues: 488 loop : -1.43 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 21 HIS 0.011 0.001 HIS E 196 PHE 0.030 0.001 PHE E 408 TYR 0.028 0.001 TYR D 40 ARG 0.017 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 951) hydrogen bonds : angle 4.79727 ( 2754) covalent geometry : bond 0.00294 (28752) covalent geometry : angle 0.67674 (39006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12005.08 seconds wall clock time: 210 minutes 8.35 seconds (12608.35 seconds total)