Starting phenix.real_space_refine on Tue Feb 20 14:05:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/02_2024/5mjs_3522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/02_2024/5mjs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/02_2024/5mjs_3522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/02_2024/5mjs_3522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/02_2024/5mjs_3522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/02_2024/5mjs_3522.pdb" } 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 Residue "D ARG 82": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 312": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 312": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 14.93, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 11.60 Conformation dependent library (CDL) restraints added in 4.6 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: 2.65 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: 8.52 Time building geometry restraints manager: 12.46 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: 95.35 - 104.04: 498 104.04 - 112.74: 14742 112.74 - 121.43: 17119 121.43 - 130.12: 6463 130.12 - 138.81: 184 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 2.440 nonbonded pdb=" O GLU E 187 " pdb=" OG SER E 191 " model vdw 2.222 2.440 nonbonded pdb=" O GLU H 187 " pdb=" OG SER H 191 " model vdw 2.222 2.440 nonbonded pdb=" O GLU F 187 " pdb=" OG SER F 191 " model vdw 2.222 2.440 nonbonded pdb=" O GLU G 187 " pdb=" OG SER G 191 " model vdw 2.222 2.440 ... (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 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.240 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 69.620 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.210 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.150 ------------------------------------------------------------------------------- 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= 0.642 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 1450 time to evaluate : 3.009 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: 0.4141 time to fit residues: 925.7527 Evaluate side-chains 952 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 948 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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: 0.3980 chunk 266 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 131 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 281 GLN A 306 HIS ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 91 ASN D 96 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 210 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 201 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 201 ASN ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 HIS ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN ** H 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN J 195 ASN J 328 GLN J 415 ASN B 134 GLN ** 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 131 GLN C 134 GLN C 195 ASN ** 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3824 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= 0.205 Angle : 0.684 8.851 39006 Z= 0.355 Chirality : 0.048 0.186 4200 Planarity : 0.007 0.085 5117 Dihedral : 10.424 156.248 3979 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.47 % Allowed : 3.52 % Favored : 96.01 % 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: -3.23 (0.12), residues: 3543 helix: -2.37 (0.11), residues: 1446 sheet: -0.64 (0.23), residues: 484 loop : -2.31 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 411 HIS 0.008 0.001 HIS C 263 PHE 0.020 0.002 PHE A 242 TYR 0.018 0.002 TYR E 165 ARG 0.008 0.001 ARG G 315 *********************** 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 1227 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1213 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8779 (t-90) cc_final: 0.8112 (t-170) REVERT: A 14 ASN cc_start: 0.9215 (m-40) cc_final: 0.9002 (m-40) REVERT: A 73 MET cc_start: 0.8324 (mmp) cc_final: 0.8046 (mmp) REVERT: A 88 ASP cc_start: 0.8492 (m-30) cc_final: 0.8025 (p0) REVERT: A 89 ASN cc_start: 0.8767 (m-40) cc_final: 0.8208 (m110) REVERT: A 134 GLN cc_start: 0.7042 (mt0) cc_final: 0.6799 (mt0) REVERT: A 136 THR cc_start: 0.8727 (m) cc_final: 0.8486 (t) REVERT: A 162 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.7489 (mmt180) REVERT: A 164 MET cc_start: 0.8176 (mmp) cc_final: 0.6876 (mmp) REVERT: A 189 MET cc_start: 0.8612 (mmt) cc_final: 0.8407 (mmp) REVERT: A 202 ILE cc_start: 0.9017 (mm) cc_final: 0.8756 (mm) REVERT: A 213 ASN cc_start: 0.9025 (m-40) cc_final: 0.8483 (t0) REVERT: A 257 MET cc_start: 0.8147 (mmp) cc_final: 0.7895 (mmp) REVERT: A 280 PHE cc_start: 0.7539 (m-10) cc_final: 0.7338 (m-10) REVERT: A 330 ARG cc_start: 0.9253 (mtm180) cc_final: 0.8909 (mtp85) REVERT: A 339 TYR cc_start: 0.8375 (m-80) cc_final: 0.8103 (m-80) REVERT: A 340 PHE cc_start: 0.7545 (m-80) cc_final: 0.7222 (m-80) REVERT: A 372 SER cc_start: 0.9354 (p) cc_final: 0.9131 (m) REVERT: D 11 TRP cc_start: 0.4894 (t60) cc_final: 0.4663 (t60) REVERT: D 71 LYS cc_start: 0.8144 (mttt) cc_final: 0.7673 (mmtp) REVERT: E 15 GLN cc_start: 0.8982 (mt0) cc_final: 0.8461 (mp10) REVERT: E 21 TRP cc_start: 0.9027 (m100) cc_final: 0.8714 (m100) REVERT: E 59 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6651 (pt0) REVERT: E 64 LYS cc_start: 0.8601 (pttm) cc_final: 0.7661 (ptpp) REVERT: E 65 PHE cc_start: 0.7378 (p90) cc_final: 0.6301 (p90) REVERT: E 73 ASP cc_start: 0.7829 (t0) cc_final: 0.7472 (t0) REVERT: E 75 GLU cc_start: 0.8210 (tp30) cc_final: 0.7986 (tp30) REVERT: E 120 ASP cc_start: 0.8574 (m-30) cc_final: 0.8329 (m-30) REVERT: E 131 ASP cc_start: 0.8011 (m-30) cc_final: 0.7794 (m-30) REVERT: E 156 LEU cc_start: 0.9577 (tt) cc_final: 0.9225 (tp) REVERT: E 192 VAL cc_start: 0.8750 (p) cc_final: 0.8416 (m) REVERT: E 201 ASN cc_start: 0.8036 (m-40) cc_final: 0.7325 (m-40) REVERT: E 213 CYS cc_start: 0.8176 (t) cc_final: 0.7834 (t) REVERT: E 243 THR cc_start: 0.8627 (p) cc_final: 0.8382 (p) REVERT: E 255 ASP cc_start: 0.8805 (t70) cc_final: 0.7938 (m-30) REVERT: E 256 LEU cc_start: 0.9138 (mt) cc_final: 0.8183 (mt) REVERT: E 260 GLN cc_start: 0.8669 (pt0) cc_final: 0.8361 (pm20) REVERT: E 270 HIS cc_start: 0.8558 (p-80) cc_final: 0.8350 (p-80) REVERT: E 274 VAL cc_start: 0.9068 (t) cc_final: 0.8862 (p) REVERT: E 308 LYS cc_start: 0.8352 (tptp) cc_final: 0.7769 (mmtp) REVERT: E 361 TYR cc_start: 0.8092 (m-80) cc_final: 0.7798 (m-80) REVERT: E 381 MET cc_start: 0.8593 (ttt) cc_final: 0.8065 (tmm) REVERT: E 402 MET cc_start: 0.9229 (mmt) cc_final: 0.8458 (mmt) REVERT: E 415 GLU cc_start: 0.6658 (pt0) cc_final: 0.6412 (pt0) REVERT: E 439 VAL cc_start: 0.8204 (t) cc_final: 0.7497 (t) REVERT: F 18 ASN cc_start: 0.9013 (m110) cc_final: 0.8764 (m110) REVERT: F 21 TRP cc_start: 0.8712 (m100) cc_final: 0.7957 (m100) REVERT: F 24 TYR cc_start: 0.8833 (m-10) cc_final: 0.8155 (m-10) REVERT: F 30 ILE cc_start: 0.9302 (mt) cc_final: 0.8984 (mt) REVERT: F 59 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7230 (pt0) REVERT: F 65 PHE cc_start: 0.7567 (p90) cc_final: 0.6050 (p90) REVERT: F 81 GLN cc_start: 0.7893 (mt0) cc_final: 0.7532 (mt0) REVERT: F 94 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7235 (tp30) REVERT: F 101 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8305 (tm-30) REVERT: F 131 ASP cc_start: 0.7578 (m-30) cc_final: 0.7276 (m-30) REVERT: F 204 CYS cc_start: 0.8652 (t) cc_final: 0.8371 (t) REVERT: F 225 ARG cc_start: 0.7910 (ptp90) cc_final: 0.7256 (mtt-85) REVERT: F 231 LEU cc_start: 0.9480 (mp) cc_final: 0.9269 (mp) REVERT: F 243 THR cc_start: 0.8696 (p) cc_final: 0.8443 (p) REVERT: F 255 ASP cc_start: 0.8264 (t70) cc_final: 0.7990 (m-30) REVERT: F 256 LEU cc_start: 0.9442 (mt) cc_final: 0.8861 (mm) REVERT: F 270 HIS cc_start: 0.8890 (p-80) cc_final: 0.7912 (p-80) REVERT: F 276 TYR cc_start: 0.8684 (t80) cc_final: 0.8468 (t80) REVERT: F 304 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8340 (t0) REVERT: F 415 GLU cc_start: 0.6495 (pt0) cc_final: 0.5849 (pt0) REVERT: F 441 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7910 (tm-30) REVERT: G 59 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5393 (pt0) REVERT: G 65 PHE cc_start: 0.7245 (p90) cc_final: 0.6019 (p90) REVERT: G 73 ASP cc_start: 0.8527 (t0) cc_final: 0.8188 (t0) REVERT: G 97 VAL cc_start: 0.9497 (p) cc_final: 0.9265 (m) REVERT: G 133 CYS cc_start: 0.8451 (m) cc_final: 0.8176 (m) REVERT: G 237 GLN cc_start: 0.8816 (mt0) cc_final: 0.8523 (tt0) REVERT: G 259 PHE cc_start: 0.7610 (m-80) cc_final: 0.7137 (m-80) REVERT: G 270 HIS cc_start: 0.8655 (p-80) cc_final: 0.8307 (p-80) REVERT: G 306 MET cc_start: 0.8323 (mmt) cc_final: 0.8105 (mmm) REVERT: G 308 LYS cc_start: 0.8733 (tptp) cc_final: 0.8527 (tppt) REVERT: G 343 ARG cc_start: 0.8467 (ptm160) cc_final: 0.8058 (mtt180) REVERT: G 374 LYS cc_start: 0.8523 (tttm) cc_final: 0.8157 (tptp) REVERT: G 381 MET cc_start: 0.9127 (tmm) cc_final: 0.8595 (tmm) REVERT: G 382 LEU cc_start: 0.9379 (mt) cc_final: 0.9136 (mp) REVERT: G 424 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8305 (pt0) REVERT: G 441 GLN cc_start: 0.9078 (mm110) cc_final: 0.8411 (tm-30) REVERT: H 80 ASP cc_start: 0.8806 (m-30) cc_final: 0.8481 (p0) REVERT: H 94 GLU cc_start: 0.8034 (tt0) cc_final: 0.7558 (tp30) REVERT: H 131 ASP cc_start: 0.8336 (m-30) cc_final: 0.8111 (m-30) REVERT: H 137 GLN cc_start: 0.8606 (mt0) cc_final: 0.8053 (mm-40) REVERT: H 192 VAL cc_start: 0.9132 (p) cc_final: 0.8930 (m) REVERT: H 206 PHE cc_start: 0.8736 (m-80) cc_final: 0.8530 (m-80) REVERT: H 209 ASP cc_start: 0.8242 (t0) cc_final: 0.8004 (t0) REVERT: H 237 GLN cc_start: 0.8892 (mt0) cc_final: 0.8445 (mt0) REVERT: H 243 THR cc_start: 0.8484 (p) cc_final: 0.8196 (p) REVERT: H 247 ARG cc_start: 0.7230 (mmt90) cc_final: 0.5173 (mmt90) REVERT: H 268 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8347 (mmm-85) REVERT: H 270 HIS cc_start: 0.8842 (p-80) cc_final: 0.7833 (p-80) REVERT: H 304 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8398 (t0) REVERT: H 317 MET cc_start: 0.7101 (mmm) cc_final: 0.6661 (tpt) REVERT: H 343 ARG cc_start: 0.8149 (ptt180) cc_final: 0.7768 (mtt180) REVERT: H 374 LYS cc_start: 0.9005 (tttm) cc_final: 0.8523 (tmtt) REVERT: H 402 MET cc_start: 0.8313 (mmp) cc_final: 0.8107 (mmp) REVERT: H 424 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8249 (mt-10) REVERT: H 441 GLN cc_start: 0.8827 (mm110) cc_final: 0.7821 (tm-30) REVERT: J 6 HIS cc_start: 0.8687 (t-90) cc_final: 0.8266 (t-170) REVERT: J 14 ASN cc_start: 0.9109 (m-40) cc_final: 0.8430 (m-40) REVERT: J 21 TRP cc_start: 0.9160 (m100) cc_final: 0.8537 (m100) REVERT: J 51 PHE cc_start: 0.9011 (m-80) cc_final: 0.8733 (m-80) REVERT: J 53 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7647 (tm-30) REVERT: J 67 ASP cc_start: 0.8187 (t0) cc_final: 0.7616 (p0) REVERT: J 84 LEU cc_start: 0.9005 (mt) cc_final: 0.8694 (mt) REVERT: J 189 MET cc_start: 0.8569 (mmt) cc_final: 0.8246 (mmp) REVERT: J 204 ASN cc_start: 0.8593 (m-40) cc_final: 0.8363 (m-40) REVERT: J 322 MET cc_start: 0.8927 (mmm) cc_final: 0.8634 (mmm) REVERT: J 343 TRP cc_start: 0.8003 (m100) cc_final: 0.7723 (m100) REVERT: J 352 VAL cc_start: 0.8848 (t) cc_final: 0.7873 (t) REVERT: J 394 LEU cc_start: 0.8715 (tp) cc_final: 0.8420 (tt) REVERT: J 405 MET cc_start: 0.8321 (tpp) cc_final: 0.8116 (tpp) REVERT: J 406 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8383 (mt-10) REVERT: B 6 HIS cc_start: 0.8890 (t70) cc_final: 0.8586 (t-170) REVERT: B 14 ASN cc_start: 0.8397 (m-40) cc_final: 0.8111 (m-40) REVERT: B 20 PHE cc_start: 0.8414 (t80) cc_final: 0.8104 (t80) REVERT: B 83 ASN cc_start: 0.8434 (m-40) cc_final: 0.8213 (m110) REVERT: B 84 LEU cc_start: 0.8796 (mt) cc_final: 0.8310 (mt) REVERT: B 85 PHE cc_start: 0.7863 (m-80) cc_final: 0.7378 (m-10) REVERT: B 101 TRP cc_start: 0.8694 (t60) cc_final: 0.8456 (t60) REVERT: B 164 MET cc_start: 0.7772 (mmp) cc_final: 0.7020 (mmp) REVERT: B 181 GLU cc_start: 0.7543 (tt0) cc_final: 0.7155 (tt0) REVERT: B 192 LEU cc_start: 0.9115 (mt) cc_final: 0.8912 (mt) REVERT: B 221 SER cc_start: 0.8988 (t) cc_final: 0.8248 (p) REVERT: B 222 TYR cc_start: 0.8625 (m-10) cc_final: 0.8404 (m-80) REVERT: B 257 MET cc_start: 0.8183 (mmp) cc_final: 0.7875 (mmp) REVERT: B 358 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7796 (pttm) REVERT: B 372 SER cc_start: 0.8726 (p) cc_final: 0.8407 (m) REVERT: B 376 ILE cc_start: 0.8688 (mm) cc_final: 0.8462 (mm) REVERT: B 394 LEU cc_start: 0.8555 (tt) cc_final: 0.8250 (tt) REVERT: B 395 HIS cc_start: 0.8514 (p-80) cc_final: 0.8294 (p-80) REVERT: B 398 THR cc_start: 0.8204 (p) cc_final: 0.7951 (p) REVERT: B 414 MET cc_start: 0.7972 (ttt) cc_final: 0.7005 (tpp) REVERT: B 417 LEU cc_start: 0.9368 (mt) cc_final: 0.9073 (mt) REVERT: C 2 ARG cc_start: 0.6912 (mtp85) cc_final: 0.6664 (mtp85) REVERT: C 6 HIS cc_start: 0.8816 (t70) cc_final: 0.8249 (t70) REVERT: C 8 GLN cc_start: 0.7897 (mt0) cc_final: 0.7622 (mt0) REVERT: C 101 TRP cc_start: 0.8993 (t60) cc_final: 0.8252 (t60) REVERT: C 202 ILE cc_start: 0.9034 (mm) cc_final: 0.8757 (mm) REVERT: C 233 MET cc_start: 0.9271 (mtm) cc_final: 0.8959 (ttp) REVERT: C 253 LEU cc_start: 0.8984 (mm) cc_final: 0.8736 (mm) REVERT: C 272 LEU cc_start: 0.8381 (tp) cc_final: 0.8059 (tp) REVERT: C 339 TYR cc_start: 0.8373 (m-80) cc_final: 0.8132 (m-80) REVERT: C 352 VAL cc_start: 0.8803 (m) cc_final: 0.8251 (m) REVERT: C 359 ASP cc_start: 0.9050 (m-30) cc_final: 0.8837 (m-30) REVERT: C 360 LEU cc_start: 0.8926 (mm) cc_final: 0.8623 (mt) REVERT: C 372 SER cc_start: 0.9410 (p) cc_final: 0.8995 (m) REVERT: C 406 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 412 SER cc_start: 0.9226 (m) cc_final: 0.8850 (p) REVERT: C 414 MET cc_start: 0.8530 (ttt) cc_final: 0.8147 (tmm) outliers start: 14 outliers final: 1 residues processed: 1217 average time/residue: 0.4245 time to fit residues: 806.2512 Evaluate side-chains 935 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 932 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 266 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 320 optimal weight: 40.0000 chunk 345 optimal weight: 30.0000 chunk 285 optimal weight: 50.0000 chunk 317 optimal weight: 0.0980 chunk 109 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN A 281 GLN A 422 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** E 15 GLN ** 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 210 ASN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 GLN 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** C 297 ASN C 422 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4814 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= 0.214 Angle : 0.653 12.196 39006 Z= 0.334 Chirality : 0.048 0.217 4200 Planarity : 0.006 0.105 5117 Dihedral : 9.924 158.654 3979 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.20 % Allowed : 3.66 % Favored : 96.14 % 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: -2.42 (0.13), residues: 3543 helix: -1.44 (0.12), residues: 1474 sheet: -0.49 (0.23), residues: 520 loop : -2.09 (0.14), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 350 HIS 0.010 0.001 HIS C 263 PHE 0.048 0.002 PHE F 408 TYR 0.017 0.002 TYR H 107 ARG 0.006 0.001 ARG J 390 *********************** 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 1107 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1101 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8709 (t-90) cc_final: 0.8068 (t-170) REVERT: A 14 ASN cc_start: 0.9178 (m-40) cc_final: 0.8973 (m-40) REVERT: A 20 PHE cc_start: 0.8237 (t80) cc_final: 0.7637 (t80) REVERT: A 88 ASP cc_start: 0.8699 (m-30) cc_final: 0.8437 (p0) REVERT: A 89 ASN cc_start: 0.9036 (m-40) cc_final: 0.8370 (m-40) REVERT: A 136 THR cc_start: 0.8829 (m) cc_final: 0.8331 (t) REVERT: A 162 ARG cc_start: 0.8643 (mmt-90) cc_final: 0.7924 (mmt180) REVERT: A 164 MET cc_start: 0.8138 (mmp) cc_final: 0.7000 (mmp) REVERT: A 199 THR cc_start: 0.8546 (m) cc_final: 0.8340 (m) REVERT: A 213 ASN cc_start: 0.8926 (m-40) cc_final: 0.8654 (t0) REVERT: A 218 LYS cc_start: 0.8615 (tptp) cc_final: 0.8063 (pptt) REVERT: A 233 MET cc_start: 0.8992 (mtm) cc_final: 0.7844 (mtm) REVERT: A 257 MET cc_start: 0.8546 (mmp) cc_final: 0.8148 (mmp) REVERT: A 293 PHE cc_start: 0.6629 (t80) cc_final: 0.5879 (t80) REVERT: A 330 ARG cc_start: 0.9229 (mtm180) cc_final: 0.8811 (mtp85) REVERT: A 339 TYR cc_start: 0.8482 (m-80) cc_final: 0.8276 (m-80) REVERT: A 340 PHE cc_start: 0.7516 (m-80) cc_final: 0.7269 (m-80) REVERT: A 375 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 380 LEU cc_start: 0.9213 (mm) cc_final: 0.8945 (tt) REVERT: A 405 MET cc_start: 0.8294 (tpp) cc_final: 0.7908 (tpp) REVERT: A 408 THR cc_start: 0.8474 (p) cc_final: 0.8232 (p) REVERT: D 32 MET cc_start: 0.6401 (mmm) cc_final: 0.5834 (mmm) REVERT: D 41 GLN cc_start: 0.7315 (tp40) cc_final: 0.7086 (tp-100) REVERT: D 66 GLN cc_start: 0.8683 (mp10) cc_final: 0.8289 (mp10) REVERT: D 71 LYS cc_start: 0.8251 (mttt) cc_final: 0.7923 (mmtp) REVERT: E 1 MET cc_start: 0.7749 (mtm) cc_final: 0.7165 (mtm) REVERT: E 15 GLN cc_start: 0.9248 (mt0) cc_final: 0.8896 (mm-40) REVERT: E 18 ASN cc_start: 0.9313 (m110) cc_final: 0.9018 (m110) REVERT: E 21 TRP cc_start: 0.8947 (m100) cc_final: 0.8539 (m100) REVERT: E 59 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6389 (pt0) REVERT: E 65 PHE cc_start: 0.7482 (p90) cc_final: 0.5890 (p90) REVERT: E 94 GLU cc_start: 0.7921 (pp20) cc_final: 0.6919 (tm-30) REVERT: E 116 LYS cc_start: 0.8929 (tmmt) cc_final: 0.8490 (ttpt) REVERT: E 131 ASP cc_start: 0.8105 (m-30) cc_final: 0.7840 (m-30) REVERT: E 156 LEU cc_start: 0.9625 (tt) cc_final: 0.9418 (tp) REVERT: E 192 VAL cc_start: 0.8871 (p) cc_final: 0.8518 (m) REVERT: E 201 ASN cc_start: 0.7951 (m-40) cc_final: 0.7252 (m-40) REVERT: E 213 CYS cc_start: 0.8345 (t) cc_final: 0.8013 (t) REVERT: E 255 ASP cc_start: 0.8592 (t70) cc_final: 0.7971 (m-30) REVERT: E 260 GLN cc_start: 0.8751 (pt0) cc_final: 0.8263 (pt0) REVERT: E 270 HIS cc_start: 0.8648 (p-80) cc_final: 0.8353 (p-80) REVERT: E 377 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7868 (mtm110) REVERT: E 402 MET cc_start: 0.9180 (mmt) cc_final: 0.8496 (mmt) REVERT: E 415 GLU cc_start: 0.7281 (pt0) cc_final: 0.6801 (pt0) REVERT: E 441 GLN cc_start: 0.8150 (tm130) cc_final: 0.7900 (tm-30) REVERT: F 14 VAL cc_start: 0.9503 (t) cc_final: 0.9287 (t) REVERT: F 21 TRP cc_start: 0.8799 (m100) cc_final: 0.8052 (m100) REVERT: F 24 TYR cc_start: 0.8901 (m-10) cc_final: 0.8220 (m-10) REVERT: F 30 ILE cc_start: 0.9324 (mt) cc_final: 0.9096 (mm) REVERT: F 59 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7005 (pt0) REVERT: F 65 PHE cc_start: 0.7962 (p90) cc_final: 0.6433 (p90) REVERT: F 94 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7456 (tm-30) REVERT: F 131 ASP cc_start: 0.7800 (m-30) cc_final: 0.7553 (m-30) REVERT: F 225 ARG cc_start: 0.7978 (ptp90) cc_final: 0.7281 (mtt-85) REVERT: F 237 GLN cc_start: 0.8748 (mt0) cc_final: 0.7978 (tt0) REVERT: F 255 ASP cc_start: 0.8539 (t70) cc_final: 0.8183 (m-30) REVERT: F 270 HIS cc_start: 0.8866 (p-80) cc_final: 0.7969 (p-80) REVERT: F 305 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8322 (mm110) REVERT: F 351 CYS cc_start: 0.8697 (t) cc_final: 0.6836 (p) REVERT: F 415 GLU cc_start: 0.6353 (pt0) cc_final: 0.6055 (pt0) REVERT: G 18 ASN cc_start: 0.9293 (m110) cc_final: 0.9086 (m110) REVERT: G 59 GLU cc_start: 0.6584 (mt-10) cc_final: 0.5726 (pt0) REVERT: G 73 ASP cc_start: 0.8582 (t0) cc_final: 0.8309 (t0) REVERT: G 94 GLU cc_start: 0.8299 (tt0) cc_final: 0.7609 (tp30) REVERT: G 189 TYR cc_start: 0.8148 (m-10) cc_final: 0.7511 (m-10) REVERT: G 206 PHE cc_start: 0.9239 (m-80) cc_final: 0.8868 (m-80) REVERT: G 215 ASP cc_start: 0.8059 (m-30) cc_final: 0.7759 (m-30) REVERT: G 260 GLN cc_start: 0.6868 (pm20) cc_final: 0.6655 (pm20) REVERT: G 270 HIS cc_start: 0.8831 (p-80) cc_final: 0.8381 (p-80) REVERT: G 308 LYS cc_start: 0.8646 (tptp) cc_final: 0.8290 (tptt) REVERT: G 343 ARG cc_start: 0.8653 (ptm160) cc_final: 0.8208 (mtt180) REVERT: G 374 LYS cc_start: 0.8682 (tttm) cc_final: 0.8296 (tmtt) REVERT: G 381 MET cc_start: 0.9197 (tmm) cc_final: 0.8650 (tmm) REVERT: G 399 PHE cc_start: 0.8546 (t80) cc_final: 0.8045 (t80) REVERT: G 402 MET cc_start: 0.8844 (mmm) cc_final: 0.8046 (mmm) REVERT: G 424 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8360 (pt0) REVERT: G 434 ARG cc_start: 0.9128 (mpt-90) cc_final: 0.8807 (mtt90) REVERT: G 441 GLN cc_start: 0.8805 (mm110) cc_final: 0.8413 (tm-30) REVERT: H 73 ASP cc_start: 0.8330 (t0) cc_final: 0.7947 (t0) REVERT: H 94 GLU cc_start: 0.8137 (tt0) cc_final: 0.7843 (tp30) REVERT: H 137 GLN cc_start: 0.8644 (mt0) cc_final: 0.7907 (mm-40) REVERT: H 143 HIS cc_start: 0.8849 (p90) cc_final: 0.8415 (p90) REVERT: H 167 LYS cc_start: 0.7606 (mmtp) cc_final: 0.7128 (mmtp) REVERT: H 247 ARG cc_start: 0.7303 (mmt90) cc_final: 0.5720 (mmt90) REVERT: H 270 HIS cc_start: 0.8594 (p-80) cc_final: 0.8133 (p-80) REVERT: H 304 ASN cc_start: 0.8718 (t0) cc_final: 0.8452 (t0) REVERT: H 305 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8672 (mm-40) REVERT: H 306 MET cc_start: 0.8655 (mmm) cc_final: 0.8390 (mmm) REVERT: H 308 LYS cc_start: 0.8593 (tptp) cc_final: 0.8173 (mmmt) REVERT: H 343 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7873 (mtt180) REVERT: H 351 CYS cc_start: 0.8371 (t) cc_final: 0.7217 (p) REVERT: H 374 LYS cc_start: 0.8954 (tttm) cc_final: 0.8645 (tmtt) REVERT: H 424 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8305 (pt0) REVERT: H 441 GLN cc_start: 0.8681 (mm110) cc_final: 0.7980 (tm-30) REVERT: J 6 HIS cc_start: 0.8848 (t-90) cc_final: 0.8322 (t-170) REVERT: J 14 ASN cc_start: 0.9226 (m-40) cc_final: 0.8761 (m-40) REVERT: J 21 TRP cc_start: 0.9034 (m100) cc_final: 0.8563 (m100) REVERT: J 51 PHE cc_start: 0.8956 (m-80) cc_final: 0.8754 (m-80) REVERT: J 53 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7603 (tm-30) REVERT: J 67 ASP cc_start: 0.8076 (t0) cc_final: 0.7859 (p0) REVERT: J 84 LEU cc_start: 0.9062 (mt) cc_final: 0.8442 (mt) REVERT: J 92 TYR cc_start: 0.8328 (p90) cc_final: 0.7847 (p90) REVERT: J 101 TRP cc_start: 0.8784 (t60) cc_final: 0.8431 (t60) REVERT: J 174 LYS cc_start: 0.9097 (mppt) cc_final: 0.8530 (mttp) REVERT: J 189 MET cc_start: 0.8655 (mmt) cc_final: 0.8299 (mmp) REVERT: J 198 GLU cc_start: 0.8921 (pm20) cc_final: 0.8707 (pm20) REVERT: J 257 MET cc_start: 0.8673 (mmp) cc_final: 0.8433 (mmp) REVERT: J 297 ASN cc_start: 0.8705 (t0) cc_final: 0.8149 (t0) REVERT: J 322 MET cc_start: 0.9126 (mmm) cc_final: 0.8840 (mmm) REVERT: J 365 THR cc_start: 0.8545 (m) cc_final: 0.8160 (p) REVERT: J 405 MET cc_start: 0.8475 (tpp) cc_final: 0.7926 (tpp) REVERT: J 412 SER cc_start: 0.9144 (m) cc_final: 0.8923 (p) REVERT: B 14 ASN cc_start: 0.8831 (m-40) cc_final: 0.8278 (m-40) REVERT: B 20 PHE cc_start: 0.8255 (t80) cc_final: 0.7774 (t80) REVERT: B 31 ASP cc_start: 0.7727 (p0) cc_final: 0.7268 (p0) REVERT: B 83 ASN cc_start: 0.8615 (m-40) cc_final: 0.8350 (m110) REVERT: B 85 PHE cc_start: 0.7965 (m-80) cc_final: 0.7503 (m-80) REVERT: B 103 LYS cc_start: 0.8613 (tttp) cc_final: 0.8299 (tttp) REVERT: B 151 LEU cc_start: 0.9539 (mt) cc_final: 0.9323 (mt) REVERT: B 152 LEU cc_start: 0.9300 (tp) cc_final: 0.9089 (tt) REVERT: B 164 MET cc_start: 0.7530 (mmp) cc_final: 0.6948 (mmp) REVERT: B 181 GLU cc_start: 0.7728 (tt0) cc_final: 0.7266 (tt0) REVERT: B 189 MET cc_start: 0.8623 (tpt) cc_final: 0.8235 (tpt) REVERT: B 193 VAL cc_start: 0.8606 (t) cc_final: 0.7019 (t) REVERT: B 222 TYR cc_start: 0.8721 (m-10) cc_final: 0.8511 (m-80) REVERT: B 247 ASN cc_start: 0.4684 (m110) cc_final: 0.4234 (m110) REVERT: B 395 HIS cc_start: 0.8846 (p-80) cc_final: 0.8260 (p-80) REVERT: B 412 SER cc_start: 0.9435 (m) cc_final: 0.9224 (p) REVERT: B 414 MET cc_start: 0.8096 (ttt) cc_final: 0.7397 (tpp) REVERT: C 6 HIS cc_start: 0.8988 (t70) cc_final: 0.7556 (t-170) REVERT: C 8 GLN cc_start: 0.8188 (mt0) cc_final: 0.7820 (mt0) REVERT: C 14 ASN cc_start: 0.9104 (m110) cc_final: 0.8795 (m-40) REVERT: C 53 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6751 (tm-30) REVERT: C 65 LEU cc_start: 0.8400 (mp) cc_final: 0.7987 (mp) REVERT: C 101 TRP cc_start: 0.8897 (t60) cc_final: 0.8047 (t60) REVERT: C 130 LEU cc_start: 0.9574 (tp) cc_final: 0.9285 (tt) REVERT: C 147 MET cc_start: 0.8503 (ppp) cc_final: 0.8232 (ppp) REVERT: C 191 GLN cc_start: 0.8669 (mm110) cc_final: 0.8403 (mm110) REVERT: C 225 LEU cc_start: 0.9138 (mp) cc_final: 0.8738 (mp) REVERT: C 233 MET cc_start: 0.9350 (mtm) cc_final: 0.9057 (ttp) REVERT: C 252 LYS cc_start: 0.9087 (mmtp) cc_final: 0.8482 (mmtp) REVERT: C 256 ASN cc_start: 0.9008 (m-40) cc_final: 0.8371 (p0) REVERT: C 339 TYR cc_start: 0.8480 (m-80) cc_final: 0.8259 (m-80) REVERT: C 352 VAL cc_start: 0.8578 (m) cc_final: 0.8246 (m) REVERT: C 359 ASP cc_start: 0.9059 (m-30) cc_final: 0.8813 (m-30) REVERT: C 405 MET cc_start: 0.8378 (tpp) cc_final: 0.8018 (tpp) outliers start: 6 outliers final: 1 residues processed: 1103 average time/residue: 0.3944 time to fit residues: 683.0882 Evaluate side-chains 906 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 905 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 20.0000 chunk 240 optimal weight: 40.0000 chunk 166 optimal weight: 20.0000 chunk 35 optimal weight: 0.0980 chunk 152 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 340 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 overall best weight: 8.4190 ------------------------------------------------------------------------------- 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 134 GLN A 204 ASN A 226 ASN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 297 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 15 GLN ** 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 237 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS J 14 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 422 GLN C 37 HIS ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28752 Z= 0.287 Angle : 0.711 10.096 39006 Z= 0.364 Chirality : 0.050 0.272 4200 Planarity : 0.006 0.068 5117 Dihedral : 9.918 158.073 3979 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.10 % Allowed : 3.12 % Favored : 96.78 % 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: -1.94 (0.14), residues: 3543 helix: -1.07 (0.13), residues: 1485 sheet: -0.19 (0.23), residues: 504 loop : -1.80 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 396 HIS 0.006 0.001 HIS B 263 PHE 0.025 0.002 PHE G 65 TYR 0.035 0.002 TYR J 222 ARG 0.016 0.001 ARG H 426 *********************** 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 1041 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1038 time to evaluate : 3.073 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: 0.8979 (t-90) cc_final: 0.7821 (t-170) REVERT: A 53 GLU cc_start: 0.8107 (mt-10) cc_final: 0.6730 (tm-30) REVERT: A 88 ASP cc_start: 0.8675 (m-30) cc_final: 0.8420 (p0) REVERT: A 136 THR cc_start: 0.8858 (m) cc_final: 0.8404 (t) REVERT: A 147 MET cc_start: 0.8466 (ppp) cc_final: 0.7887 (ppp) REVERT: A 157 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 196 SER cc_start: 0.9442 (t) cc_final: 0.9153 (p) REVERT: A 197 ASP cc_start: 0.8412 (t70) cc_final: 0.8147 (t0) REVERT: A 218 LYS cc_start: 0.8657 (tptp) cc_final: 0.8300 (pptt) REVERT: A 233 MET cc_start: 0.9096 (mtm) cc_final: 0.8783 (ttp) REVERT: A 252 LYS cc_start: 0.9081 (mptt) cc_final: 0.8864 (mptt) REVERT: A 257 MET cc_start: 0.8518 (mmp) cc_final: 0.8119 (mmp) REVERT: A 293 PHE cc_start: 0.6742 (t80) cc_final: 0.6352 (t80) REVERT: A 294 ASP cc_start: 0.9313 (t0) cc_final: 0.9111 (t70) REVERT: A 297 ASN cc_start: 0.9370 (m-40) cc_final: 0.8722 (t0) REVERT: A 365 THR cc_start: 0.8884 (m) cc_final: 0.8636 (p) REVERT: A 412 SER cc_start: 0.9057 (m) cc_final: 0.8818 (p) REVERT: D 5 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.6695 (ttp80) REVERT: D 11 TRP cc_start: 0.5509 (t60) cc_final: 0.5147 (t60) REVERT: D 32 MET cc_start: 0.6799 (mmm) cc_final: 0.6515 (mmm) REVERT: D 65 LEU cc_start: 0.8799 (mm) cc_final: 0.8566 (mm) REVERT: D 71 LYS cc_start: 0.8359 (mttt) cc_final: 0.7950 (mmtp) REVERT: E 24 TYR cc_start: 0.8833 (m-10) cc_final: 0.8407 (m-10) REVERT: E 59 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6397 (pt0) REVERT: E 65 PHE cc_start: 0.8022 (p90) cc_final: 0.6095 (p90) REVERT: E 94 GLU cc_start: 0.8184 (pp20) cc_final: 0.7196 (tm-30) REVERT: E 131 ASP cc_start: 0.8070 (m-30) cc_final: 0.7760 (m-30) REVERT: E 156 LEU cc_start: 0.9656 (tt) cc_final: 0.9310 (tp) REVERT: E 184 SER cc_start: 0.7585 (p) cc_final: 0.7291 (m) REVERT: E 186 VAL cc_start: 0.9445 (m) cc_final: 0.9156 (p) REVERT: E 192 VAL cc_start: 0.9178 (p) cc_final: 0.8737 (m) REVERT: E 201 ASN cc_start: 0.8225 (m-40) cc_final: 0.7622 (m-40) REVERT: E 255 ASP cc_start: 0.8471 (t70) cc_final: 0.7884 (m-30) REVERT: E 260 GLN cc_start: 0.8895 (pt0) cc_final: 0.8305 (pt0) REVERT: E 270 HIS cc_start: 0.8699 (p-80) cc_final: 0.8205 (p-80) REVERT: E 273 LEU cc_start: 0.8420 (tp) cc_final: 0.8111 (tp) REVERT: E 308 LYS cc_start: 0.8312 (tptp) cc_final: 0.7514 (mtpp) REVERT: E 350 TRP cc_start: 0.7066 (m-10) cc_final: 0.6821 (m-10) REVERT: E 381 MET cc_start: 0.8781 (tmm) cc_final: 0.7811 (tmm) REVERT: E 396 ASP cc_start: 0.9602 (t0) cc_final: 0.9360 (t0) REVERT: E 402 MET cc_start: 0.9182 (mmt) cc_final: 0.8765 (mmt) REVERT: F 21 TRP cc_start: 0.8869 (m100) cc_final: 0.8275 (m100) REVERT: F 24 TYR cc_start: 0.8925 (m-10) cc_final: 0.8286 (m-10) REVERT: F 59 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7266 (pt0) REVERT: F 131 ASP cc_start: 0.7948 (m-30) cc_final: 0.7673 (m-30) REVERT: F 215 ASP cc_start: 0.7638 (m-30) cc_final: 0.7352 (m-30) REVERT: F 247 ARG cc_start: 0.7234 (mmt90) cc_final: 0.4644 (mmt90) REVERT: F 255 ASP cc_start: 0.8578 (t70) cc_final: 0.8178 (m-30) REVERT: F 260 GLN cc_start: 0.8512 (pm20) cc_final: 0.8158 (pm20) REVERT: F 270 HIS cc_start: 0.8900 (p-80) cc_final: 0.8045 (p-80) REVERT: F 276 TYR cc_start: 0.8711 (t80) cc_final: 0.8122 (t80) REVERT: F 317 MET cc_start: 0.6347 (tpt) cc_final: 0.5849 (tpt) REVERT: F 356 LYS cc_start: 0.8791 (tptt) cc_final: 0.8172 (tppt) REVERT: G 3 GLU cc_start: 0.7045 (mt-10) cc_final: 0.5676 (mt-10) REVERT: G 23 LEU cc_start: 0.9204 (tp) cc_final: 0.8611 (tt) REVERT: G 27 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7636 (mt-10) REVERT: G 59 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5333 (pt0) REVERT: G 65 PHE cc_start: 0.7721 (p90) cc_final: 0.6630 (p90) REVERT: G 74 LEU cc_start: 0.8634 (mt) cc_final: 0.8423 (mp) REVERT: G 94 GLU cc_start: 0.8449 (tt0) cc_final: 0.8027 (tm-30) REVERT: G 124 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8386 (tt0) REVERT: G 125 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7607 (mtt90) REVERT: G 143 HIS cc_start: 0.8706 (p90) cc_final: 0.8490 (p90) REVERT: G 149 THR cc_start: 0.8875 (m) cc_final: 0.8558 (m) REVERT: G 204 CYS cc_start: 0.9405 (p) cc_final: 0.9154 (p) REVERT: G 206 PHE cc_start: 0.9342 (m-80) cc_final: 0.8578 (m-80) REVERT: G 308 LYS cc_start: 0.8532 (tptp) cc_final: 0.8265 (tppt) REVERT: G 326 ASP cc_start: 0.7905 (p0) cc_final: 0.7581 (p0) REVERT: G 343 ARG cc_start: 0.8677 (ptm160) cc_final: 0.8226 (mtt180) REVERT: G 374 LYS cc_start: 0.8983 (tttm) cc_final: 0.8298 (tmtt) REVERT: G 380 CYS cc_start: 0.8718 (t) cc_final: 0.8435 (p) REVERT: G 381 MET cc_start: 0.9204 (tmm) cc_final: 0.8493 (tmm) REVERT: G 434 ARG cc_start: 0.9084 (mpt-90) cc_final: 0.8772 (mtt90) REVERT: G 441 GLN cc_start: 0.8861 (mm110) cc_final: 0.8463 (tm-30) REVERT: H 15 GLN cc_start: 0.8550 (mt0) cc_final: 0.8319 (mt0) REVERT: H 20 CYS cc_start: 0.8703 (m) cc_final: 0.8453 (m) REVERT: H 27 GLU cc_start: 0.8510 (tt0) cc_final: 0.8300 (tt0) REVERT: H 73 ASP cc_start: 0.8365 (t0) cc_final: 0.7928 (t0) REVERT: H 80 ASP cc_start: 0.8309 (m-30) cc_final: 0.7956 (p0) REVERT: H 94 GLU cc_start: 0.8185 (tt0) cc_final: 0.7727 (tp30) REVERT: H 100 LYS cc_start: 0.8629 (mttm) cc_final: 0.8410 (mmtm) REVERT: H 116 LYS cc_start: 0.8589 (ptmt) cc_final: 0.8382 (ptmt) REVERT: H 131 ASP cc_start: 0.8419 (m-30) cc_final: 0.8211 (m-30) REVERT: H 137 GLN cc_start: 0.8819 (mt0) cc_final: 0.8187 (mm-40) REVERT: H 143 HIS cc_start: 0.8737 (p90) cc_final: 0.8171 (p90) REVERT: H 237 GLN cc_start: 0.8576 (mt0) cc_final: 0.7653 (tt0) REVERT: H 270 HIS cc_start: 0.8818 (p-80) cc_final: 0.8452 (p-80) REVERT: H 276 TYR cc_start: 0.8176 (t80) cc_final: 0.6894 (t80) REVERT: H 287 HIS cc_start: 0.7699 (m170) cc_final: 0.7388 (m170) REVERT: H 306 MET cc_start: 0.8301 (mmm) cc_final: 0.8089 (mmm) REVERT: H 343 ARG cc_start: 0.8566 (ptt180) cc_final: 0.8077 (mtt180) REVERT: H 351 CYS cc_start: 0.8063 (t) cc_final: 0.6700 (p) REVERT: H 374 LYS cc_start: 0.8940 (tttm) cc_final: 0.8511 (tmtt) REVERT: H 381 MET cc_start: 0.8908 (tmm) cc_final: 0.8481 (tmm) REVERT: H 415 GLU cc_start: 0.6732 (pt0) cc_final: 0.6407 (pt0) REVERT: H 441 GLN cc_start: 0.8739 (mm110) cc_final: 0.8156 (tm-30) REVERT: J 1 MET cc_start: 0.8494 (tpt) cc_final: 0.8082 (tpp) REVERT: J 14 ASN cc_start: 0.9123 (m110) cc_final: 0.8728 (m-40) REVERT: J 51 PHE cc_start: 0.8941 (m-80) cc_final: 0.8659 (m-80) REVERT: J 53 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7580 (tm-30) REVERT: J 83 ASN cc_start: 0.8953 (m-40) cc_final: 0.8751 (m110) REVERT: J 84 LEU cc_start: 0.9048 (mt) cc_final: 0.8704 (mt) REVERT: J 136 THR cc_start: 0.9066 (m) cc_final: 0.8732 (t) REVERT: J 196 SER cc_start: 0.9431 (t) cc_final: 0.9056 (p) REVERT: J 197 ASP cc_start: 0.7705 (t0) cc_final: 0.7473 (t0) REVERT: J 198 GLU cc_start: 0.9021 (pm20) cc_final: 0.8157 (pm20) REVERT: J 216 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8709 (mmmt) REVERT: J 297 ASN cc_start: 0.8883 (t0) cc_final: 0.8448 (t0) REVERT: J 322 MET cc_start: 0.9183 (mmm) cc_final: 0.8961 (mmm) REVERT: J 365 THR cc_start: 0.8666 (m) cc_final: 0.8386 (p) REVERT: J 403 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7206 (t0) REVERT: J 405 MET cc_start: 0.8581 (tpp) cc_final: 0.7234 (tpp) REVERT: J 406 GLU cc_start: 0.8923 (pt0) cc_final: 0.8251 (tm-30) REVERT: J 408 THR cc_start: 0.9079 (p) cc_final: 0.8743 (p) REVERT: J 409 GLU cc_start: 0.8946 (pt0) cc_final: 0.8624 (pt0) REVERT: B 14 ASN cc_start: 0.8993 (m-40) cc_final: 0.8686 (m-40) REVERT: B 20 PHE cc_start: 0.8291 (t80) cc_final: 0.7828 (t80) REVERT: B 21 TRP cc_start: 0.9320 (m100) cc_final: 0.9049 (m100) REVERT: B 53 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7244 (tm-30) REVERT: B 85 PHE cc_start: 0.8052 (m-80) cc_final: 0.7619 (m-80) REVERT: B 152 LEU cc_start: 0.9272 (tp) cc_final: 0.9064 (tt) REVERT: B 164 MET cc_start: 0.7848 (mmp) cc_final: 0.7370 (mmp) REVERT: B 174 LYS cc_start: 0.8858 (mppt) cc_final: 0.8585 (mppt) REVERT: B 181 GLU cc_start: 0.7844 (tt0) cc_final: 0.7410 (tt0) REVERT: B 256 ASN cc_start: 0.9179 (m-40) cc_final: 0.8948 (m-40) REVERT: B 395 HIS cc_start: 0.8871 (p-80) cc_final: 0.8407 (p-80) REVERT: B 412 SER cc_start: 0.9423 (m) cc_final: 0.9210 (p) REVERT: B 414 MET cc_start: 0.8192 (ttt) cc_final: 0.7576 (tpp) REVERT: C 6 HIS cc_start: 0.9007 (t70) cc_final: 0.7711 (t-170) REVERT: C 8 GLN cc_start: 0.8423 (mt0) cc_final: 0.8101 (mt0) REVERT: C 14 ASN cc_start: 0.9102 (m110) cc_final: 0.8708 (m-40) REVERT: C 53 GLU cc_start: 0.7794 (mt-10) cc_final: 0.6887 (tm-30) REVERT: C 101 TRP cc_start: 0.8922 (t60) cc_final: 0.8108 (t60) REVERT: C 164 MET cc_start: 0.7788 (mmm) cc_final: 0.7244 (mmm) REVERT: C 224 ASP cc_start: 0.9104 (m-30) cc_final: 0.8870 (m-30) REVERT: C 233 MET cc_start: 0.9288 (mtm) cc_final: 0.9037 (ttp) REVERT: C 359 ASP cc_start: 0.9146 (m-30) cc_final: 0.8930 (m-30) REVERT: C 405 MET cc_start: 0.8277 (tpp) cc_final: 0.7848 (tpp) REVERT: C 408 THR cc_start: 0.8731 (p) cc_final: 0.8494 (p) outliers start: 3 outliers final: 0 residues processed: 1040 average time/residue: 0.3806 time to fit residues: 632.5498 Evaluate side-chains 838 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 837 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 253 optimal weight: 40.0000 chunk 140 optimal weight: 20.0000 chunk 290 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 173 optimal weight: 0.0020 chunk 305 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 overall best weight: 4.7594 ------------------------------------------------------------------------------- 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 226 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 91 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 132 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN G 18 ASN G 162 ASN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS J 99 ASN B 263 HIS ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28752 Z= 0.204 Angle : 0.634 11.054 39006 Z= 0.319 Chirality : 0.047 0.170 4200 Planarity : 0.005 0.066 5117 Dihedral : 9.565 160.027 3979 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.68 (0.14), residues: 3543 helix: -0.71 (0.13), residues: 1523 sheet: -0.13 (0.23), residues: 512 loop : -1.81 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 396 HIS 0.007 0.001 HIS A 395 PHE 0.029 0.002 PHE E 65 TYR 0.016 0.001 TYR F 436 ARG 0.008 0.001 ARG E 247 *********************** 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 1019 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1017 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: A 6 HIS cc_start: 0.8972 (t-90) cc_final: 0.8035 (t-170) REVERT: A 20 PHE cc_start: 0.8169 (t80) cc_final: 0.7735 (t80) REVERT: A 35 ILE cc_start: 0.8583 (mp) cc_final: 0.8083 (mm) REVERT: A 53 GLU cc_start: 0.8094 (mt-10) cc_final: 0.6728 (tm-30) REVERT: A 67 ASP cc_start: 0.8322 (t0) cc_final: 0.8078 (t70) REVERT: A 73 MET cc_start: 0.7939 (mmp) cc_final: 0.7624 (mmm) REVERT: A 136 THR cc_start: 0.8943 (m) cc_final: 0.8633 (p) REVERT: A 139 LEU cc_start: 0.8471 (mt) cc_final: 0.8143 (mt) REVERT: A 147 MET cc_start: 0.8388 (ppp) cc_final: 0.7790 (ppp) REVERT: A 157 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 196 SER cc_start: 0.9405 (t) cc_final: 0.9134 (p) REVERT: A 197 ASP cc_start: 0.8618 (t70) cc_final: 0.8366 (t0) REVERT: A 199 THR cc_start: 0.8090 (m) cc_final: 0.7848 (m) REVERT: A 218 LYS cc_start: 0.8564 (tptp) cc_final: 0.8254 (pptt) REVERT: A 227 HIS cc_start: 0.8358 (t-90) cc_final: 0.8052 (t-90) REVERT: A 257 MET cc_start: 0.8563 (mmp) cc_final: 0.8260 (mmp) REVERT: A 293 PHE cc_start: 0.6687 (t80) cc_final: 0.6335 (t80) REVERT: A 297 ASN cc_start: 0.9330 (m-40) cc_final: 0.8742 (t0) REVERT: A 349 LEU cc_start: 0.6007 (mt) cc_final: 0.5412 (tp) REVERT: A 352 VAL cc_start: 0.8350 (m) cc_final: 0.8059 (m) REVERT: A 365 THR cc_start: 0.8885 (m) cc_final: 0.8597 (p) REVERT: A 380 LEU cc_start: 0.9331 (mm) cc_final: 0.8907 (tp) REVERT: D 32 MET cc_start: 0.6616 (mmm) cc_final: 0.6396 (mmm) REVERT: D 71 LYS cc_start: 0.8287 (mttt) cc_final: 0.7965 (mmtp) REVERT: E 15 GLN cc_start: 0.9142 (mt0) cc_final: 0.8776 (mt0) REVERT: E 18 ASN cc_start: 0.9147 (m110) cc_final: 0.8255 (t0) REVERT: E 21 TRP cc_start: 0.8940 (m100) cc_final: 0.8470 (m100) REVERT: E 24 TYR cc_start: 0.8672 (m-10) cc_final: 0.8322 (m-10) REVERT: E 59 GLU cc_start: 0.7426 (mt-10) cc_final: 0.5891 (pt0) REVERT: E 65 PHE cc_start: 0.7917 (p90) cc_final: 0.6691 (p90) REVERT: E 94 GLU cc_start: 0.8252 (pp20) cc_final: 0.7376 (tm-30) REVERT: E 107 TYR cc_start: 0.9079 (t80) cc_final: 0.8873 (t80) REVERT: E 131 ASP cc_start: 0.8026 (m-30) cc_final: 0.7648 (m-30) REVERT: E 156 LEU cc_start: 0.9610 (tt) cc_final: 0.9354 (tp) REVERT: E 186 VAL cc_start: 0.9489 (m) cc_final: 0.9195 (p) REVERT: E 192 VAL cc_start: 0.9082 (p) cc_final: 0.8749 (m) REVERT: E 201 ASN cc_start: 0.8048 (m-40) cc_final: 0.7510 (m-40) REVERT: E 255 ASP cc_start: 0.8415 (t70) cc_final: 0.7891 (m-30) REVERT: E 260 GLN cc_start: 0.8603 (pt0) cc_final: 0.8001 (pt0) REVERT: E 270 HIS cc_start: 0.8632 (p-80) cc_final: 0.8070 (p-80) REVERT: E 273 LEU cc_start: 0.8362 (tp) cc_final: 0.8077 (tp) REVERT: E 350 TRP cc_start: 0.6681 (m-10) cc_final: 0.6339 (m-10) REVERT: E 381 MET cc_start: 0.8824 (tmm) cc_final: 0.8000 (tmm) REVERT: E 402 MET cc_start: 0.9229 (mmt) cc_final: 0.8655 (mmt) REVERT: E 439 VAL cc_start: 0.8128 (t) cc_final: 0.7649 (t) REVERT: F 18 ASN cc_start: 0.8972 (m110) cc_final: 0.8760 (m110) REVERT: F 21 TRP cc_start: 0.8794 (m100) cc_final: 0.8073 (m100) REVERT: F 24 TYR cc_start: 0.8696 (m-10) cc_final: 0.8092 (m-10) REVERT: F 59 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7290 (pt0) REVERT: F 120 ASP cc_start: 0.8625 (m-30) cc_final: 0.8220 (p0) REVERT: F 131 ASP cc_start: 0.7877 (m-30) cc_final: 0.7596 (m-30) REVERT: F 211 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8411 (mt-10) REVERT: F 237 GLN cc_start: 0.8720 (mt0) cc_final: 0.8044 (tt0) REVERT: F 247 ARG cc_start: 0.6760 (mmt90) cc_final: 0.4672 (mmt90) REVERT: F 255 ASP cc_start: 0.8539 (t70) cc_final: 0.8136 (m-30) REVERT: F 270 HIS cc_start: 0.8626 (p-80) cc_final: 0.7805 (p-80) REVERT: F 276 TYR cc_start: 0.8487 (t80) cc_final: 0.7850 (t80) REVERT: F 308 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8190 (mmtm) REVERT: F 381 MET cc_start: 0.8138 (ttt) cc_final: 0.7442 (ttp) REVERT: F 415 GLU cc_start: 0.6938 (pt0) cc_final: 0.6639 (pt0) REVERT: F 441 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8236 (tm-30) REVERT: G 23 LEU cc_start: 0.9205 (tp) cc_final: 0.8626 (tt) REVERT: G 27 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7594 (mt-10) REVERT: G 59 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6212 (pp20) REVERT: G 65 PHE cc_start: 0.7867 (p90) cc_final: 0.6572 (p90) REVERT: G 94 GLU cc_start: 0.8268 (tt0) cc_final: 0.7729 (tp30) REVERT: G 124 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8313 (tt0) REVERT: G 167 LYS cc_start: 0.7926 (mptt) cc_final: 0.7686 (ptmt) REVERT: G 206 PHE cc_start: 0.9289 (m-80) cc_final: 0.8846 (m-80) REVERT: G 209 ASP cc_start: 0.7807 (t0) cc_final: 0.7157 (t0) REVERT: G 215 ASP cc_start: 0.8071 (m-30) cc_final: 0.7438 (m-30) REVERT: G 304 ASN cc_start: 0.9295 (t0) cc_final: 0.8965 (t0) REVERT: G 308 LYS cc_start: 0.8443 (tptp) cc_final: 0.8173 (mmtt) REVERT: G 343 ARG cc_start: 0.8688 (ptm160) cc_final: 0.8208 (mtt180) REVERT: G 346 GLN cc_start: 0.7139 (pp30) cc_final: 0.6753 (pp30) REVERT: G 374 LYS cc_start: 0.9026 (tttm) cc_final: 0.8364 (tmtt) REVERT: G 377 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7824 (mtm110) REVERT: G 381 MET cc_start: 0.9327 (tmm) cc_final: 0.8929 (tmm) REVERT: G 402 MET cc_start: 0.8645 (mmt) cc_final: 0.8348 (mmm) REVERT: G 441 GLN cc_start: 0.8922 (mm110) cc_final: 0.8519 (tm-30) REVERT: H 2 ARG cc_start: 0.7078 (mtp180) cc_final: 0.5979 (mtt180) REVERT: H 20 CYS cc_start: 0.8749 (m) cc_final: 0.8495 (m) REVERT: H 27 GLU cc_start: 0.8603 (tt0) cc_final: 0.8314 (tt0) REVERT: H 73 ASP cc_start: 0.7945 (t0) cc_final: 0.7488 (t0) REVERT: H 80 ASP cc_start: 0.8304 (m-30) cc_final: 0.7991 (p0) REVERT: H 116 LYS cc_start: 0.8556 (ptmt) cc_final: 0.8329 (ptmt) REVERT: H 131 ASP cc_start: 0.8387 (m-30) cc_final: 0.8184 (m-30) REVERT: H 137 GLN cc_start: 0.8526 (mt0) cc_final: 0.8223 (mm-40) REVERT: H 143 HIS cc_start: 0.8569 (p90) cc_final: 0.8214 (p90) REVERT: H 270 HIS cc_start: 0.8727 (p-80) cc_final: 0.8479 (p-80) REVERT: H 343 ARG cc_start: 0.8528 (ptt180) cc_final: 0.8060 (mtt180) REVERT: H 351 CYS cc_start: 0.8142 (t) cc_final: 0.6905 (p) REVERT: H 374 LYS cc_start: 0.8968 (tttm) cc_final: 0.8558 (tmtt) REVERT: H 435 ASP cc_start: 0.8770 (t0) cc_final: 0.8555 (t0) REVERT: H 441 GLN cc_start: 0.8781 (mm110) cc_final: 0.8286 (tm-30) REVERT: J 1 MET cc_start: 0.8691 (tpt) cc_final: 0.8442 (tpp) REVERT: J 21 TRP cc_start: 0.9033 (m100) cc_final: 0.8514 (m100) REVERT: J 51 PHE cc_start: 0.8805 (m-80) cc_final: 0.8439 (m-80) REVERT: J 53 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7373 (tm-30) REVERT: J 84 LEU cc_start: 0.9127 (mt) cc_final: 0.8818 (mt) REVERT: J 174 LYS cc_start: 0.8930 (mppt) cc_final: 0.8280 (mtmm) REVERT: J 190 HIS cc_start: 0.8634 (t-90) cc_final: 0.8420 (t-90) REVERT: J 192 LEU cc_start: 0.9457 (mt) cc_final: 0.9249 (mt) REVERT: J 196 SER cc_start: 0.9394 (t) cc_final: 0.9001 (p) REVERT: J 198 GLU cc_start: 0.8998 (pm20) cc_final: 0.8093 (tp30) REVERT: J 216 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8788 (mmmt) REVERT: J 297 ASN cc_start: 0.9024 (t0) cc_final: 0.8776 (t0) REVERT: J 322 MET cc_start: 0.9094 (mmm) cc_final: 0.8783 (mmm) REVERT: J 365 THR cc_start: 0.8574 (m) cc_final: 0.8158 (p) REVERT: J 394 LEU cc_start: 0.8731 (tt) cc_final: 0.8448 (tt) REVERT: J 398 THR cc_start: 0.8532 (p) cc_final: 0.8214 (p) REVERT: J 405 MET cc_start: 0.8271 (tpp) cc_final: 0.7557 (tpp) REVERT: J 406 GLU cc_start: 0.8655 (pt0) cc_final: 0.8058 (tm-30) REVERT: J 408 THR cc_start: 0.9193 (p) cc_final: 0.8928 (p) REVERT: J 409 GLU cc_start: 0.8945 (pt0) cc_final: 0.8429 (pt0) REVERT: J 412 SER cc_start: 0.9172 (m) cc_final: 0.8882 (p) REVERT: B 14 ASN cc_start: 0.8932 (m-40) cc_final: 0.8595 (m-40) REVERT: B 20 PHE cc_start: 0.8351 (t80) cc_final: 0.8103 (t80) REVERT: B 21 TRP cc_start: 0.9429 (m100) cc_final: 0.8594 (m100) REVERT: B 85 PHE cc_start: 0.7762 (m-80) cc_final: 0.7091 (m-80) REVERT: B 147 MET cc_start: 0.8550 (tmm) cc_final: 0.7973 (tmm) REVERT: B 151 LEU cc_start: 0.9554 (mt) cc_final: 0.9168 (mt) REVERT: B 164 MET cc_start: 0.8008 (mmp) cc_final: 0.7269 (mmp) REVERT: B 174 LYS cc_start: 0.8845 (mppt) cc_final: 0.8593 (mppt) REVERT: B 181 GLU cc_start: 0.7838 (tt0) cc_final: 0.7429 (tt0) REVERT: B 199 THR cc_start: 0.7755 (m) cc_final: 0.7460 (m) REVERT: B 207 LEU cc_start: 0.8930 (tt) cc_final: 0.8612 (tt) REVERT: B 222 TYR cc_start: 0.8898 (m-10) cc_final: 0.8691 (m-80) REVERT: B 225 LEU cc_start: 0.9526 (mp) cc_final: 0.9181 (mp) REVERT: B 233 MET cc_start: 0.9207 (mtm) cc_final: 0.8489 (mmm) REVERT: B 247 ASN cc_start: 0.5862 (m-40) cc_final: 0.5506 (m110) REVERT: B 352 VAL cc_start: 0.8862 (t) cc_final: 0.8101 (t) REVERT: B 394 LEU cc_start: 0.8872 (tt) cc_final: 0.8661 (tt) REVERT: B 395 HIS cc_start: 0.8952 (p-80) cc_final: 0.8523 (p-80) REVERT: B 414 MET cc_start: 0.8405 (ttt) cc_final: 0.8173 (mmm) REVERT: C 2 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7534 (mtp180) REVERT: C 6 HIS cc_start: 0.9037 (t70) cc_final: 0.7674 (t-170) REVERT: C 14 ASN cc_start: 0.9101 (m110) cc_final: 0.8743 (m-40) REVERT: C 35 ILE cc_start: 0.8732 (mp) cc_final: 0.8305 (mm) REVERT: C 53 GLU cc_start: 0.7801 (mt-10) cc_final: 0.6740 (tm-30) REVERT: C 101 TRP cc_start: 0.8676 (t60) cc_final: 0.8258 (t60) REVERT: C 228 LEU cc_start: 0.9460 (tp) cc_final: 0.9223 (tp) REVERT: C 233 MET cc_start: 0.9279 (mtm) cc_final: 0.8919 (ttp) REVERT: C 252 LYS cc_start: 0.8978 (mptt) cc_final: 0.8625 (mmtp) REVERT: C 359 ASP cc_start: 0.9108 (m-30) cc_final: 0.8801 (m-30) REVERT: C 397 TYR cc_start: 0.8828 (m-80) cc_final: 0.8607 (m-80) REVERT: C 405 MET cc_start: 0.8020 (mmt) cc_final: 0.7571 (tpp) REVERT: C 408 THR cc_start: 0.8860 (p) cc_final: 0.8610 (p) REVERT: C 423 GLN cc_start: 0.8299 (mt0) cc_final: 0.8043 (tt0) outliers start: 2 outliers final: 0 residues processed: 1019 average time/residue: 0.3833 time to fit residues: 621.0817 Evaluate side-chains 852 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 852 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 4.9990 chunk 306 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 340 optimal weight: 0.5980 chunk 282 optimal weight: 50.0000 chunk 157 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN E 172 GLN E 210 ASN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN E 441 GLN F 8 HIS ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 237 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN J 99 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28752 Z= 0.177 Angle : 0.619 10.007 39006 Z= 0.307 Chirality : 0.046 0.162 4200 Planarity : 0.005 0.079 5117 Dihedral : 9.261 161.815 3979 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.77 % 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: -1.36 (0.14), residues: 3543 helix: -0.45 (0.13), residues: 1507 sheet: 0.04 (0.24), residues: 512 loop : -1.63 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 396 HIS 0.011 0.001 HIS B 6 PHE 0.021 0.001 PHE F 408 TYR 0.016 0.001 TYR H 24 ARG 0.014 0.001 ARG G 426 *********************** 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 1028 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1026 time to evaluate : 3.084 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 6 HIS cc_start: 0.8939 (t-90) cc_final: 0.8043 (t-170) REVERT: A 20 PHE cc_start: 0.8244 (t80) cc_final: 0.7417 (t80) REVERT: A 35 ILE cc_start: 0.8623 (mp) cc_final: 0.8205 (mm) REVERT: A 67 ASP cc_start: 0.8383 (t0) cc_final: 0.7967 (t70) REVERT: A 73 MET cc_start: 0.7989 (mmp) cc_final: 0.7736 (mmm) REVERT: A 136 THR cc_start: 0.8948 (m) cc_final: 0.8712 (p) REVERT: A 147 MET cc_start: 0.8428 (ppp) cc_final: 0.7835 (ppp) REVERT: A 199 THR cc_start: 0.7929 (m) cc_final: 0.7573 (m) REVERT: A 218 LYS cc_start: 0.8576 (tptp) cc_final: 0.8350 (pptt) REVERT: A 227 HIS cc_start: 0.8084 (t-90) cc_final: 0.7877 (t-90) REVERT: A 233 MET cc_start: 0.9024 (mtm) cc_final: 0.7916 (mtm) REVERT: A 293 PHE cc_start: 0.6652 (t80) cc_final: 0.6345 (t80) REVERT: A 297 ASN cc_start: 0.9289 (m-40) cc_final: 0.8841 (t0) REVERT: A 352 VAL cc_start: 0.8385 (m) cc_final: 0.8132 (m) REVERT: A 380 LEU cc_start: 0.9251 (mm) cc_final: 0.8964 (tp) REVERT: A 423 GLN cc_start: 0.8441 (mt0) cc_final: 0.7558 (mp10) REVERT: D 32 MET cc_start: 0.6519 (mmm) cc_final: 0.6291 (mmm) REVERT: D 65 LEU cc_start: 0.8756 (mm) cc_final: 0.8434 (mm) REVERT: D 71 LYS cc_start: 0.8088 (mttt) cc_final: 0.7634 (mmtp) REVERT: E 18 ASN cc_start: 0.9168 (m110) cc_final: 0.8375 (t0) REVERT: E 21 TRP cc_start: 0.8853 (m100) cc_final: 0.8526 (m100) REVERT: E 24 TYR cc_start: 0.8557 (m-10) cc_final: 0.8226 (m-10) REVERT: E 59 GLU cc_start: 0.7552 (mt-10) cc_final: 0.5779 (pt0) REVERT: E 65 PHE cc_start: 0.7819 (p90) cc_final: 0.6072 (p90) REVERT: E 94 GLU cc_start: 0.8277 (pp20) cc_final: 0.7322 (tm-30) REVERT: E 97 VAL cc_start: 0.8768 (p) cc_final: 0.8394 (m) REVERT: E 116 LYS cc_start: 0.8994 (tmmt) cc_final: 0.8462 (ttpt) REVERT: E 131 ASP cc_start: 0.7999 (m-30) cc_final: 0.7697 (m-30) REVERT: E 163 MET cc_start: 0.8866 (mmp) cc_final: 0.8421 (mmm) REVERT: E 192 VAL cc_start: 0.9195 (p) cc_final: 0.8970 (m) REVERT: E 201 ASN cc_start: 0.8046 (m-40) cc_final: 0.7402 (m-40) REVERT: E 255 ASP cc_start: 0.8558 (t70) cc_final: 0.7923 (m-30) REVERT: E 260 GLN cc_start: 0.8787 (pt0) cc_final: 0.8285 (pt0) REVERT: E 270 HIS cc_start: 0.8508 (p-80) cc_final: 0.8018 (p-80) REVERT: E 361 TYR cc_start: 0.8172 (m-80) cc_final: 0.7950 (m-80) REVERT: E 381 MET cc_start: 0.8841 (tmm) cc_final: 0.7885 (tmm) REVERT: E 402 MET cc_start: 0.9132 (mmt) cc_final: 0.8578 (mmt) REVERT: F 1 MET cc_start: 0.7847 (ptp) cc_final: 0.7605 (ptp) REVERT: F 21 TRP cc_start: 0.8677 (m100) cc_final: 0.7987 (m100) REVERT: F 24 TYR cc_start: 0.8476 (m-10) cc_final: 0.8157 (m-10) REVERT: F 59 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6724 (pt0) REVERT: F 65 PHE cc_start: 0.7647 (p90) cc_final: 0.6655 (p90) REVERT: F 131 ASP cc_start: 0.7849 (m-30) cc_final: 0.7581 (m-30) REVERT: F 237 GLN cc_start: 0.8573 (mt0) cc_final: 0.7725 (tt0) REVERT: F 247 ARG cc_start: 0.6793 (mmt90) cc_final: 0.4663 (mmt90) REVERT: F 255 ASP cc_start: 0.8512 (t70) cc_final: 0.8123 (m-30) REVERT: F 270 HIS cc_start: 0.8638 (p-80) cc_final: 0.7763 (p-80) REVERT: F 276 TYR cc_start: 0.8293 (t80) cc_final: 0.7747 (t80) REVERT: F 317 MET cc_start: 0.6633 (tpt) cc_final: 0.6342 (tpt) REVERT: F 361 TYR cc_start: 0.8348 (m-80) cc_final: 0.8016 (m-80) REVERT: F 441 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8285 (tm-30) REVERT: G 23 LEU cc_start: 0.9096 (tp) cc_final: 0.8349 (tp) REVERT: G 27 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7544 (mt-10) REVERT: G 59 GLU cc_start: 0.6851 (mt-10) cc_final: 0.5254 (pt0) REVERT: G 65 PHE cc_start: 0.7562 (p90) cc_final: 0.6214 (p90) REVERT: G 94 GLU cc_start: 0.8085 (tt0) cc_final: 0.7715 (tm-30) REVERT: G 124 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8447 (mt-10) REVERT: G 206 PHE cc_start: 0.9368 (m-80) cc_final: 0.8770 (m-80) REVERT: G 209 ASP cc_start: 0.7897 (t0) cc_final: 0.7259 (t0) REVERT: G 215 ASP cc_start: 0.7984 (m-30) cc_final: 0.7699 (m-30) REVERT: G 279 ILE cc_start: 0.8672 (mm) cc_final: 0.8414 (mm) REVERT: G 301 GLU cc_start: 0.8809 (tt0) cc_final: 0.8584 (tt0) REVERT: G 304 ASN cc_start: 0.9248 (t0) cc_final: 0.8824 (t0) REVERT: G 308 LYS cc_start: 0.8348 (tptp) cc_final: 0.8032 (ttmt) REVERT: G 317 MET cc_start: 0.7271 (mmm) cc_final: 0.6993 (mtp) REVERT: G 343 ARG cc_start: 0.8831 (ptm160) cc_final: 0.8153 (mtt180) REVERT: G 351 CYS cc_start: 0.8572 (t) cc_final: 0.7492 (p) REVERT: G 374 LYS cc_start: 0.9044 (tttm) cc_final: 0.8513 (tptp) REVERT: G 380 CYS cc_start: 0.8872 (t) cc_final: 0.8567 (p) REVERT: G 381 MET cc_start: 0.9362 (tmm) cc_final: 0.8572 (tmm) REVERT: G 441 GLN cc_start: 0.8802 (mm110) cc_final: 0.8446 (tm-30) REVERT: H 2 ARG cc_start: 0.6867 (mtp180) cc_final: 0.5366 (mmt180) REVERT: H 20 CYS cc_start: 0.8738 (m) cc_final: 0.8405 (m) REVERT: H 27 GLU cc_start: 0.8521 (tt0) cc_final: 0.8200 (tt0) REVERT: H 57 PHE cc_start: 0.8194 (m-80) cc_final: 0.6896 (m-80) REVERT: H 80 ASP cc_start: 0.8256 (m-30) cc_final: 0.7809 (p0) REVERT: H 94 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7218 (tp30) REVERT: H 116 LYS cc_start: 0.8483 (ptmt) cc_final: 0.8251 (ptmt) REVERT: H 131 ASP cc_start: 0.8378 (m-30) cc_final: 0.8171 (m-30) REVERT: H 137 GLN cc_start: 0.8470 (mt0) cc_final: 0.8067 (mm-40) REVERT: H 140 LEU cc_start: 0.8228 (tp) cc_final: 0.7953 (mt) REVERT: H 143 HIS cc_start: 0.8519 (p90) cc_final: 0.8177 (p90) REVERT: H 237 GLN cc_start: 0.8510 (mt0) cc_final: 0.7568 (tt0) REVERT: H 276 TYR cc_start: 0.7945 (t80) cc_final: 0.6842 (t80) REVERT: H 330 ARG cc_start: 0.5289 (mtt180) cc_final: 0.5072 (mtm-85) REVERT: H 343 ARG cc_start: 0.8418 (ptt180) cc_final: 0.7996 (mtt180) REVERT: H 351 CYS cc_start: 0.8122 (t) cc_final: 0.7023 (p) REVERT: H 374 LYS cc_start: 0.8926 (tttm) cc_final: 0.8535 (tmtt) REVERT: H 415 GLU cc_start: 0.6562 (pt0) cc_final: 0.5919 (pt0) REVERT: H 429 LEU cc_start: 0.9245 (mm) cc_final: 0.9036 (mm) REVERT: H 441 GLN cc_start: 0.8868 (mm110) cc_final: 0.8433 (tm-30) REVERT: J 6 HIS cc_start: 0.8942 (t70) cc_final: 0.8720 (t-170) REVERT: J 21 TRP cc_start: 0.8952 (m100) cc_final: 0.8350 (m100) REVERT: J 53 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7344 (tm-30) REVERT: J 89 ASN cc_start: 0.9113 (m110) cc_final: 0.8837 (m110) REVERT: J 136 THR cc_start: 0.8709 (m) cc_final: 0.8368 (t) REVERT: J 157 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8182 (tm-30) REVERT: J 174 LYS cc_start: 0.9036 (mppt) cc_final: 0.8476 (mtmm) REVERT: J 192 LEU cc_start: 0.9422 (mt) cc_final: 0.9215 (mt) REVERT: J 196 SER cc_start: 0.9231 (t) cc_final: 0.8850 (p) REVERT: J 198 GLU cc_start: 0.9009 (pm20) cc_final: 0.8134 (tp30) REVERT: J 216 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8768 (mmmt) REVERT: J 266 MET cc_start: 0.8693 (mtm) cc_final: 0.8279 (mtm) REVERT: J 322 MET cc_start: 0.9130 (mmm) cc_final: 0.8849 (mmm) REVERT: J 405 MET cc_start: 0.8190 (tpp) cc_final: 0.7793 (tpp) REVERT: J 406 GLU cc_start: 0.8641 (pt0) cc_final: 0.8192 (tm-30) REVERT: J 409 GLU cc_start: 0.8908 (pt0) cc_final: 0.8441 (pt0) REVERT: J 412 SER cc_start: 0.9078 (m) cc_final: 0.8867 (p) REVERT: B 14 ASN cc_start: 0.8853 (m-40) cc_final: 0.8639 (m-40) REVERT: B 51 PHE cc_start: 0.9052 (m-80) cc_final: 0.8844 (m-80) REVERT: B 85 PHE cc_start: 0.7784 (m-80) cc_final: 0.7303 (m-80) REVERT: B 147 MET cc_start: 0.8211 (tmm) cc_final: 0.7606 (tmm) REVERT: B 151 LEU cc_start: 0.9503 (mt) cc_final: 0.9140 (mt) REVERT: B 164 MET cc_start: 0.7771 (mmp) cc_final: 0.7234 (mmp) REVERT: B 174 LYS cc_start: 0.8883 (mppt) cc_final: 0.8677 (mppt) REVERT: B 181 GLU cc_start: 0.7857 (tt0) cc_final: 0.7396 (tt0) REVERT: B 215 LEU cc_start: 0.9183 (mm) cc_final: 0.8805 (mm) REVERT: B 257 MET cc_start: 0.7643 (mmm) cc_final: 0.7433 (mmm) REVERT: B 299 MET cc_start: 0.9137 (mmp) cc_final: 0.8921 (mmt) REVERT: B 344 ILE cc_start: 0.9113 (mt) cc_final: 0.8886 (mt) REVERT: B 352 VAL cc_start: 0.8809 (t) cc_final: 0.8160 (t) REVERT: B 359 ASP cc_start: 0.9345 (m-30) cc_final: 0.9011 (m-30) REVERT: B 395 HIS cc_start: 0.8827 (p-80) cc_final: 0.8434 (p-80) REVERT: B 405 MET cc_start: 0.8528 (tpt) cc_final: 0.8092 (tpt) REVERT: B 414 MET cc_start: 0.8373 (ttt) cc_final: 0.8172 (mmm) REVERT: C 3 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6924 (tm-30) REVERT: C 6 HIS cc_start: 0.8962 (t70) cc_final: 0.7830 (t-170) REVERT: C 8 GLN cc_start: 0.8400 (mt0) cc_final: 0.8043 (mt0) REVERT: C 14 ASN cc_start: 0.9110 (m110) cc_final: 0.8691 (m-40) REVERT: C 20 PHE cc_start: 0.8289 (t80) cc_final: 0.7602 (t80) REVERT: C 35 ILE cc_start: 0.8715 (mp) cc_final: 0.8323 (mm) REVERT: C 53 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6971 (tm-30) REVERT: C 157 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8594 (tm-30) REVERT: C 189 MET cc_start: 0.8463 (tpp) cc_final: 0.8195 (tpp) REVERT: C 252 LYS cc_start: 0.9031 (mptt) cc_final: 0.8770 (mmtp) REVERT: C 297 ASN cc_start: 0.9238 (m-40) cc_final: 0.8827 (t0) REVERT: C 359 ASP cc_start: 0.9078 (m-30) cc_final: 0.8797 (m-30) REVERT: C 405 MET cc_start: 0.7916 (mmt) cc_final: 0.7303 (tpp) REVERT: C 408 THR cc_start: 0.8868 (p) cc_final: 0.8480 (p) outliers start: 2 outliers final: 1 residues processed: 1028 average time/residue: 0.3813 time to fit residues: 619.2454 Evaluate side-chains 859 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 858 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 192 optimal weight: 40.0000 chunk 286 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 339 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 172 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN C 44 HIS C 184 ASN C 256 ASN C 328 GLN C 423 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28752 Z= 0.269 Angle : 0.682 10.203 39006 Z= 0.345 Chirality : 0.049 0.191 4200 Planarity : 0.005 0.082 5117 Dihedral : 9.442 160.733 3979 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -0.56 (0.13), residues: 1549 sheet: 0.12 (0.24), residues: 516 loop : -1.54 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G 411 HIS 0.008 0.001 HIS B 44 PHE 0.053 0.002 PHE E 408 TYR 0.020 0.002 TYR A 222 ARG 0.009 0.001 ARG E 247 *********************** 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 985 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 985 time to evaluate : 3.531 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: A 6 HIS cc_start: 0.9049 (t-90) cc_final: 0.8147 (t70) REVERT: A 14 ASN cc_start: 0.9069 (m-40) cc_final: 0.8863 (m-40) REVERT: A 20 PHE cc_start: 0.8160 (t80) cc_final: 0.7764 (t80) REVERT: A 53 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7229 (tm-30) REVERT: A 136 THR cc_start: 0.9013 (m) cc_final: 0.8764 (p) REVERT: A 139 LEU cc_start: 0.8571 (mt) cc_final: 0.8260 (mt) REVERT: A 147 MET cc_start: 0.8434 (ppp) cc_final: 0.7764 (ppp) REVERT: A 151 LEU cc_start: 0.9472 (mt) cc_final: 0.9242 (mt) REVERT: A 157 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 199 THR cc_start: 0.7942 (m) cc_final: 0.7604 (m) REVERT: A 213 ASN cc_start: 0.8878 (m-40) cc_final: 0.8534 (t0) REVERT: A 227 HIS cc_start: 0.8240 (t-90) cc_final: 0.7975 (t-90) REVERT: A 265 PHE cc_start: 0.8177 (p90) cc_final: 0.7905 (p90) REVERT: A 293 PHE cc_start: 0.6987 (t80) cc_final: 0.6557 (t80) REVERT: A 297 ASN cc_start: 0.9414 (m-40) cc_final: 0.8868 (t0) REVERT: A 352 VAL cc_start: 0.8335 (m) cc_final: 0.8062 (m) REVERT: A 376 ILE cc_start: 0.8972 (pt) cc_final: 0.8715 (pt) REVERT: A 423 GLN cc_start: 0.8422 (mt0) cc_final: 0.7619 (mp10) REVERT: D 71 LYS cc_start: 0.8130 (mttt) cc_final: 0.7667 (mmtp) REVERT: D 92 LEU cc_start: 0.7881 (mt) cc_final: 0.7363 (pp) REVERT: E 18 ASN cc_start: 0.9189 (m110) cc_final: 0.8481 (t0) REVERT: E 21 TRP cc_start: 0.8940 (m100) cc_final: 0.8552 (m100) REVERT: E 24 TYR cc_start: 0.8727 (m-10) cc_final: 0.8420 (m-10) REVERT: E 59 GLU cc_start: 0.7601 (mt-10) cc_final: 0.5774 (pt0) REVERT: E 65 PHE cc_start: 0.8019 (p90) cc_final: 0.6081 (p90) REVERT: E 73 ASP cc_start: 0.8469 (t0) cc_final: 0.8027 (t0) REVERT: E 94 GLU cc_start: 0.8369 (pp20) cc_final: 0.7406 (tm-30) REVERT: E 97 VAL cc_start: 0.8885 (p) cc_final: 0.8480 (m) REVERT: E 116 LYS cc_start: 0.9167 (tmmt) cc_final: 0.8656 (ttmt) REVERT: E 131 ASP cc_start: 0.8085 (m-30) cc_final: 0.7718 (m-30) REVERT: E 133 CYS cc_start: 0.8839 (m) cc_final: 0.8285 (m) REVERT: E 186 VAL cc_start: 0.9457 (m) cc_final: 0.9216 (p) REVERT: E 192 VAL cc_start: 0.9231 (p) cc_final: 0.8993 (m) REVERT: E 201 ASN cc_start: 0.8184 (m-40) cc_final: 0.7692 (m-40) REVERT: E 219 ARG cc_start: 0.7275 (mtm110) cc_final: 0.6407 (ptm160) REVERT: E 255 ASP cc_start: 0.8528 (t70) cc_final: 0.7924 (m-30) REVERT: E 260 GLN cc_start: 0.8759 (pt0) cc_final: 0.8275 (pt0) REVERT: E 270 HIS cc_start: 0.8627 (p-80) cc_final: 0.8122 (p-80) REVERT: E 303 TYR cc_start: 0.8658 (m-10) cc_final: 0.8335 (m-10) REVERT: E 308 LYS cc_start: 0.8425 (tptp) cc_final: 0.7819 (mtpp) REVERT: E 381 MET cc_start: 0.8945 (tmm) cc_final: 0.8018 (tmm) REVERT: E 402 MET cc_start: 0.9123 (mmt) cc_final: 0.8657 (mmt) REVERT: F 21 TRP cc_start: 0.8823 (m100) cc_final: 0.8214 (m100) REVERT: F 24 TYR cc_start: 0.8757 (m-10) cc_final: 0.8489 (m-10) REVERT: F 59 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6425 (pt0) REVERT: F 131 ASP cc_start: 0.7914 (m-30) cc_final: 0.7637 (m-30) REVERT: F 149 THR cc_start: 0.8166 (m) cc_final: 0.7952 (m) REVERT: F 237 GLN cc_start: 0.8645 (mt0) cc_final: 0.7789 (tt0) REVERT: F 247 ARG cc_start: 0.7210 (mmt90) cc_final: 0.4888 (mmt90) REVERT: F 255 ASP cc_start: 0.8561 (t70) cc_final: 0.8019 (m-30) REVERT: F 257 ASN cc_start: 0.8835 (t0) cc_final: 0.8397 (t0) REVERT: F 260 GLN cc_start: 0.8563 (pm20) cc_final: 0.8307 (pm20) REVERT: F 270 HIS cc_start: 0.8736 (p-80) cc_final: 0.7897 (p-80) REVERT: F 276 TYR cc_start: 0.8579 (t80) cc_final: 0.7682 (t80) REVERT: F 317 MET cc_start: 0.6578 (tpt) cc_final: 0.5295 (tpt) REVERT: F 361 TYR cc_start: 0.8430 (m-80) cc_final: 0.8166 (m-80) REVERT: F 426 ARG cc_start: 0.9008 (mmp80) cc_final: 0.8725 (mmp80) REVERT: F 441 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8319 (tm-30) REVERT: G 23 LEU cc_start: 0.9153 (tp) cc_final: 0.8409 (tp) REVERT: G 27 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7674 (mt-10) REVERT: G 59 GLU cc_start: 0.6809 (mt-10) cc_final: 0.5284 (pt0) REVERT: G 65 PHE cc_start: 0.7908 (p90) cc_final: 0.6544 (p90) REVERT: G 75 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8040 (tm-30) REVERT: G 94 GLU cc_start: 0.8074 (tt0) cc_final: 0.7627 (tm-30) REVERT: G 124 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8547 (tt0) REVERT: G 143 HIS cc_start: 0.8872 (p90) cc_final: 0.8307 (p90) REVERT: G 206 PHE cc_start: 0.9413 (m-80) cc_final: 0.8700 (m-80) REVERT: G 279 ILE cc_start: 0.8705 (mm) cc_final: 0.8491 (mm) REVERT: G 304 ASN cc_start: 0.9194 (t0) cc_final: 0.8870 (t0) REVERT: G 330 ARG cc_start: 0.5250 (mtt180) cc_final: 0.4951 (mtm180) REVERT: G 343 ARG cc_start: 0.8828 (ptm160) cc_final: 0.8180 (mtt180) REVERT: G 374 LYS cc_start: 0.9136 (tttm) cc_final: 0.8530 (tmtt) REVERT: G 379 VAL cc_start: 0.8666 (t) cc_final: 0.8277 (t) REVERT: G 380 CYS cc_start: 0.8907 (t) cc_final: 0.8463 (p) REVERT: G 381 MET cc_start: 0.9316 (tmm) cc_final: 0.8573 (tmm) REVERT: G 434 ARG cc_start: 0.9114 (mpt-90) cc_final: 0.8798 (mtt90) REVERT: G 441 GLN cc_start: 0.8802 (mm110) cc_final: 0.8445 (tm-30) REVERT: H 2 ARG cc_start: 0.7169 (mtp180) cc_final: 0.5800 (mtt180) REVERT: H 20 CYS cc_start: 0.8732 (m) cc_final: 0.8470 (m) REVERT: H 80 ASP cc_start: 0.8468 (m-30) cc_final: 0.7987 (p0) REVERT: H 131 ASP cc_start: 0.8409 (m-30) cc_final: 0.8168 (m-30) REVERT: H 143 HIS cc_start: 0.8601 (p90) cc_final: 0.8150 (p90) REVERT: H 204 CYS cc_start: 0.8822 (p) cc_final: 0.8579 (p) REVERT: H 209 ASP cc_start: 0.8321 (t0) cc_final: 0.8091 (t0) REVERT: H 237 GLN cc_start: 0.8490 (mt0) cc_final: 0.7565 (tt0) REVERT: H 266 TYR cc_start: 0.8841 (m-80) cc_final: 0.8582 (m-80) REVERT: H 276 TYR cc_start: 0.8237 (t80) cc_final: 0.7140 (t80) REVERT: H 306 MET cc_start: 0.8176 (mmm) cc_final: 0.7884 (mmm) REVERT: H 308 LYS cc_start: 0.8619 (tptp) cc_final: 0.8213 (mmtm) REVERT: H 343 ARG cc_start: 0.8509 (ptt180) cc_final: 0.8021 (mtt180) REVERT: H 351 CYS cc_start: 0.8106 (t) cc_final: 0.7883 (t) REVERT: H 441 GLN cc_start: 0.8873 (mm110) cc_final: 0.8458 (tm-30) REVERT: J 6 HIS cc_start: 0.9009 (t70) cc_final: 0.8553 (t-170) REVERT: J 14 ASN cc_start: 0.9245 (m-40) cc_final: 0.8959 (m-40) REVERT: J 21 TRP cc_start: 0.9006 (m100) cc_final: 0.8466 (m100) REVERT: J 53 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7384 (tm-30) REVERT: J 136 THR cc_start: 0.8738 (m) cc_final: 0.8504 (p) REVERT: J 157 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8203 (tm-30) REVERT: J 174 LYS cc_start: 0.9036 (mppt) cc_final: 0.8461 (mtmm) REVERT: J 198 GLU cc_start: 0.9014 (pm20) cc_final: 0.8153 (tp30) REVERT: J 216 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8783 (mmmt) REVERT: J 265 PHE cc_start: 0.7851 (p90) cc_final: 0.7647 (p90) REVERT: J 266 MET cc_start: 0.8807 (mtm) cc_final: 0.8400 (mtm) REVERT: J 315 LEU cc_start: 0.9038 (mt) cc_final: 0.8771 (mt) REVERT: J 322 MET cc_start: 0.9214 (mmm) cc_final: 0.8915 (mmm) REVERT: J 365 THR cc_start: 0.8675 (m) cc_final: 0.8355 (p) REVERT: J 405 MET cc_start: 0.8321 (tpp) cc_final: 0.7782 (tpp) REVERT: J 406 GLU cc_start: 0.8722 (pt0) cc_final: 0.8145 (tm-30) REVERT: J 409 GLU cc_start: 0.8898 (pt0) cc_final: 0.8149 (pt0) REVERT: J 412 SER cc_start: 0.9148 (m) cc_final: 0.8924 (p) REVERT: B 14 ASN cc_start: 0.8853 (m-40) cc_final: 0.8614 (m-40) REVERT: B 20 PHE cc_start: 0.8011 (t80) cc_final: 0.7796 (t80) REVERT: B 21 TRP cc_start: 0.9325 (m100) cc_final: 0.8452 (m100) REVERT: B 53 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7248 (tm-30) REVERT: B 84 LEU cc_start: 0.8726 (mt) cc_final: 0.7940 (mt) REVERT: B 85 PHE cc_start: 0.7933 (m-80) cc_final: 0.7327 (m-80) REVERT: B 130 LEU cc_start: 0.9163 (tp) cc_final: 0.8868 (tp) REVERT: B 162 ARG cc_start: 0.7665 (mmt-90) cc_final: 0.7186 (mmt180) REVERT: B 164 MET cc_start: 0.7728 (mmp) cc_final: 0.7254 (mmp) REVERT: B 174 LYS cc_start: 0.8981 (mppt) cc_final: 0.8758 (mppt) REVERT: B 181 GLU cc_start: 0.7870 (tt0) cc_final: 0.7378 (tt0) REVERT: B 198 GLU cc_start: 0.8906 (pm20) cc_final: 0.8537 (pm20) REVERT: B 233 MET cc_start: 0.8315 (mtm) cc_final: 0.8053 (mtm) REVERT: B 299 MET cc_start: 0.9147 (mmp) cc_final: 0.8828 (mmt) REVERT: B 343 TRP cc_start: 0.7470 (m100) cc_final: 0.6879 (m100) REVERT: B 352 VAL cc_start: 0.8714 (t) cc_final: 0.8024 (t) REVERT: B 405 MET cc_start: 0.8728 (tpt) cc_final: 0.8441 (tpp) REVERT: C 3 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7097 (tm-30) REVERT: C 6 HIS cc_start: 0.9047 (t70) cc_final: 0.7982 (t-170) REVERT: C 8 GLN cc_start: 0.8582 (mt0) cc_final: 0.8146 (mt0) REVERT: C 14 ASN cc_start: 0.9145 (m110) cc_final: 0.8543 (m-40) REVERT: C 35 ILE cc_start: 0.8776 (mp) cc_final: 0.8361 (mm) REVERT: C 53 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6748 (tm-30) REVERT: C 101 TRP cc_start: 0.8329 (t60) cc_final: 0.7854 (t60) REVERT: C 157 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 189 MET cc_start: 0.8642 (tpp) cc_final: 0.8335 (tpp) REVERT: C 228 LEU cc_start: 0.9445 (tp) cc_final: 0.9165 (tp) REVERT: C 241 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7258 (mtm110) REVERT: C 297 ASN cc_start: 0.9213 (m-40) cc_final: 0.8837 (t0) REVERT: C 359 ASP cc_start: 0.9085 (m-30) cc_final: 0.8794 (m-30) REVERT: C 375 GLU cc_start: 0.8063 (tt0) cc_final: 0.7564 (tm-30) REVERT: C 376 ILE cc_start: 0.8875 (pt) cc_final: 0.8659 (pt) REVERT: C 405 MET cc_start: 0.8107 (mmt) cc_final: 0.7770 (tpp) REVERT: C 408 THR cc_start: 0.8979 (p) cc_final: 0.8107 (p) outliers start: 0 outliers final: 0 residues processed: 985 average time/residue: 0.3865 time to fit residues: 604.8393 Evaluate side-chains 815 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 815 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 202 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 215 optimal weight: 0.0070 chunk 231 optimal weight: 2.9990 chunk 167 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 266 optimal weight: 0.0570 overall best weight: 3.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN E 210 ASN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN F 8 HIS ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** 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 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 226 ASN B 256 ASN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28752 Z= 0.187 Angle : 0.650 10.913 39006 Z= 0.321 Chirality : 0.047 0.263 4200 Planarity : 0.005 0.069 5117 Dihedral : 9.202 159.728 3979 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % 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: -1.20 (0.14), residues: 3543 helix: -0.33 (0.13), residues: 1528 sheet: 0.24 (0.24), residues: 516 loop : -1.59 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 350 HIS 0.005 0.001 HIS E 366 PHE 0.027 0.001 PHE G 408 TYR 0.019 0.001 TYR J 106 ARG 0.010 0.001 ARG F 426 *********************** 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 1004 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1004 time to evaluate : 3.316 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: 0.9021 (t-90) cc_final: 0.8066 (t-170) REVERT: A 20 PHE cc_start: 0.8045 (t80) cc_final: 0.7685 (t80) REVERT: A 35 ILE cc_start: 0.8702 (mp) cc_final: 0.8236 (mm) REVERT: A 53 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7180 (tm-30) REVERT: A 136 THR cc_start: 0.9005 (m) cc_final: 0.8785 (p) REVERT: A 157 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 176 SER cc_start: 0.7879 (t) cc_final: 0.6946 (t) REVERT: A 199 THR cc_start: 0.7858 (m) cc_final: 0.7515 (m) REVERT: A 227 HIS cc_start: 0.8000 (t-90) cc_final: 0.7765 (t-90) REVERT: A 265 PHE cc_start: 0.7952 (p90) cc_final: 0.7658 (p90) REVERT: A 293 PHE cc_start: 0.6876 (t80) cc_final: 0.6480 (t80) REVERT: A 297 ASN cc_start: 0.9320 (m-40) cc_final: 0.8651 (t0) REVERT: A 350 LYS cc_start: 0.8569 (ptpt) cc_final: 0.8368 (mtmm) REVERT: A 352 VAL cc_start: 0.8293 (m) cc_final: 0.8018 (m) REVERT: A 375 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 380 LEU cc_start: 0.9314 (mm) cc_final: 0.8824 (tt) REVERT: A 423 GLN cc_start: 0.8450 (mt0) cc_final: 0.7588 (mp10) REVERT: D 32 MET cc_start: 0.6731 (mmm) cc_final: 0.6004 (mmm) REVERT: D 40 TYR cc_start: 0.8195 (m-10) cc_final: 0.7782 (m-10) REVERT: D 65 LEU cc_start: 0.8731 (mm) cc_final: 0.8502 (mm) REVERT: D 71 LYS cc_start: 0.8090 (mttt) cc_final: 0.7673 (mmtp) REVERT: D 92 LEU cc_start: 0.7891 (mt) cc_final: 0.7213 (pp) REVERT: E 18 ASN cc_start: 0.9141 (m110) cc_final: 0.8430 (t0) REVERT: E 21 TRP cc_start: 0.8834 (m100) cc_final: 0.8417 (m100) REVERT: E 24 TYR cc_start: 0.8571 (m-10) cc_final: 0.8332 (m-10) REVERT: E 59 GLU cc_start: 0.7636 (mt-10) cc_final: 0.5725 (pt0) REVERT: E 65 PHE cc_start: 0.7904 (p90) cc_final: 0.6039 (p90) REVERT: E 73 ASP cc_start: 0.8400 (t0) cc_final: 0.7947 (t0) REVERT: E 94 GLU cc_start: 0.8262 (pp20) cc_final: 0.7437 (pp20) REVERT: E 97 VAL cc_start: 0.8879 (p) cc_final: 0.8517 (m) REVERT: E 116 LYS cc_start: 0.9057 (tmmt) cc_final: 0.8569 (ttmt) REVERT: E 131 ASP cc_start: 0.7797 (m-30) cc_final: 0.7589 (m-30) REVERT: E 133 CYS cc_start: 0.9073 (m) cc_final: 0.8504 (m) REVERT: E 186 VAL cc_start: 0.9400 (m) cc_final: 0.9138 (p) REVERT: E 201 ASN cc_start: 0.7921 (m-40) cc_final: 0.7395 (m-40) REVERT: E 255 ASP cc_start: 0.8566 (t70) cc_final: 0.7995 (m-30) REVERT: E 260 GLN cc_start: 0.8682 (pt0) cc_final: 0.8220 (pt0) REVERT: E 270 HIS cc_start: 0.8426 (p-80) cc_final: 0.8052 (p-80) REVERT: E 306 MET cc_start: 0.8246 (tpp) cc_final: 0.8015 (tpp) REVERT: E 308 LYS cc_start: 0.8441 (tptp) cc_final: 0.8146 (mmmt) REVERT: E 317 MET cc_start: 0.7502 (ttp) cc_final: 0.6737 (ttp) REVERT: E 381 MET cc_start: 0.8961 (tmm) cc_final: 0.8075 (tmm) REVERT: E 402 MET cc_start: 0.9156 (mmt) cc_final: 0.8598 (mmt) REVERT: E 408 PHE cc_start: 0.5158 (m-10) cc_final: 0.4946 (m-80) REVERT: E 412 TYR cc_start: 0.7643 (t80) cc_final: 0.7045 (t80) REVERT: F 21 TRP cc_start: 0.8669 (m100) cc_final: 0.8087 (m100) REVERT: F 24 TYR cc_start: 0.8729 (m-10) cc_final: 0.8348 (m-10) REVERT: F 59 GLU cc_start: 0.7721 (mt-10) cc_final: 0.6541 (pt0) REVERT: F 131 ASP cc_start: 0.7874 (m-30) cc_final: 0.7585 (m-30) REVERT: F 204 CYS cc_start: 0.9027 (t) cc_final: 0.8764 (t) REVERT: F 239 VAL cc_start: 0.8871 (t) cc_final: 0.8623 (t) REVERT: F 247 ARG cc_start: 0.6867 (mmt90) cc_final: 0.4776 (mmt180) REVERT: F 255 ASP cc_start: 0.8406 (t70) cc_final: 0.8064 (m-30) REVERT: F 257 ASN cc_start: 0.8962 (t0) cc_final: 0.8518 (t0) REVERT: F 270 HIS cc_start: 0.8508 (p-80) cc_final: 0.7752 (p-80) REVERT: F 276 TYR cc_start: 0.8345 (t80) cc_final: 0.7988 (t80) REVERT: F 320 CYS cc_start: 0.8737 (t) cc_final: 0.8167 (t) REVERT: F 349 ASP cc_start: 0.6979 (t0) cc_final: 0.6751 (p0) REVERT: F 426 ARG cc_start: 0.8980 (mmp80) cc_final: 0.8655 (mmp80) REVERT: F 441 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8500 (tm-30) REVERT: G 23 LEU cc_start: 0.9139 (tp) cc_final: 0.8401 (tp) REVERT: G 27 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7605 (mt-10) REVERT: G 59 GLU cc_start: 0.6798 (mt-10) cc_final: 0.5585 (pt0) REVERT: G 94 GLU cc_start: 0.7871 (tt0) cc_final: 0.7313 (tm-30) REVERT: G 124 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8387 (tt0) REVERT: G 143 HIS cc_start: 0.8546 (p90) cc_final: 0.8051 (p90) REVERT: G 206 PHE cc_start: 0.9326 (m-80) cc_final: 0.8753 (m-80) REVERT: G 220 ASN cc_start: 0.9304 (m-40) cc_final: 0.9082 (m110) REVERT: G 279 ILE cc_start: 0.8677 (mm) cc_final: 0.8438 (mm) REVERT: G 304 ASN cc_start: 0.9162 (t0) cc_final: 0.8852 (t0) REVERT: G 317 MET cc_start: 0.7241 (mtp) cc_final: 0.6754 (mtp) REVERT: G 343 ARG cc_start: 0.8841 (ptm160) cc_final: 0.8025 (mtt180) REVERT: G 345 ILE cc_start: 0.9665 (pt) cc_final: 0.9452 (tp) REVERT: G 351 CYS cc_start: 0.8572 (t) cc_final: 0.7602 (p) REVERT: G 374 LYS cc_start: 0.9171 (tttm) cc_final: 0.8582 (tmtt) REVERT: G 380 CYS cc_start: 0.8933 (t) cc_final: 0.8468 (p) REVERT: G 381 MET cc_start: 0.9320 (tmm) cc_final: 0.8630 (tmm) REVERT: G 399 PHE cc_start: 0.8770 (t80) cc_final: 0.8447 (t80) REVERT: G 426 ARG cc_start: 0.9044 (mmp80) cc_final: 0.8583 (mmp80) REVERT: G 441 GLN cc_start: 0.8723 (mm110) cc_final: 0.8458 (tm-30) REVERT: H 2 ARG cc_start: 0.5308 (mtp180) cc_final: 0.4762 (mmt180) REVERT: H 20 CYS cc_start: 0.8559 (m) cc_final: 0.8241 (m) REVERT: H 140 LEU cc_start: 0.8235 (tp) cc_final: 0.7879 (mm) REVERT: H 142 PHE cc_start: 0.8496 (m-10) cc_final: 0.8196 (m-10) REVERT: H 173 PHE cc_start: 0.8077 (m-10) cc_final: 0.7831 (m-80) REVERT: H 204 CYS cc_start: 0.8700 (p) cc_final: 0.8469 (p) REVERT: H 237 GLN cc_start: 0.8515 (mt0) cc_final: 0.7591 (tt0) REVERT: H 266 TYR cc_start: 0.8838 (m-80) cc_final: 0.8584 (m-80) REVERT: H 276 TYR cc_start: 0.8047 (t80) cc_final: 0.7146 (t80) REVERT: H 301 GLU cc_start: 0.8660 (tt0) cc_final: 0.8449 (tt0) REVERT: H 343 ARG cc_start: 0.8494 (ptt180) cc_final: 0.8283 (mtt180) REVERT: H 346 GLN cc_start: 0.8390 (mp10) cc_final: 0.7845 (tp40) REVERT: H 351 CYS cc_start: 0.8427 (t) cc_final: 0.8188 (t) REVERT: H 429 LEU cc_start: 0.9380 (mm) cc_final: 0.9165 (mm) REVERT: H 441 GLN cc_start: 0.8882 (mm110) cc_final: 0.8479 (tm-30) REVERT: J 6 HIS cc_start: 0.8896 (t70) cc_final: 0.8415 (t-170) REVERT: J 21 TRP cc_start: 0.9026 (m100) cc_final: 0.8533 (m100) REVERT: J 53 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7260 (tm-30) REVERT: J 83 ASN cc_start: 0.8993 (m-40) cc_final: 0.8756 (m110) REVERT: J 86 ARG cc_start: 0.6826 (ptm160) cc_final: 0.6589 (ptp-170) REVERT: J 111 GLU cc_start: 0.7867 (tt0) cc_final: 0.7569 (tp30) REVERT: J 157 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8293 (tm-30) REVERT: J 189 MET cc_start: 0.8869 (mmt) cc_final: 0.8635 (mmp) REVERT: J 198 GLU cc_start: 0.8961 (pm20) cc_final: 0.8022 (tp30) REVERT: J 215 LEU cc_start: 0.9104 (mm) cc_final: 0.8719 (mm) REVERT: J 216 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8779 (mmmt) REVERT: J 228 LEU cc_start: 0.9401 (tp) cc_final: 0.9173 (tp) REVERT: J 257 MET cc_start: 0.7957 (mmm) cc_final: 0.7525 (mmm) REVERT: J 266 MET cc_start: 0.8665 (mtm) cc_final: 0.8251 (mtm) REVERT: J 322 MET cc_start: 0.9075 (mmm) cc_final: 0.8702 (mmm) REVERT: J 365 THR cc_start: 0.8669 (m) cc_final: 0.8214 (p) REVERT: J 376 ILE cc_start: 0.9051 (pt) cc_final: 0.8254 (pt) REVERT: J 405 MET cc_start: 0.8476 (tpp) cc_final: 0.7900 (tpp) REVERT: J 406 GLU cc_start: 0.8575 (pt0) cc_final: 0.7954 (tm-30) REVERT: J 409 GLU cc_start: 0.8800 (pt0) cc_final: 0.8000 (pt0) REVERT: J 412 SER cc_start: 0.9146 (m) cc_final: 0.8899 (p) REVERT: B 85 PHE cc_start: 0.7858 (m-80) cc_final: 0.7235 (m-80) REVERT: B 130 LEU cc_start: 0.9200 (tp) cc_final: 0.8910 (tp) REVERT: B 147 MET cc_start: 0.8362 (tmm) cc_final: 0.7787 (tmm) REVERT: B 151 LEU cc_start: 0.9542 (mt) cc_final: 0.9167 (mt) REVERT: B 162 ARG cc_start: 0.7619 (mmt-90) cc_final: 0.7095 (mmt180) REVERT: B 164 MET cc_start: 0.7590 (mmp) cc_final: 0.7148 (mmp) REVERT: B 174 LYS cc_start: 0.8943 (mppt) cc_final: 0.8725 (mppt) REVERT: B 181 GLU cc_start: 0.7823 (tt0) cc_final: 0.7439 (tt0) REVERT: B 198 GLU cc_start: 0.8911 (pm20) cc_final: 0.8522 (pm20) REVERT: B 202 ILE cc_start: 0.8888 (mm) cc_final: 0.8665 (mm) REVERT: B 225 LEU cc_start: 0.9447 (mt) cc_final: 0.9242 (mt) REVERT: B 233 MET cc_start: 0.8237 (mtm) cc_final: 0.8036 (mtm) REVERT: B 395 HIS cc_start: 0.8834 (p-80) cc_final: 0.8284 (p-80) REVERT: B 402 MET cc_start: 0.6454 (mtm) cc_final: 0.6204 (mtp) REVERT: B 405 MET cc_start: 0.8672 (tpt) cc_final: 0.8186 (tpp) REVERT: C 6 HIS cc_start: 0.9021 (t70) cc_final: 0.7924 (t-170) REVERT: C 8 GLN cc_start: 0.8339 (mt0) cc_final: 0.7979 (mt0) REVERT: C 14 ASN cc_start: 0.9113 (m110) cc_final: 0.8633 (m-40) REVERT: C 20 PHE cc_start: 0.8335 (t80) cc_final: 0.7616 (t80) REVERT: C 21 TRP cc_start: 0.9209 (m100) cc_final: 0.8996 (m100) REVERT: C 35 ILE cc_start: 0.8795 (mp) cc_final: 0.8384 (mm) REVERT: C 53 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6749 (tm-30) REVERT: C 101 TRP cc_start: 0.8226 (t60) cc_final: 0.7841 (t60) REVERT: C 157 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 164 MET cc_start: 0.8301 (mmm) cc_final: 0.7735 (mmm) REVERT: C 189 MET cc_start: 0.8570 (tpp) cc_final: 0.8263 (tpp) REVERT: C 202 ILE cc_start: 0.9061 (mm) cc_final: 0.8834 (tp) REVERT: C 297 ASN cc_start: 0.9259 (m-40) cc_final: 0.8896 (t0) REVERT: C 359 ASP cc_start: 0.9077 (m-30) cc_final: 0.8776 (m-30) REVERT: C 375 GLU cc_start: 0.8032 (tt0) cc_final: 0.7503 (tm-30) REVERT: C 376 ILE cc_start: 0.8856 (pt) cc_final: 0.8616 (pt) REVERT: C 405 MET cc_start: 0.7679 (mmt) cc_final: 0.6765 (tpp) REVERT: C 408 THR cc_start: 0.8910 (p) cc_final: 0.8189 (p) outliers start: 0 outliers final: 0 residues processed: 1004 average time/residue: 0.3825 time to fit residues: 607.6370 Evaluate side-chains 824 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 824 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 299 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN F 8 HIS ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN F 237 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 184 ASN C 256 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28752 Z= 0.218 Angle : 0.658 9.886 39006 Z= 0.329 Chirality : 0.048 0.188 4200 Planarity : 0.005 0.074 5117 Dihedral : 9.165 161.372 3979 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.15 (0.14), residues: 3543 helix: -0.25 (0.14), residues: 1514 sheet: 0.21 (0.24), residues: 516 loop : -1.58 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 411 HIS 0.010 0.001 HIS F 8 PHE 0.037 0.002 PHE E 408 TYR 0.018 0.002 TYR G 176 ARG 0.009 0.001 ARG F 426 *********************** 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 979 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 979 time to evaluate : 3.409 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: A 6 HIS cc_start: 0.9085 (t-90) cc_final: 0.8078 (t-170) REVERT: A 20 PHE cc_start: 0.8043 (t80) cc_final: 0.7598 (t80) REVERT: A 35 ILE cc_start: 0.8642 (mp) cc_final: 0.8170 (mm) REVERT: A 51 PHE cc_start: 0.9070 (m-80) cc_final: 0.8815 (m-10) REVERT: A 53 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7234 (tm-30) REVERT: A 157 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 176 SER cc_start: 0.7933 (t) cc_final: 0.6967 (t) REVERT: A 199 THR cc_start: 0.7834 (m) cc_final: 0.7495 (m) REVERT: A 227 HIS cc_start: 0.8124 (t-90) cc_final: 0.7872 (t-90) REVERT: A 269 PHE cc_start: 0.8093 (t80) cc_final: 0.7735 (t80) REVERT: A 293 PHE cc_start: 0.7080 (t80) cc_final: 0.6668 (t80) REVERT: A 297 ASN cc_start: 0.9355 (m-40) cc_final: 0.8751 (t0) REVERT: A 365 THR cc_start: 0.8891 (m) cc_final: 0.8677 (p) REVERT: A 380 LEU cc_start: 0.9289 (mm) cc_final: 0.8817 (tt) REVERT: A 423 GLN cc_start: 0.8451 (mt0) cc_final: 0.7591 (mp10) REVERT: D 32 MET cc_start: 0.6686 (mmm) cc_final: 0.5818 (mmm) REVERT: D 71 LYS cc_start: 0.8039 (mttt) cc_final: 0.7579 (mmtp) REVERT: D 92 LEU cc_start: 0.7913 (mt) cc_final: 0.7267 (pp) REVERT: E 18 ASN cc_start: 0.9151 (m110) cc_final: 0.8460 (t0) REVERT: E 21 TRP cc_start: 0.8776 (m100) cc_final: 0.8348 (m100) REVERT: E 23 LEU cc_start: 0.8968 (tt) cc_final: 0.8595 (tt) REVERT: E 27 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7655 (mt-10) REVERT: E 59 GLU cc_start: 0.7641 (mt-10) cc_final: 0.5763 (pt0) REVERT: E 65 PHE cc_start: 0.7993 (p90) cc_final: 0.5950 (p90) REVERT: E 73 ASP cc_start: 0.8382 (t0) cc_final: 0.7980 (t0) REVERT: E 94 GLU cc_start: 0.8247 (pp20) cc_final: 0.7461 (tm-30) REVERT: E 97 VAL cc_start: 0.8899 (p) cc_final: 0.8533 (m) REVERT: E 116 LYS cc_start: 0.9124 (tmmt) cc_final: 0.8706 (ttmt) REVERT: E 131 ASP cc_start: 0.7786 (m-30) cc_final: 0.7513 (m-30) REVERT: E 133 CYS cc_start: 0.9000 (m) cc_final: 0.8500 (m) REVERT: E 201 ASN cc_start: 0.8038 (m-40) cc_final: 0.7498 (m-40) REVERT: E 215 ASP cc_start: 0.7866 (m-30) cc_final: 0.7630 (m-30) REVERT: E 219 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6573 (ttp-170) REVERT: E 255 ASP cc_start: 0.8572 (t70) cc_final: 0.7992 (m-30) REVERT: E 260 GLN cc_start: 0.8710 (pt0) cc_final: 0.8161 (pt0) REVERT: E 270 HIS cc_start: 0.8378 (p-80) cc_final: 0.8004 (p-80) REVERT: E 273 LEU cc_start: 0.8331 (tp) cc_final: 0.8102 (tp) REVERT: E 306 MET cc_start: 0.8268 (tpp) cc_final: 0.8039 (tpp) REVERT: E 308 LYS cc_start: 0.8319 (tptp) cc_final: 0.7687 (mmmt) REVERT: E 381 MET cc_start: 0.9047 (tmm) cc_final: 0.8185 (tmm) REVERT: E 402 MET cc_start: 0.9151 (mmt) cc_final: 0.8834 (mmt) REVERT: F 1 MET cc_start: 0.7788 (ptp) cc_final: 0.7506 (ptp) REVERT: F 21 TRP cc_start: 0.8653 (m100) cc_final: 0.8026 (m100) REVERT: F 24 TYR cc_start: 0.8912 (m-10) cc_final: 0.8324 (m-10) REVERT: F 59 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6661 (pt0) REVERT: F 131 ASP cc_start: 0.7892 (m-30) cc_final: 0.7607 (m-30) REVERT: F 239 VAL cc_start: 0.8951 (t) cc_final: 0.8682 (t) REVERT: F 247 ARG cc_start: 0.7031 (mmt90) cc_final: 0.5018 (mmt90) REVERT: F 255 ASP cc_start: 0.8427 (t70) cc_final: 0.8058 (m-30) REVERT: F 257 ASN cc_start: 0.9042 (t0) cc_final: 0.8503 (t0) REVERT: F 270 HIS cc_start: 0.8431 (p-80) cc_final: 0.7815 (p-80) REVERT: F 276 TYR cc_start: 0.8450 (t80) cc_final: 0.8186 (t80) REVERT: F 306 MET cc_start: 0.8272 (mmm) cc_final: 0.8070 (tpp) REVERT: F 426 ARG cc_start: 0.9022 (mmp80) cc_final: 0.8801 (mmp80) REVERT: F 441 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8523 (tm-30) REVERT: G 23 LEU cc_start: 0.9165 (tp) cc_final: 0.8366 (tp) REVERT: G 27 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7661 (mt-10) REVERT: G 59 GLU cc_start: 0.6747 (mt-10) cc_final: 0.5642 (pt0) REVERT: G 124 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8425 (tt0) REVERT: G 140 LEU cc_start: 0.8797 (tp) cc_final: 0.8558 (mp) REVERT: G 143 HIS cc_start: 0.8690 (p90) cc_final: 0.8253 (p90) REVERT: G 180 GLN cc_start: 0.8929 (pm20) cc_final: 0.7652 (pm20) REVERT: G 181 VAL cc_start: 0.8415 (t) cc_final: 0.7982 (t) REVERT: G 204 CYS cc_start: 0.9494 (p) cc_final: 0.9222 (p) REVERT: G 206 PHE cc_start: 0.9326 (m-80) cc_final: 0.8675 (m-10) REVERT: G 211 GLU cc_start: 0.8691 (mp0) cc_final: 0.8155 (tm-30) REVERT: G 215 ASP cc_start: 0.8051 (m-30) cc_final: 0.7541 (m-30) REVERT: G 220 ASN cc_start: 0.9308 (m-40) cc_final: 0.9092 (m110) REVERT: G 279 ILE cc_start: 0.8713 (mm) cc_final: 0.8498 (mm) REVERT: G 304 ASN cc_start: 0.9225 (t0) cc_final: 0.8923 (t0) REVERT: G 308 LYS cc_start: 0.8262 (tptp) cc_final: 0.7999 (mmmt) REVERT: G 343 ARG cc_start: 0.8856 (ptm160) cc_final: 0.8045 (mtt180) REVERT: G 345 ILE cc_start: 0.9660 (pt) cc_final: 0.9441 (tp) REVERT: G 351 CYS cc_start: 0.8533 (t) cc_final: 0.7509 (p) REVERT: G 374 LYS cc_start: 0.9172 (tttm) cc_final: 0.8605 (tmtt) REVERT: G 380 CYS cc_start: 0.8845 (t) cc_final: 0.8516 (p) REVERT: G 381 MET cc_start: 0.9337 (tmm) cc_final: 0.8623 (tmm) REVERT: G 426 ARG cc_start: 0.9166 (mmp80) cc_final: 0.8780 (mmp80) REVERT: G 441 GLN cc_start: 0.8710 (mm110) cc_final: 0.8464 (tm-30) REVERT: H 20 CYS cc_start: 0.8731 (m) cc_final: 0.8394 (m) REVERT: H 57 PHE cc_start: 0.8152 (m-80) cc_final: 0.6778 (m-80) REVERT: H 131 ASP cc_start: 0.8392 (m-30) cc_final: 0.8165 (m-30) REVERT: H 140 LEU cc_start: 0.8226 (tp) cc_final: 0.7969 (mt) REVERT: H 143 HIS cc_start: 0.8722 (p90) cc_final: 0.8440 (p90) REVERT: H 204 CYS cc_start: 0.8855 (p) cc_final: 0.8560 (p) REVERT: H 209 ASP cc_start: 0.8282 (t0) cc_final: 0.8046 (t0) REVERT: H 237 GLN cc_start: 0.8561 (mt0) cc_final: 0.7605 (tt0) REVERT: H 266 TYR cc_start: 0.8861 (m-80) cc_final: 0.8615 (m-80) REVERT: H 276 TYR cc_start: 0.8144 (t80) cc_final: 0.7233 (t80) REVERT: H 301 GLU cc_start: 0.8760 (tt0) cc_final: 0.8436 (tt0) REVERT: H 308 LYS cc_start: 0.8607 (tptp) cc_final: 0.8255 (mmtt) REVERT: H 346 GLN cc_start: 0.8392 (mp10) cc_final: 0.7826 (tp40) REVERT: H 351 CYS cc_start: 0.8379 (t) cc_final: 0.7388 (p) REVERT: H 429 LEU cc_start: 0.9388 (mm) cc_final: 0.9175 (mm) REVERT: H 441 GLN cc_start: 0.8889 (mm110) cc_final: 0.8487 (tm-30) REVERT: J 6 HIS cc_start: 0.8886 (t70) cc_final: 0.8489 (t-170) REVERT: J 21 TRP cc_start: 0.9059 (m100) cc_final: 0.8595 (m100) REVERT: J 50 TYR cc_start: 0.8053 (m-10) cc_final: 0.7759 (m-10) REVERT: J 53 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7304 (tm-30) REVERT: J 101 TRP cc_start: 0.8506 (t60) cc_final: 0.8280 (t60) REVERT: J 157 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8254 (tm-30) REVERT: J 198 GLU cc_start: 0.8938 (pm20) cc_final: 0.8059 (tp30) REVERT: J 216 LYS cc_start: 0.9203 (mmtt) cc_final: 0.8764 (mmmt) REVERT: J 228 LEU cc_start: 0.9434 (tp) cc_final: 0.9132 (tp) REVERT: J 287 GLU cc_start: 0.8863 (tt0) cc_final: 0.8463 (tt0) REVERT: J 322 MET cc_start: 0.9109 (mmm) cc_final: 0.8895 (mmm) REVERT: J 362 MET cc_start: 0.8807 (mmm) cc_final: 0.8577 (mmm) REVERT: J 365 THR cc_start: 0.8670 (m) cc_final: 0.8139 (p) REVERT: J 394 LEU cc_start: 0.8858 (tt) cc_final: 0.8567 (tt) REVERT: J 396 TRP cc_start: 0.8486 (m100) cc_final: 0.8257 (m100) REVERT: J 398 THR cc_start: 0.8557 (p) cc_final: 0.8208 (p) REVERT: J 405 MET cc_start: 0.8421 (tpp) cc_final: 0.7884 (tpp) REVERT: J 406 GLU cc_start: 0.8598 (pt0) cc_final: 0.7944 (tm-30) REVERT: J 409 GLU cc_start: 0.8784 (pt0) cc_final: 0.8025 (pt0) REVERT: J 412 SER cc_start: 0.9145 (m) cc_final: 0.8897 (p) REVERT: B 14 ASN cc_start: 0.8704 (m-40) cc_final: 0.8439 (m-40) REVERT: B 53 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7157 (tm-30) REVERT: B 85 PHE cc_start: 0.7878 (m-80) cc_final: 0.7302 (m-80) REVERT: B 130 LEU cc_start: 0.9250 (tp) cc_final: 0.8972 (tp) REVERT: B 147 MET cc_start: 0.8368 (tmm) cc_final: 0.8058 (tmm) REVERT: B 151 LEU cc_start: 0.9579 (mt) cc_final: 0.9304 (mt) REVERT: B 162 ARG cc_start: 0.7598 (mmt-90) cc_final: 0.7107 (mmt180) REVERT: B 164 MET cc_start: 0.7613 (mmp) cc_final: 0.7101 (mmp) REVERT: B 174 LYS cc_start: 0.8980 (mppt) cc_final: 0.8772 (mppt) REVERT: B 181 GLU cc_start: 0.7881 (tt0) cc_final: 0.7448 (tt0) REVERT: B 198 GLU cc_start: 0.8961 (pm20) cc_final: 0.8464 (pm20) REVERT: B 343 TRP cc_start: 0.7565 (m100) cc_final: 0.6943 (m100) REVERT: B 395 HIS cc_start: 0.8846 (p-80) cc_final: 0.8268 (p-80) REVERT: B 402 MET cc_start: 0.6871 (mtm) cc_final: 0.6649 (mtp) REVERT: C 2 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7535 (mtp180) REVERT: C 6 HIS cc_start: 0.9002 (t70) cc_final: 0.7878 (t-170) REVERT: C 8 GLN cc_start: 0.8408 (mt0) cc_final: 0.7975 (mt0) REVERT: C 14 ASN cc_start: 0.9114 (m110) cc_final: 0.8639 (m-40) REVERT: C 20 PHE cc_start: 0.8443 (t80) cc_final: 0.7616 (t80) REVERT: C 35 ILE cc_start: 0.8849 (mp) cc_final: 0.8436 (mm) REVERT: C 53 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6792 (tm-30) REVERT: C 101 TRP cc_start: 0.8220 (t60) cc_final: 0.7866 (t60) REVERT: C 157 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8554 (tm-30) REVERT: C 189 MET cc_start: 0.8631 (tpp) cc_final: 0.8315 (tpp) REVERT: C 241 ARG cc_start: 0.7490 (mtm110) cc_final: 0.7215 (mtm110) REVERT: C 297 ASN cc_start: 0.9224 (m-40) cc_final: 0.8883 (t0) REVERT: C 359 ASP cc_start: 0.9035 (m-30) cc_final: 0.8788 (m-30) REVERT: C 375 GLU cc_start: 0.7923 (tt0) cc_final: 0.7403 (tm-30) REVERT: C 376 ILE cc_start: 0.8837 (pt) cc_final: 0.8598 (pt) REVERT: C 405 MET cc_start: 0.7805 (mmt) cc_final: 0.7003 (tpp) REVERT: C 408 THR cc_start: 0.8921 (p) cc_final: 0.8363 (p) outliers start: 0 outliers final: 0 residues processed: 979 average time/residue: 0.3823 time to fit residues: 592.4671 Evaluate side-chains 831 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 831 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 334 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 232 optimal weight: 0.7980 chunk 350 optimal weight: 7.9990 chunk 322 optimal weight: 0.0060 chunk 279 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- 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 D 13 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN E 210 ASN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN F 106 ASN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 226 ASN B 256 ASN C 256 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28752 Z= 0.176 Angle : 0.644 10.802 39006 Z= 0.317 Chirality : 0.047 0.189 4200 Planarity : 0.005 0.070 5117 Dihedral : 8.905 162.247 3979 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.04 (0.14), residues: 3543 helix: -0.12 (0.14), residues: 1496 sheet: 0.22 (0.24), residues: 500 loop : -1.54 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP F 350 HIS 0.005 0.001 HIS B 6 PHE 0.023 0.001 PHE H 408 TYR 0.022 0.001 TYR H 214 ARG 0.010 0.001 ARG A 390 ********************** 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 1037 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1036 time to evaluate : 3.338 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: A 6 HIS cc_start: 0.8905 (t-90) cc_final: 0.8068 (t-170) REVERT: A 20 PHE cc_start: 0.8056 (t80) cc_final: 0.7544 (t80) REVERT: A 35 ILE cc_start: 0.8595 (mp) cc_final: 0.8137 (mm) REVERT: A 53 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7179 (tm-30) REVERT: A 147 MET cc_start: 0.8090 (ppp) cc_final: 0.7821 (ppp) REVERT: A 161 ASP cc_start: 0.8693 (m-30) cc_final: 0.8439 (t0) REVERT: A 176 SER cc_start: 0.7852 (t) cc_final: 0.6756 (t) REVERT: A 199 THR cc_start: 0.7726 (m) cc_final: 0.7409 (m) REVERT: A 269 PHE cc_start: 0.8217 (t80) cc_final: 0.7827 (t80) REVERT: A 293 PHE cc_start: 0.7096 (t80) cc_final: 0.6675 (t80) REVERT: A 297 ASN cc_start: 0.9234 (m-40) cc_final: 0.8794 (t0) REVERT: A 365 THR cc_start: 0.8997 (m) cc_final: 0.8716 (p) REVERT: A 375 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 380 LEU cc_start: 0.9243 (mm) cc_final: 0.8711 (tt) REVERT: A 394 LEU cc_start: 0.8556 (tp) cc_final: 0.8350 (tp) REVERT: A 423 GLN cc_start: 0.8333 (mt0) cc_final: 0.7666 (mp10) REVERT: D 32 MET cc_start: 0.6615 (mmm) cc_final: 0.6074 (mmm) REVERT: D 35 ILE cc_start: 0.8021 (mt) cc_final: 0.7757 (mt) REVERT: D 40 TYR cc_start: 0.7943 (m-10) cc_final: 0.7439 (m-10) REVERT: D 71 LYS cc_start: 0.7894 (mttt) cc_final: 0.7680 (mmtp) REVERT: D 92 LEU cc_start: 0.7824 (mt) cc_final: 0.7251 (pp) REVERT: E 18 ASN cc_start: 0.9128 (m110) cc_final: 0.8360 (t0) REVERT: E 21 TRP cc_start: 0.8702 (m100) cc_final: 0.8295 (m100) REVERT: E 23 LEU cc_start: 0.8934 (tt) cc_final: 0.8368 (tp) REVERT: E 24 TYR cc_start: 0.8694 (m-10) cc_final: 0.8386 (m-10) REVERT: E 27 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7426 (mt-10) REVERT: E 59 GLU cc_start: 0.7701 (mt-10) cc_final: 0.5919 (pt0) REVERT: E 65 PHE cc_start: 0.7768 (p90) cc_final: 0.5902 (p90) REVERT: E 73 ASP cc_start: 0.8275 (t0) cc_final: 0.7928 (t0) REVERT: E 94 GLU cc_start: 0.8270 (pp20) cc_final: 0.7206 (tm-30) REVERT: E 97 VAL cc_start: 0.8840 (p) cc_final: 0.8471 (m) REVERT: E 116 LYS cc_start: 0.9078 (tmmt) cc_final: 0.8687 (ttmt) REVERT: E 131 ASP cc_start: 0.7840 (m-30) cc_final: 0.7587 (m-30) REVERT: E 201 ASN cc_start: 0.7920 (m-40) cc_final: 0.7341 (m-40) REVERT: E 255 ASP cc_start: 0.8436 (t70) cc_final: 0.7951 (m-30) REVERT: E 260 GLN cc_start: 0.8668 (pt0) cc_final: 0.8169 (pt0) REVERT: E 270 HIS cc_start: 0.8190 (p-80) cc_final: 0.7903 (p-80) REVERT: E 308 LYS cc_start: 0.8384 (tptp) cc_final: 0.7792 (mmmt) REVERT: E 356 LYS cc_start: 0.8925 (tptm) cc_final: 0.8560 (tppt) REVERT: E 381 MET cc_start: 0.9033 (tmm) cc_final: 0.8132 (tmm) REVERT: F 1 MET cc_start: 0.7824 (ptp) cc_final: 0.7504 (ptp) REVERT: F 21 TRP cc_start: 0.8473 (m100) cc_final: 0.7513 (m100) REVERT: F 24 TYR cc_start: 0.8780 (m-10) cc_final: 0.8229 (m-10) REVERT: F 30 ILE cc_start: 0.9359 (mt) cc_final: 0.9087 (mm) REVERT: F 69 SER cc_start: 0.8947 (p) cc_final: 0.8302 (p) REVERT: F 131 ASP cc_start: 0.7873 (m-30) cc_final: 0.7576 (m-30) REVERT: F 173 PHE cc_start: 0.8486 (m-10) cc_final: 0.8142 (m-10) REVERT: F 239 VAL cc_start: 0.8841 (t) cc_final: 0.8520 (t) REVERT: F 247 ARG cc_start: 0.6596 (mmt90) cc_final: 0.5174 (mmt180) REVERT: F 255 ASP cc_start: 0.8495 (t70) cc_final: 0.8217 (m-30) REVERT: F 257 ASN cc_start: 0.9018 (t0) cc_final: 0.8516 (t0) REVERT: F 320 CYS cc_start: 0.8577 (t) cc_final: 0.7655 (t) REVERT: F 381 MET cc_start: 0.8292 (ttt) cc_final: 0.7503 (ttp) REVERT: F 399 PHE cc_start: 0.8355 (t80) cc_final: 0.8148 (t80) REVERT: F 429 LEU cc_start: 0.8860 (tp) cc_final: 0.8582 (tp) REVERT: F 441 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8603 (tm-30) REVERT: G 14 VAL cc_start: 0.9461 (t) cc_final: 0.8815 (t) REVERT: G 23 LEU cc_start: 0.9193 (tp) cc_final: 0.8384 (tp) REVERT: G 27 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7609 (mt-10) REVERT: G 59 GLU cc_start: 0.6827 (mt-10) cc_final: 0.5577 (pt0) REVERT: G 71 TYR cc_start: 0.6571 (m-80) cc_final: 0.5989 (m-80) REVERT: G 94 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7952 (tp30) REVERT: G 124 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8589 (tt0) REVERT: G 143 HIS cc_start: 0.8630 (p90) cc_final: 0.8110 (p90) REVERT: G 180 GLN cc_start: 0.8849 (pm20) cc_final: 0.8623 (pm20) REVERT: G 206 PHE cc_start: 0.9155 (m-80) cc_final: 0.8769 (m-80) REVERT: G 304 ASN cc_start: 0.9152 (t0) cc_final: 0.8949 (t0) REVERT: G 343 ARG cc_start: 0.8816 (ptm160) cc_final: 0.8031 (mtt180) REVERT: G 351 CYS cc_start: 0.8659 (t) cc_final: 0.8397 (t) REVERT: G 374 LYS cc_start: 0.9165 (tttm) cc_final: 0.8607 (tptp) REVERT: G 380 CYS cc_start: 0.8954 (t) cc_final: 0.8580 (p) REVERT: G 381 MET cc_start: 0.9300 (tmm) cc_final: 0.8568 (tmm) REVERT: G 399 PHE cc_start: 0.8730 (t80) cc_final: 0.8444 (t80) REVERT: G 426 ARG cc_start: 0.9128 (mmp80) cc_final: 0.8765 (mmp80) REVERT: H 2 ARG cc_start: 0.5281 (mtp180) cc_final: 0.4630 (mmt180) REVERT: H 20 CYS cc_start: 0.8648 (m) cc_final: 0.8398 (m) REVERT: H 57 PHE cc_start: 0.8047 (m-80) cc_final: 0.6825 (m-80) REVERT: H 204 CYS cc_start: 0.8616 (p) cc_final: 0.8328 (p) REVERT: H 219 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7128 (mtm110) REVERT: H 237 GLN cc_start: 0.8527 (mt0) cc_final: 0.7637 (tt0) REVERT: H 266 TYR cc_start: 0.8859 (m-80) cc_final: 0.8617 (m-80) REVERT: H 276 TYR cc_start: 0.8012 (t80) cc_final: 0.7194 (t80) REVERT: H 308 LYS cc_start: 0.8622 (tptp) cc_final: 0.8231 (mmtt) REVERT: H 346 GLN cc_start: 0.8437 (mp10) cc_final: 0.7770 (tp40) REVERT: H 351 CYS cc_start: 0.8497 (t) cc_final: 0.7617 (p) REVERT: H 441 GLN cc_start: 0.8830 (mm110) cc_final: 0.8419 (tm-30) REVERT: J 6 HIS cc_start: 0.8911 (t70) cc_final: 0.8599 (t-170) REVERT: J 8 GLN cc_start: 0.8334 (mt0) cc_final: 0.8039 (mt0) REVERT: J 21 TRP cc_start: 0.9003 (m100) cc_final: 0.8464 (m100) REVERT: J 50 TYR cc_start: 0.7986 (m-10) cc_final: 0.7559 (m-10) REVERT: J 53 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7206 (tm-30) REVERT: J 111 GLU cc_start: 0.7965 (tt0) cc_final: 0.7659 (tp30) REVERT: J 157 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8271 (tm-30) REVERT: J 189 MET cc_start: 0.8905 (mmt) cc_final: 0.8552 (mmp) REVERT: J 198 GLU cc_start: 0.8893 (pm20) cc_final: 0.8039 (tp30) REVERT: J 216 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8761 (mmmt) REVERT: J 228 LEU cc_start: 0.9392 (tp) cc_final: 0.9101 (tp) REVERT: J 266 MET cc_start: 0.8678 (mtm) cc_final: 0.8244 (mtm) REVERT: J 292 MET cc_start: 0.8028 (mpp) cc_final: 0.7643 (mpp) REVERT: J 322 MET cc_start: 0.9049 (mmm) cc_final: 0.8661 (mmm) REVERT: J 362 MET cc_start: 0.8837 (mmm) cc_final: 0.8563 (mmm) REVERT: J 365 THR cc_start: 0.8657 (m) cc_final: 0.7951 (p) REVERT: J 405 MET cc_start: 0.8309 (tpp) cc_final: 0.7815 (tpp) REVERT: J 406 GLU cc_start: 0.8618 (pt0) cc_final: 0.7838 (tm-30) REVERT: J 409 GLU cc_start: 0.8748 (pt0) cc_final: 0.8066 (pt0) REVERT: J 412 SER cc_start: 0.9146 (m) cc_final: 0.8905 (p) REVERT: J 423 GLN cc_start: 0.8254 (mt0) cc_final: 0.7594 (mp10) REVERT: B 21 TRP cc_start: 0.9089 (m100) cc_final: 0.8509 (m100) REVERT: B 85 PHE cc_start: 0.7771 (m-80) cc_final: 0.7157 (m-10) REVERT: B 86 ARG cc_start: 0.7536 (ptp-170) cc_final: 0.7306 (ptp-170) REVERT: B 103 LYS cc_start: 0.8502 (tttp) cc_final: 0.8298 (tttp) REVERT: B 147 MET cc_start: 0.8238 (tmm) cc_final: 0.7874 (tmm) REVERT: B 151 LEU cc_start: 0.9596 (mt) cc_final: 0.9379 (mt) REVERT: B 164 MET cc_start: 0.7646 (mmp) cc_final: 0.7086 (mmp) REVERT: B 174 LYS cc_start: 0.8951 (mppt) cc_final: 0.8746 (mppt) REVERT: B 181 GLU cc_start: 0.7716 (tt0) cc_final: 0.7384 (tt0) REVERT: B 198 GLU cc_start: 0.8934 (pm20) cc_final: 0.8455 (pm20) REVERT: B 343 TRP cc_start: 0.7505 (m100) cc_final: 0.7301 (m100) REVERT: B 395 HIS cc_start: 0.8793 (p-80) cc_final: 0.8206 (p-80) REVERT: B 420 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7362 (mm-30) REVERT: C 6 HIS cc_start: 0.8952 (t70) cc_final: 0.7858 (t-170) REVERT: C 8 GLN cc_start: 0.8233 (mt0) cc_final: 0.7803 (mt0) REVERT: C 14 ASN cc_start: 0.9044 (m110) cc_final: 0.8619 (m-40) REVERT: C 20 PHE cc_start: 0.8292 (t80) cc_final: 0.7550 (t80) REVERT: C 35 ILE cc_start: 0.8723 (mp) cc_final: 0.8320 (mm) REVERT: C 53 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6572 (tm-30) REVERT: C 101 TRP cc_start: 0.8052 (t60) cc_final: 0.7615 (t60) REVERT: C 147 MET cc_start: 0.7885 (ppp) cc_final: 0.7393 (ppp) REVERT: C 157 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8509 (tm-30) REVERT: C 163 MET cc_start: 0.7059 (pmm) cc_final: 0.6419 (pmm) REVERT: C 164 MET cc_start: 0.8274 (mmm) cc_final: 0.7590 (mmm) REVERT: C 189 MET cc_start: 0.8592 (tpp) cc_final: 0.8278 (tpp) REVERT: C 223 ASP cc_start: 0.8795 (m-30) cc_final: 0.8123 (t70) REVERT: C 232 VAL cc_start: 0.9348 (t) cc_final: 0.9109 (p) REVERT: C 241 ARG cc_start: 0.7306 (mtm110) cc_final: 0.7097 (mtm110) REVERT: C 297 ASN cc_start: 0.9101 (m-40) cc_final: 0.8851 (t0) REVERT: C 359 ASP cc_start: 0.9025 (m-30) cc_final: 0.8772 (m-30) REVERT: C 361 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8609 (ttmm) REVERT: C 375 GLU cc_start: 0.7892 (tt0) cc_final: 0.7504 (tm-30) REVERT: C 376 ILE cc_start: 0.8805 (pt) cc_final: 0.8528 (pt) REVERT: C 395 HIS cc_start: 0.8992 (p-80) cc_final: 0.8673 (p-80) REVERT: C 405 MET cc_start: 0.7844 (mmt) cc_final: 0.7168 (tpp) REVERT: C 408 THR cc_start: 0.8922 (p) cc_final: 0.8629 (p) outliers start: 1 outliers final: 0 residues processed: 1037 average time/residue: 0.3815 time to fit residues: 625.7202 Evaluate side-chains 830 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 830 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 257 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 8 HIS E 132 ASN E 172 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN F 8 HIS F 106 ASN F 210 ASN F 237 GLN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 83 ASN C 184 ASN C 256 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.118936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102957 restraints weight = 61596.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106544 restraints weight = 35797.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108966 restraints weight = 22834.487| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.7351 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= 0.217 Angle : 0.667 10.622 39006 Z= 0.332 Chirality : 0.048 0.180 4200 Planarity : 0.005 0.081 5117 Dihedral : 8.926 163.199 3979 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.07 % Allowed : 0.30 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.08 (0.14), residues: 3543 helix: -0.11 (0.14), residues: 1500 sheet: 0.19 (0.24), residues: 524 loop : -1.62 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP F 350 HIS 0.009 0.001 HIS F 8 PHE 0.037 0.002 PHE F 408 TYR 0.029 0.002 TYR H 107 ARG 0.009 0.001 ARG J 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9271.91 seconds wall clock time: 166 minutes 49.29 seconds (10009.29 seconds total)