Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 14:26:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/04_2023/5mjs_3522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/04_2023/5mjs_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_3522/04_2023/5mjs_3522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/04_2023/5mjs_3522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/04_2023/5mjs_3522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mjs_3522/04_2023/5mjs_3522.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 15.05, per 1000 atoms: 0.54 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: 11.15 Conformation dependent library (CDL) restraints added in 5.2 seconds 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6578 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 28 sheets defined 45.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 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: 8.27 Time building geometry restraints manager: 12.10 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: 0.150 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: 3.280 Check model and map are aligned: 0.420 Set scattering table: 0.220 Process input model: 68.110 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.190 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.900 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 3.127 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 outliers start: 20 outliers final: 3 residues processed: 1459 average time/residue: 0.4298 time to fit residues: 963.6200 Evaluate side-chains 877 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 874 time to evaluate : 3.431 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2887 time to fit residues: 6.0349 ------------------------------------------------------------------------------- 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: 9.9990 chunk 148 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 319 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 134 GLN 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 61 ASN D 66 GLN 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 210 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 201 ASN ** F 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 ASN 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 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN H 441 GLN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 191 GLN J 195 ASN J 415 ASN B 134 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN 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: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4082 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= 0.211 Angle : 0.708 11.654 39006 Z= 0.367 Chirality : 0.049 0.234 4200 Planarity : 0.007 0.076 5117 Dihedral : 10.563 156.473 3979 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.43 % 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: 1434 sheet: -0.80 (0.22), residues: 512 loop : -2.28 (0.14), residues: 1597 *********************** 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 1184 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1171 time to evaluate : 2.998 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 outliers start: 13 outliers final: 1 residues processed: 1174 average time/residue: 0.4061 time to fit residues: 775.9826 Evaluate side-chains 866 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 865 time to evaluate : 3.287 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2766 time to fit residues: 5.0254 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 40.0000 chunk 345 optimal weight: 40.0000 chunk 285 optimal weight: 40.0000 chunk 317 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 chunk 256 optimal weight: 30.0000 overall best weight: 7.5792 ------------------------------------------------------------------------------- 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 134 GLN 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 91 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** F 333 GLN ** 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 230 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 134 GLN B 190 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 28752 Z= 0.278 Angle : 0.707 9.523 39006 Z= 0.364 Chirality : 0.049 0.265 4200 Planarity : 0.006 0.077 5117 Dihedral : 10.098 156.748 3979 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.13), residues: 3543 helix: -1.60 (0.12), residues: 1450 sheet: -0.67 (0.22), residues: 536 loop : -2.03 (0.15), residues: 1557 *********************** 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 1056 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1049 time to evaluate : 3.311 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 outliers start: 7 outliers final: 1 residues processed: 1053 average time/residue: 0.4060 time to fit residues: 678.4461 Evaluate side-chains 842 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 841 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2516 time to fit residues: 4.9208 ------------------------------------------------------------------------------- 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: 6.9990 chunk 240 optimal weight: 40.0000 chunk 166 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 321 optimal weight: 20.0000 chunk 340 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 overall best weight: 8.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 83 ASN A 226 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 328 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** G 92 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** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN H 230 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 422 GLN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 328 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 28752 Z= 0.304 Angle : 0.727 10.702 39006 Z= 0.373 Chirality : 0.051 0.319 4200 Planarity : 0.006 0.079 5117 Dihedral : 9.962 157.137 3979 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 0.27 % 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: -2.23 (0.13), residues: 3543 helix: -1.30 (0.13), residues: 1460 sheet: -0.37 (0.23), residues: 516 loop : -1.97 (0.15), residues: 1567 *********************** 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 992 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 984 time to evaluate : 3.509 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 outliers start: 8 outliers final: 1 residues processed: 990 average time/residue: 0.3862 time to fit residues: 611.3902 Evaluate side-chains 792 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 791 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2600 time to fit residues: 4.8975 ------------------------------------------------------------------------------- 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: 9.9990 chunk 193 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 253 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 290 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 173 optimal weight: 0.5980 chunk 305 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 296 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 172 GLN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 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 256 ASN C 297 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 28752 Z= 0.217 Angle : 0.659 10.444 39006 Z= 0.332 Chirality : 0.048 0.213 4200 Planarity : 0.005 0.077 5117 Dihedral : 9.546 159.058 3979 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.93 (0.14), residues: 3543 helix: -0.97 (0.13), residues: 1464 sheet: -0.25 (0.23), residues: 516 loop : -1.88 (0.15), residues: 1563 *********************** 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 991 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 989 time to evaluate : 3.100 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 outliers start: 2 outliers final: 0 residues processed: 991 average time/residue: 0.3879 time to fit residues: 611.1111 Evaluate side-chains 810 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 3.073 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1877 ------------------------------------------------------------------------------- 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: 20.0000 chunk 306 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 83 optimal weight: 40.0000 chunk 340 optimal weight: 30.0000 chunk 282 optimal weight: 40.0000 chunk 157 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 178 optimal weight: 6.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 28 HIS E 106 ASN E 172 GLN E 237 GLN E 262 ASN F 28 HIS ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN J 99 ASN ** J 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 297 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 28752 Z= 0.335 Angle : 0.752 9.056 39006 Z= 0.385 Chirality : 0.052 0.247 4200 Planarity : 0.006 0.067 5117 Dihedral : 9.762 157.126 3979 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer Outliers : 0.07 % 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: -1.96 (0.14), residues: 3543 helix: -0.96 (0.13), residues: 1423 sheet: -0.24 (0.23), residues: 516 loop : -1.92 (0.15), residues: 1604 *********************** 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 952 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 950 time to evaluate : 3.367 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 outliers start: 2 outliers final: 0 residues processed: 951 average time/residue: 0.4017 time to fit residues: 611.2847 Evaluate side-chains 781 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 781 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3550 ------------------------------------------------------------------------------- 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: 8.9990 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 190 optimal weight: 0.0980 chunk 339 optimal weight: 10.0000 chunk 212 optimal weight: 50.0000 chunk 206 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 226 ASN ** A 247 ASN ** 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** 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 270 HIS ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 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 256 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 28752 Z= 0.212 Angle : 0.679 15.220 39006 Z= 0.341 Chirality : 0.048 0.246 4200 Planarity : 0.005 0.062 5117 Dihedral : 9.370 159.105 3979 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.03 % 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: -1.67 (0.14), residues: 3543 helix: -0.64 (0.13), residues: 1421 sheet: -0.19 (0.24), residues: 500 loop : -1.80 (0.15), residues: 1622 *********************** 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 973 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 972 time to evaluate : 3.260 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 outliers start: 1 outliers final: 0 residues processed: 972 average time/residue: 0.3969 time to fit residues: 612.8650 Evaluate side-chains 794 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 794 time to evaluate : 3.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8307 ------------------------------------------------------------------------------- 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: 30.0000 chunk 135 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 134 GLN A 226 ASN 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 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN E 237 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 256 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** 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: 0.8021 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 28752 Z= 0.256 Angle : 0.707 12.401 39006 Z= 0.357 Chirality : 0.050 0.293 4200 Planarity : 0.005 0.069 5117 Dihedral : 9.352 158.446 3979 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.03 % 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: -1.75 (0.14), residues: 3543 helix: -0.74 (0.13), residues: 1488 sheet: -0.11 (0.24), residues: 496 loop : -1.88 (0.15), residues: 1559 *********************** 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 946 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 945 time to evaluate : 3.309 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 outliers start: 1 outliers final: 0 residues processed: 945 average time/residue: 0.3940 time to fit residues: 594.3622 Evaluate side-chains 785 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 785 time to evaluate : 3.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1719 ------------------------------------------------------------------------------- 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: 7.9990 chunk 296 optimal weight: 7.9990 chunk 316 optimal weight: 0.0670 chunk 324 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 299 optimal weight: 30.0000 overall best weight: 6.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 172 GLN E 237 GLN E 262 ASN F 62 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN H 210 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS J 44 HIS ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 28752 Z= 0.245 Angle : 0.698 11.205 39006 Z= 0.352 Chirality : 0.049 0.209 4200 Planarity : 0.005 0.075 5117 Dihedral : 9.310 158.380 3979 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 0.07 % 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: -1.67 (0.14), residues: 3543 helix: -0.67 (0.13), residues: 1488 sheet: -0.15 (0.24), residues: 508 loop : -1.82 (0.15), residues: 1547 *********************** 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 936 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 934 time to evaluate : 3.302 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 outliers start: 2 outliers final: 0 residues processed: 935 average time/residue: 0.3941 time to fit residues: 587.2131 Evaluate side-chains 769 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 769 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3195 ------------------------------------------------------------------------------- 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: 0.7980 chunk 207 optimal weight: 2.9990 chunk 334 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 322 optimal weight: 30.0000 chunk 279 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 215 optimal weight: 0.2980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 99 ASN A 134 GLN D 13 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 172 GLN E 237 GLN E 262 ASN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 210 ASN F 237 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 HIS ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 89 ASN B 226 ASN B 296 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.7576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 28752 Z= 0.196 Angle : 0.690 11.824 39006 Z= 0.343 Chirality : 0.048 0.196 4200 Planarity : 0.005 0.067 5117 Dihedral : 9.084 160.170 3979 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.51 (0.14), residues: 3543 helix: -0.51 (0.13), residues: 1488 sheet: -0.08 (0.24), residues: 500 loop : -1.75 (0.15), residues: 1555 ********************** 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 961 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 957 time to evaluate : 3.302 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 outliers start: 4 outliers final: 0 residues processed: 961 average time/residue: 0.3993 time to fit residues: 613.6709 Evaluate side-chains 777 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 777 time to evaluate : 3.275 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4280 ------------------------------------------------------------------------------- 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: 30.0000 chunk 221 optimal weight: 4.9990 chunk 297 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 279 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 287 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 99 ASN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 106 ASN E 172 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN F 28 HIS ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 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 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** 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** H 143 HIS H 210 ASN H 237 GLN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS B 8 GLN B 83 ASN B 89 ASN B 226 ASN B 297 ASN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 281 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.122212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106385 restraints weight = 61030.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.109980 restraints weight = 34885.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112429 restraints weight = 21988.996| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 28752 Z= 0.187 Angle : 0.691 17.388 39006 Z= 0.342 Chirality : 0.048 0.198 4200 Planarity : 0.005 0.063 5117 Dihedral : 8.933 162.784 3979 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.07 % 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: -1.43 (0.14), residues: 3543 helix: -0.48 (0.13), residues: 1511 sheet: 0.08 (0.24), residues: 504 loop : -1.75 (0.15), residues: 1528 =============================================================================== Job complete usr+sys time: 8960.04 seconds wall clock time: 161 minutes 19.45 seconds (9679.45 seconds total)