Starting phenix.real_space_refine on Thu Mar 5 17:29:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l70_23209/03_2026/7l70_23209_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l70_23209/03_2026/7l70_23209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l70_23209/03_2026/7l70_23209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l70_23209/03_2026/7l70_23209.map" model { file = "/net/cci-nas-00/data/ceres_data/7l70_23209/03_2026/7l70_23209_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l70_23209/03_2026/7l70_23209_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.073 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: 4 Type Number sf(0) Gaussians S 137 5.16 5 C 15414 2.51 5 N 4221 2.21 5 O 4415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24187 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3195 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3195 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2479 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2734 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2693 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328} Chain: "G" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1977 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1966 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1682 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 205} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1794 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 5.63, per 1000 atoms: 0.23 Number of scatterers: 24187 At special positions: 0 Unit cell: (134.435, 174.515, 125.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 137 16.00 O 4415 8.00 N 4221 7.00 C 15414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 31 sheets defined 44.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.797A pdb=" N ASP A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.738A pdb=" N LEU A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.621A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.623A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.657A pdb=" N CYS A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.959A pdb=" N SER A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.752A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.957A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.609A pdb=" N ALA A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.797A pdb=" N ASP B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.621A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.623A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.657A pdb=" N CYS B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.959A pdb=" N SER B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.753A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.957A pdb=" N ASN B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.608A pdb=" N ALA B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 25 removed outlier: 3.648A pdb=" N GLY C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.545A pdb=" N ASP C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.917A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 98 removed outlier: 3.868A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.515A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 removed outlier: 3.955A pdb=" N ALA C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.529A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.653A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.975A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 304' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.532A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.736A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.679A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 98 removed outlier: 3.624A pdb=" N MET D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 153 removed outlier: 4.355A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.892A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.571A pdb=" N LEU D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.769A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 4.213A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.810A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.978A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 3.729A pdb=" N LEU E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 removed outlier: 3.544A pdb=" N ALA E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP E 305 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 325 removed outlier: 4.352A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 380 removed outlier: 4.134A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 removed outlier: 3.534A pdb=" N VAL E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 418 through 430 removed outlier: 4.687A pdb=" N GLN E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 423 " --> pdb=" O GLY E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.804A pdb=" N LYS E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 443' Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.540A pdb=" N ASP E 462 " --> pdb=" O ASP E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 511 through 517 Processing helix chain 'F' and resid 204 through 217 Processing helix chain 'F' and resid 221 through 239 removed outlier: 3.594A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.380A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 313 through 323 removed outlier: 3.783A pdb=" N GLN F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 319 " --> pdb=" O ALA F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 353 removed outlier: 3.740A pdb=" N GLY F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 378 removed outlier: 4.056A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.577A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.575A pdb=" N VAL F 497 " --> pdb=" O PRO F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 517 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.609A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 3.636A pdb=" N GLY G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.838A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 116 removed outlier: 4.646A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 143 Processing helix chain 'G' and resid 160 through 170 removed outlier: 3.565A pdb=" N HIS G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.835A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 221 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.888A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE G 235 " --> pdb=" O SER G 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 231 through 235' Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.699A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 295 through 304 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 21 through 35 removed outlier: 3.813A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 60 Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.695A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 106 removed outlier: 4.004A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.656A pdb=" N LEU H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 143 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 186 through 190 Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.834A pdb=" N LYS H 234 " --> pdb=" O GLU H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.580A pdb=" N LYS H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.567A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 43 removed outlier: 3.617A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 113 through 123 removed outlier: 4.153A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 223 through 234 removed outlier: 4.770A pdb=" N ILE I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 4.020A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 28 removed outlier: 3.562A pdb=" N LEU J 28 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 44 removed outlier: 3.744A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 3.612A pdb=" N ILE J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 124 removed outlier: 4.014A pdb=" N VAL J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 208 through 218 removed outlier: 4.084A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN J 218 " --> pdb=" O PHE J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 236 Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.906A pdb=" N SER J 331 " --> pdb=" O PRO J 327 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.484A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 149 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 251 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 180 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 214 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.537A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.262A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.278A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.891A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.689A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 448 " --> pdb=" O GLU A 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.484A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 149 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 251 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 180 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN B 286 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 181 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE B 287 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 214 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS J 196 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE J 158 " --> pdb=" O HIS J 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.538A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.263A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.277A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 401 through 402 removed outlier: 6.891A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 430 through 431 removed outlier: 6.690A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 448 " --> pdb=" O GLU B 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.487A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 231 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.508A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.466A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR F 336 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY F 404 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.853A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.237A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.445A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY G 196 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC7, first strand: chain 'H' and resid 177 through 178 removed outlier: 7.218A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 286 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AC9, first strand: chain 'I' and resid 51 through 53 removed outlier: 3.872A pdb=" N ALA I 202 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AD2, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AD3, first strand: chain 'J' and resid 101 through 103 Processing sheet with id=AD4, first strand: chain 'J' and resid 132 through 134 973 hydrogen bonds defined for protein. 2724 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: 4.99 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3950 1.31 - 1.44: 6229 1.44 - 1.56: 14247 1.56 - 1.69: 2 1.69 - 1.81: 208 Bond restraints: 24636 Sorted by residual: bond pdb=" CA SER H 62 " pdb=" C SER H 62 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.23e-02 6.61e+03 1.59e+01 bond pdb=" CA ARG G 46 " pdb=" C ARG G 46 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.32e-02 5.74e+03 1.56e+01 bond pdb=" C LEU H 56 " pdb=" O LEU H 56 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.40e+01 bond pdb=" C ASP H 60 " pdb=" O ASP H 60 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.34e+01 bond pdb=" C SER H 62 " pdb=" O SER H 62 " ideal model delta sigma weight residual 1.234 1.188 0.046 1.26e-02 6.30e+03 1.32e+01 ... (remaining 24631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 33103 2.51 - 5.02: 276 5.02 - 7.54: 42 7.54 - 10.05: 5 10.05 - 12.56: 5 Bond angle restraints: 33431 Sorted by residual: angle pdb=" C ASP G 19 " pdb=" N MET G 20 " pdb=" CA MET G 20 " ideal model delta sigma weight residual 120.90 130.06 -9.16 1.41e+00 5.03e-01 4.22e+01 angle pdb=" N PRO G 18 " pdb=" CA PRO G 18 " pdb=" C PRO G 18 " ideal model delta sigma weight residual 113.53 122.30 -8.77 1.39e+00 5.18e-01 3.98e+01 angle pdb=" CA GLU A 104 " pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " ideal model delta sigma weight residual 114.10 126.66 -12.56 2.00e+00 2.50e-01 3.95e+01 angle pdb=" CA GLU B 104 " pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " ideal model delta sigma weight residual 114.10 126.64 -12.54 2.00e+00 2.50e-01 3.93e+01 angle pdb=" N ASP G 60 " pdb=" CA ASP G 60 " pdb=" C ASP G 60 " ideal model delta sigma weight residual 107.62 119.31 -11.69 1.97e+00 2.58e-01 3.52e+01 ... (remaining 33426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 14145 24.05 - 48.10: 628 48.10 - 72.14: 131 72.14 - 96.19: 25 96.19 - 120.24: 2 Dihedral angle restraints: 14931 sinusoidal: 5787 harmonic: 9144 Sorted by residual: dihedral pdb=" CA PHE A 57 " pdb=" C PHE A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 59.76 120.24 0 5.00e+00 4.00e-02 5.78e+02 dihedral pdb=" CA PHE B 57 " pdb=" C PHE B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual 180.00 59.89 120.11 0 5.00e+00 4.00e-02 5.77e+02 dihedral pdb=" CA GLU C 281 " pdb=" C GLU C 281 " pdb=" N GLU C 282 " pdb=" CA GLU C 282 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 14928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.556: 3963 0.556 - 1.112: 4 1.112 - 1.668: 0 1.668 - 2.224: 0 2.224 - 2.780: 1 Chirality restraints: 3968 Sorted by residual: chirality pdb=" CG LEU G 49 " pdb=" CB LEU G 49 " pdb=" CD1 LEU G 49 " pdb=" CD2 LEU G 49 " both_signs ideal model delta sigma weight residual False -2.59 0.19 -2.78 2.00e-01 2.50e+01 1.93e+02 chirality pdb=" CG LEU A 70 " pdb=" CB LEU A 70 " pdb=" CD1 LEU A 70 " pdb=" CD2 LEU A 70 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CG LEU B 70 " pdb=" CB LEU B 70 " pdb=" CD1 LEU B 70 " pdb=" CD2 LEU B 70 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.31e+01 ... (remaining 3965 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 13 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLN G 13 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN G 13 " 0.023 2.00e-02 2.50e+03 pdb=" N MET G 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 384 " 0.019 2.00e-02 2.50e+03 2.13e-02 6.79e+00 pdb=" CG HIS B 384 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS B 384 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 384 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS B 384 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 384 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 384 " -0.019 2.00e-02 2.50e+03 2.12e-02 6.77e+00 pdb=" CG HIS A 384 " 0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS A 384 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 384 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 384 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 384 " -0.006 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 65 2.44 - 3.05: 15438 3.05 - 3.67: 35504 3.67 - 4.28: 52752 4.28 - 4.90: 90401 Nonbonded interactions: 194160 Sorted by model distance: nonbonded pdb=" O ASN G 48 " pdb=" OG SER G 51 " model vdw 1.824 3.040 nonbonded pdb=" OG1 THR D 76 " pdb=" OG1 THR D 238 " model vdw 1.958 3.040 nonbonded pdb=" OG SER B 130 " pdb=" O GLN B 267 " model vdw 2.030 3.040 nonbonded pdb=" OG SER A 130 " pdb=" O GLN A 267 " model vdw 2.030 3.040 nonbonded pdb=" O LYS J 328 " pdb=" OG SER J 331 " model vdw 2.052 3.040 ... (remaining 194155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 279 or (resid 280 through 283 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 through 351)) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 172 through 517) selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 9 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 14 or (resid 15 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 74 or (resi \ d 75 through 76 and (name N or name CA or name C or name O or name CB )) or resi \ d 77 or resid 91 through 305)) selection = (chain 'H' and (resid 9 through 58 or (resid 59 through 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 305)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB )) or resid 58 through 60 or resid 85 through 106 or (resi \ d 107 and (name N or name CA or name C or name O or name CB )) or resid 108 thro \ ugh 135 or (resid 157 and (name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 158 through \ 236 or resid 298 through 334)) } 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 individual isotropic 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.320 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.003 0.073 24636 Z= 0.191 Angle : 0.583 12.562 33431 Z= 0.336 Chirality : 0.071 2.780 3968 Planarity : 0.003 0.065 4248 Dihedral : 14.391 120.238 8985 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 13.31 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.14), residues: 3080 helix: -0.15 (0.15), residues: 1187 sheet: -2.05 (0.23), residues: 425 loop : -2.31 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 274 TYR 0.007 0.001 TYR J 210 PHE 0.017 0.001 PHE A 57 TRP 0.005 0.000 TRP C 51 HIS 0.024 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00310 (24636) covalent geometry : angle 0.58266 (33431) hydrogen bonds : bond 0.18038 ( 973) hydrogen bonds : angle 5.78493 ( 2724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 381 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7197 (t-100) cc_final: 0.6366 (t60) REVERT: A 173 LYS cc_start: 0.6795 (mptt) cc_final: 0.6566 (mptt) REVERT: B 109 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 370 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7883 (m) REVERT: B 371 ASN cc_start: 0.7987 (m-40) cc_final: 0.7498 (p0) REVERT: C 203 MET cc_start: 0.8027 (ttt) cc_final: 0.7787 (ttm) REVERT: E 235 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7534 (tp-100) REVERT: E 249 SER cc_start: 0.8243 (t) cc_final: 0.7730 (m) REVERT: E 467 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7175 (mmm160) REVERT: F 495 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7238 (pt0) REVERT: G 45 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7321 (tm) REVERT: G 54 GLU cc_start: 0.5415 (tp30) cc_final: 0.4940 (tp30) REVERT: H 139 GLU cc_start: 0.7952 (tt0) cc_final: 0.7494 (tm-30) REVERT: I 100 ASP cc_start: 0.7979 (m-30) cc_final: 0.7701 (m-30) REVERT: I 320 MET cc_start: 0.8380 (mmt) cc_final: 0.8174 (pp-130) REVERT: J 50 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7551 (mt-10) outliers start: 70 outliers final: 23 residues processed: 444 average time/residue: 0.6467 time to fit residues: 327.7852 Evaluate side-chains 230 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain J residue 158 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 44 GLN B 337 HIS B 376 ASN B 410 GLN C 130 GLN C 158 HIS C 160 HIS C 252 HIS D 80 ASN D 158 HIS D 160 HIS D 331 ASN E 213 GLN ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS E 431 ASN E 448 GLN F 213 GLN F 448 GLN F 455 ASN F 464 GLN G 222 GLN G 243 GLN H 43 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 GLN H 243 GLN J 41 ASN J 236 GLN J 303 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.110978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089725 restraints weight = 49239.047| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.72 r_work: 0.3401 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24636 Z= 0.223 Angle : 0.662 9.571 33431 Z= 0.335 Chirality : 0.046 0.168 3968 Planarity : 0.005 0.096 4248 Dihedral : 6.253 126.968 3415 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 4.45 % Allowed : 17.03 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 3080 helix: 0.74 (0.15), residues: 1191 sheet: -1.54 (0.23), residues: 413 loop : -1.49 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 28 TYR 0.039 0.002 TYR C 126 PHE 0.024 0.002 PHE B 57 TRP 0.007 0.001 TRP A 317 HIS 0.007 0.001 HIS J 196 Details of bonding type rmsd covalent geometry : bond 0.00539 (24636) covalent geometry : angle 0.66212 (33431) hydrogen bonds : bond 0.04300 ( 973) hydrogen bonds : angle 4.22177 ( 2724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 222 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7616 (t-100) cc_final: 0.6334 (t60) REVERT: A 181 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8225 (ttp) REVERT: A 305 MET cc_start: 0.7967 (tpt) cc_final: 0.7658 (tpp) REVERT: B 54 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7899 (ttt180) REVERT: B 109 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.7603 (p) REVERT: B 370 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7234 (m) REVERT: B 371 ASN cc_start: 0.7899 (m-40) cc_final: 0.7042 (p0) REVERT: C 340 MET cc_start: 0.7747 (mtm) cc_final: 0.7317 (tpp) REVERT: D 213 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6191 (tm-30) REVERT: E 171 LYS cc_start: 0.8413 (ptmm) cc_final: 0.8070 (pmtt) REVERT: E 235 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8001 (mm-40) REVERT: E 247 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7838 (tm-30) REVERT: E 467 ARG cc_start: 0.7822 (mpt180) cc_final: 0.6982 (mmm160) REVERT: F 235 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: F 415 MET cc_start: 0.8673 (tmm) cc_final: 0.8395 (tpp) REVERT: G 164 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7495 (tpt) REVERT: H 139 GLU cc_start: 0.8233 (tt0) cc_final: 0.7476 (tm-30) REVERT: I 100 ASP cc_start: 0.8405 (m-30) cc_final: 0.7884 (m-30) REVERT: I 227 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7928 (mt-10) REVERT: I 320 MET cc_start: 0.8637 (mmt) cc_final: 0.8167 (pp-130) REVERT: J 49 GLU cc_start: 0.7948 (pm20) cc_final: 0.7320 (pm20) REVERT: J 50 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7602 (mt-10) outliers start: 117 outliers final: 49 residues processed: 326 average time/residue: 0.5551 time to fit residues: 212.3651 Evaluate side-chains 244 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 68 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 376 ASN B 302 ASN B 359 ASN C 80 ASN D 331 ASN ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 185 GLN F 223 ASN G 244 GLN H 43 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.108190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086978 restraints weight = 49367.361| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.66 r_work: 0.3427 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24636 Z= 0.123 Angle : 0.548 7.913 33431 Z= 0.278 Chirality : 0.043 0.149 3968 Planarity : 0.004 0.120 4248 Dihedral : 5.195 77.970 3398 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 4.56 % Allowed : 17.11 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3080 helix: 1.22 (0.16), residues: 1185 sheet: -1.21 (0.24), residues: 404 loop : -1.13 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 46 TYR 0.030 0.001 TYR C 126 PHE 0.017 0.001 PHE D 272 TRP 0.007 0.001 TRP I 37 HIS 0.005 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00292 (24636) covalent geometry : angle 0.54797 (33431) hydrogen bonds : bond 0.03558 ( 973) hydrogen bonds : angle 3.89368 ( 2724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 209 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7627 (t-100) cc_final: 0.6445 (t60) REVERT: A 130 SER cc_start: 0.7052 (OUTLIER) cc_final: 0.6584 (t) REVERT: A 187 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: A 246 ASP cc_start: 0.8782 (t0) cc_final: 0.8527 (t0) REVERT: A 324 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: A 359 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8346 (p0) REVERT: B 54 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7711 (ttt180) REVERT: B 109 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.7640 (p) REVERT: B 305 MET cc_start: 0.7427 (tpt) cc_final: 0.7131 (tpp) REVERT: C 126 TYR cc_start: 0.7185 (p90) cc_final: 0.6741 (p90) REVERT: C 340 MET cc_start: 0.7692 (mtm) cc_final: 0.7288 (tpp) REVERT: D 58 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7418 (mtp) REVERT: D 213 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: D 305 LYS cc_start: 0.8790 (mmpt) cc_final: 0.8489 (mmtp) REVERT: E 214 TYR cc_start: 0.7904 (m-10) cc_final: 0.7597 (m-10) REVERT: E 235 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7936 (mm-40) REVERT: E 467 ARG cc_start: 0.7833 (mpt180) cc_final: 0.6994 (mmm160) REVERT: F 207 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7426 (mpt) REVERT: F 235 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: F 415 MET cc_start: 0.8668 (tmm) cc_final: 0.8391 (tpp) REVERT: G 28 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.8027 (mtp85) REVERT: G 120 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8214 (mptt) REVERT: H 139 GLU cc_start: 0.8243 (tt0) cc_final: 0.7529 (tm-30) REVERT: H 198 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7259 (mp0) REVERT: I 320 MET cc_start: 0.8598 (mmt) cc_final: 0.8076 (pp-130) REVERT: J 49 GLU cc_start: 0.8001 (pm20) cc_final: 0.7309 (pm20) REVERT: J 50 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7615 (mt-10) outliers start: 120 outliers final: 47 residues processed: 312 average time/residue: 0.5629 time to fit residues: 205.8601 Evaluate side-chains 246 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 130 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 201 optimal weight: 0.0040 chunk 228 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 384 HIS B 255 GLN B 359 ASN E 281 ASN E 431 ASN H 43 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.105474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.084222 restraints weight = 49774.087| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.64 r_work: 0.3358 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24636 Z= 0.176 Angle : 0.586 8.529 33431 Z= 0.297 Chirality : 0.045 0.189 3968 Planarity : 0.005 0.106 4248 Dihedral : 5.118 73.181 3393 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 4.68 % Allowed : 17.72 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3080 helix: 1.28 (0.16), residues: 1185 sheet: -1.15 (0.24), residues: 408 loop : -0.91 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 46 TYR 0.024 0.002 TYR I 92 PHE 0.026 0.002 PHE G 100 TRP 0.007 0.001 TRP J 37 HIS 0.005 0.001 HIS J 196 Details of bonding type rmsd covalent geometry : bond 0.00429 (24636) covalent geometry : angle 0.58644 (33431) hydrogen bonds : bond 0.03767 ( 973) hydrogen bonds : angle 3.93312 ( 2724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 196 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7667 (t-100) cc_final: 0.6497 (t60) REVERT: A 128 TYR cc_start: 0.6890 (m-80) cc_final: 0.6542 (m-80) REVERT: A 130 SER cc_start: 0.7008 (OUTLIER) cc_final: 0.6790 (t) REVERT: A 181 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8376 (ttp) REVERT: A 187 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8302 (pt0) REVERT: B 54 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7823 (ttt180) REVERT: B 109 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7715 (p) REVERT: B 152 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8506 (m-10) REVERT: C 340 MET cc_start: 0.7687 (mtm) cc_final: 0.7214 (tpp) REVERT: D 58 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7457 (mtp) REVERT: D 213 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: D 305 LYS cc_start: 0.8692 (mmpt) cc_final: 0.8399 (mmtp) REVERT: E 214 TYR cc_start: 0.8001 (m-10) cc_final: 0.7771 (m-10) REVERT: E 235 GLN cc_start: 0.8498 (mm-40) cc_final: 0.7999 (mm-40) REVERT: E 247 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 467 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7055 (mmm160) REVERT: F 207 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7476 (mpt) REVERT: F 230 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7485 (mp) REVERT: F 235 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: F 415 MET cc_start: 0.8668 (tmm) cc_final: 0.8410 (tpp) REVERT: G 164 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7402 (tpt) REVERT: H 139 GLU cc_start: 0.8219 (tt0) cc_final: 0.7553 (tm-30) REVERT: H 198 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7220 (mp0) REVERT: H 244 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: I 58 ASP cc_start: 0.8265 (p0) cc_final: 0.8030 (m-30) REVERT: I 100 ASP cc_start: 0.8321 (m-30) cc_final: 0.7817 (m-30) REVERT: I 320 MET cc_start: 0.8605 (mmt) cc_final: 0.8066 (pp-130) REVERT: J 49 GLU cc_start: 0.8083 (pm20) cc_final: 0.7404 (pm20) REVERT: J 50 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7572 (mt-10) REVERT: J 179 GLU cc_start: 0.7466 (pm20) cc_final: 0.7210 (pp20) REVERT: J 306 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6860 (mmtm) outliers start: 123 outliers final: 56 residues processed: 297 average time/residue: 0.5705 time to fit residues: 197.7464 Evaluate side-chains 251 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 244 GLN Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 218 ASN Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 306 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 213 optimal weight: 3.9990 chunk 223 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 115 optimal weight: 0.0030 chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN D 331 ASN E 238 GLN E 431 ASN G 244 GLN H 43 GLN H 214 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.110306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089212 restraints weight = 49011.230| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.69 r_work: 0.3389 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24636 Z= 0.138 Angle : 0.558 8.602 33431 Z= 0.281 Chirality : 0.044 0.182 3968 Planarity : 0.004 0.095 4248 Dihedral : 4.808 68.458 3387 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 4.75 % Allowed : 18.25 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 3080 helix: 1.45 (0.16), residues: 1190 sheet: -0.99 (0.25), residues: 408 loop : -0.76 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 46 TYR 0.026 0.001 TYR I 92 PHE 0.024 0.001 PHE G 100 TRP 0.008 0.001 TRP B 111 HIS 0.004 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00334 (24636) covalent geometry : angle 0.55789 (33431) hydrogen bonds : bond 0.03373 ( 973) hydrogen bonds : angle 3.79426 ( 2724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 200 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7687 (t-100) cc_final: 0.6603 (t60) REVERT: A 175 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: A 181 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8347 (ttp) REVERT: A 187 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: B 54 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7733 (mtp180) REVERT: B 109 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7662 (p) REVERT: B 152 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8496 (m-10) REVERT: B 305 MET cc_start: 0.7341 (tpt) cc_final: 0.7114 (tpp) REVERT: C 56 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: C 340 MET cc_start: 0.7666 (mtm) cc_final: 0.7213 (tpp) REVERT: D 58 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7444 (mtp) REVERT: D 213 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6131 (tm-30) REVERT: E 235 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8026 (mm-40) REVERT: E 247 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7621 (tm-30) REVERT: E 467 ARG cc_start: 0.7826 (mpt180) cc_final: 0.7076 (mmm160) REVERT: E 510 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8634 (p) REVERT: F 173 TYR cc_start: 0.8554 (t80) cc_final: 0.8227 (t80) REVERT: F 235 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: F 415 MET cc_start: 0.8672 (tmm) cc_final: 0.8446 (tpp) REVERT: G 70 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: G 164 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7431 (tpt) REVERT: H 139 GLU cc_start: 0.8180 (tt0) cc_final: 0.7582 (tm-30) REVERT: H 198 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7234 (mp0) REVERT: I 100 ASP cc_start: 0.8330 (m-30) cc_final: 0.7841 (m-30) REVERT: I 320 MET cc_start: 0.8576 (mmt) cc_final: 0.8136 (pp-130) REVERT: I 321 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8288 (mm-30) REVERT: J 35 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5949 (tm) REVERT: J 50 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7896 (mp0) REVERT: J 111 ASP cc_start: 0.7808 (p0) cc_final: 0.7582 (p0) REVERT: J 306 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6845 (mmtm) REVERT: J 320 MET cc_start: 0.8607 (mmm) cc_final: 0.8338 (mmm) REVERT: J 321 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8791 (mm-30) REVERT: J 326 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7578 (p) REVERT: J 331 SER cc_start: 0.9033 (p) cc_final: 0.8789 (t) outliers start: 125 outliers final: 61 residues processed: 308 average time/residue: 0.5725 time to fit residues: 205.1588 Evaluate side-chains 255 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 179 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 306 LYS Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 140 optimal weight: 0.1980 chunk 224 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 359 ASN D 331 ASN E 254 ASN E 431 ASN E 479 HIS F 254 ASN G 244 GLN H 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.104787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083495 restraints weight = 49733.339| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.63 r_work: 0.3365 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24636 Z= 0.180 Angle : 0.591 8.844 33431 Z= 0.298 Chirality : 0.045 0.187 3968 Planarity : 0.005 0.082 4248 Dihedral : 4.852 66.603 3386 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 5.51 % Allowed : 17.91 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 3080 helix: 1.38 (0.16), residues: 1199 sheet: -0.92 (0.25), residues: 406 loop : -0.66 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 250 TYR 0.027 0.002 TYR I 92 PHE 0.024 0.002 PHE G 100 TRP 0.009 0.001 TRP B 111 HIS 0.005 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00438 (24636) covalent geometry : angle 0.59148 (33431) hydrogen bonds : bond 0.03681 ( 973) hydrogen bonds : angle 3.84077 ( 2724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 187 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7779 (t-100) cc_final: 0.6695 (t60) REVERT: A 128 TYR cc_start: 0.6976 (m-80) cc_final: 0.6617 (m-80) REVERT: A 130 SER cc_start: 0.7032 (OUTLIER) cc_final: 0.6802 (t) REVERT: A 181 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8374 (ttp) REVERT: A 187 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: B 54 ARG cc_start: 0.8009 (mtp180) cc_final: 0.6857 (mtp180) REVERT: B 57 PHE cc_start: 0.7792 (t80) cc_final: 0.7570 (t80) REVERT: B 152 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8603 (m-10) REVERT: B 209 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6781 (p) REVERT: B 305 MET cc_start: 0.7566 (tpt) cc_final: 0.7302 (tpp) REVERT: B 418 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: C 56 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: C 68 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7361 (mpp) REVERT: C 203 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7963 (ttm) REVERT: C 340 MET cc_start: 0.7827 (mtm) cc_final: 0.7336 (tpp) REVERT: D 58 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7482 (mtp) REVERT: D 64 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: D 213 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6139 (tm-30) REVERT: E 192 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8514 (tt) REVERT: E 196 MET cc_start: 0.7796 (mtm) cc_final: 0.7274 (ptp) REVERT: E 235 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8132 (mm-40) REVERT: E 247 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7743 (tm-30) REVERT: E 292 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8068 (mtm-85) REVERT: E 467 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7048 (mmm160) REVERT: F 173 TYR cc_start: 0.8624 (t80) cc_final: 0.8422 (t80) REVERT: F 196 MET cc_start: 0.7750 (mtt) cc_final: 0.7518 (mtt) REVERT: F 235 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: F 415 MET cc_start: 0.8730 (tmm) cc_final: 0.8494 (tpp) REVERT: G 70 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: H 53 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8690 (mp) REVERT: H 139 GLU cc_start: 0.8215 (tt0) cc_final: 0.7587 (tm-30) REVERT: H 198 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7543 (mp0) REVERT: I 100 ASP cc_start: 0.8376 (m-30) cc_final: 0.7880 (m-30) REVERT: I 320 MET cc_start: 0.8625 (mmt) cc_final: 0.8100 (pp-130) REVERT: J 35 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5997 (tm) REVERT: J 50 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7928 (mp0) REVERT: J 111 ASP cc_start: 0.7966 (p0) cc_final: 0.7764 (p0) REVERT: J 179 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6813 (pp20) REVERT: J 326 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7588 (p) outliers start: 145 outliers final: 82 residues processed: 313 average time/residue: 0.5465 time to fit residues: 200.8489 Evaluate side-chains 278 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 176 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 179 GLU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 138 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN E 431 ASN G 244 GLN H 43 GLN H 128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.110834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089779 restraints weight = 48911.687| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.70 r_work: 0.3398 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24636 Z= 0.114 Angle : 0.549 9.556 33431 Z= 0.277 Chirality : 0.043 0.191 3968 Planarity : 0.004 0.073 4248 Dihedral : 4.598 63.038 3385 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 4.33 % Allowed : 19.20 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 3080 helix: 1.58 (0.16), residues: 1203 sheet: -0.82 (0.25), residues: 413 loop : -0.53 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 250 TYR 0.028 0.001 TYR I 92 PHE 0.022 0.001 PHE G 100 TRP 0.008 0.001 TRP B 111 HIS 0.004 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00269 (24636) covalent geometry : angle 0.54919 (33431) hydrogen bonds : bond 0.03115 ( 973) hydrogen bonds : angle 3.70410 ( 2724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 187 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7720 (t-100) cc_final: 0.6669 (t60) REVERT: A 128 TYR cc_start: 0.6734 (m-80) cc_final: 0.6432 (m-80) REVERT: A 130 SER cc_start: 0.7034 (OUTLIER) cc_final: 0.6767 (t) REVERT: A 175 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: A 187 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: B 54 ARG cc_start: 0.7937 (mtp180) cc_final: 0.6723 (mtp180) REVERT: B 57 PHE cc_start: 0.7765 (t80) cc_final: 0.7527 (t80) REVERT: B 152 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8506 (m-10) REVERT: B 305 MET cc_start: 0.7348 (tpt) cc_final: 0.7096 (tpp) REVERT: C 56 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: C 340 MET cc_start: 0.7657 (mtm) cc_final: 0.7202 (tpp) REVERT: D 58 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7429 (mtp) REVERT: D 64 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: D 213 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.5902 (tm-30) REVERT: E 192 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8734 (tt) REVERT: E 235 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8013 (mm-40) REVERT: E 467 ARG cc_start: 0.7833 (mpt180) cc_final: 0.7039 (mmm160) REVERT: E 510 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8663 (p) REVERT: F 173 TYR cc_start: 0.8606 (t80) cc_final: 0.8372 (t80) REVERT: F 196 MET cc_start: 0.7664 (mtt) cc_final: 0.7414 (mtt) REVERT: F 235 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: F 250 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8184 (ttp-110) REVERT: F 415 MET cc_start: 0.8646 (tmm) cc_final: 0.8411 (tpp) REVERT: G 70 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: G 164 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7466 (tpt) REVERT: H 53 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8663 (mp) REVERT: H 139 GLU cc_start: 0.8125 (tt0) cc_final: 0.7529 (tm-30) REVERT: H 198 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7316 (mp0) REVERT: I 100 ASP cc_start: 0.8316 (m-30) cc_final: 0.7824 (m-30) REVERT: I 320 MET cc_start: 0.8561 (mmt) cc_final: 0.8057 (pp-130) REVERT: J 35 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5963 (tm) REVERT: J 50 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7923 (mp0) REVERT: J 326 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.7612 (p) outliers start: 114 outliers final: 61 residues processed: 289 average time/residue: 0.5683 time to fit residues: 191.0760 Evaluate side-chains 252 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 175 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 208 optimal weight: 0.0060 chunk 232 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN D 331 ASN E 238 GLN F 479 HIS G 244 GLN H 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.106732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085524 restraints weight = 49304.719| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.67 r_work: 0.3398 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24636 Z= 0.119 Angle : 0.557 9.580 33431 Z= 0.280 Chirality : 0.043 0.186 3968 Planarity : 0.004 0.067 4248 Dihedral : 4.529 60.921 3384 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 4.14 % Allowed : 19.73 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 3080 helix: 1.64 (0.16), residues: 1203 sheet: -0.71 (0.26), residues: 413 loop : -0.45 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 46 TYR 0.026 0.001 TYR I 92 PHE 0.021 0.001 PHE G 100 TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00286 (24636) covalent geometry : angle 0.55716 (33431) hydrogen bonds : bond 0.03126 ( 973) hydrogen bonds : angle 3.65874 ( 2724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 192 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7766 (t-100) cc_final: 0.6675 (t60) REVERT: A 128 TYR cc_start: 0.6768 (m-80) cc_final: 0.6285 (m-80) REVERT: A 130 SER cc_start: 0.6999 (OUTLIER) cc_final: 0.6728 (t) REVERT: A 175 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: A 181 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8276 (ttp) REVERT: A 387 ASP cc_start: 0.8783 (m-30) cc_final: 0.8199 (t0) REVERT: B 54 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7640 (mmm-85) REVERT: B 152 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: B 305 MET cc_start: 0.7300 (tpt) cc_final: 0.7045 (tpp) REVERT: C 56 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7979 (pm20) REVERT: C 166 MET cc_start: 0.7791 (ttp) cc_final: 0.7587 (ttp) REVERT: C 203 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7309 (tpp) REVERT: C 340 MET cc_start: 0.7621 (mtm) cc_final: 0.7156 (tpp) REVERT: D 58 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7416 (mtp) REVERT: D 64 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: D 213 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.5908 (tm-30) REVERT: E 192 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8720 (tt) REVERT: E 235 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7981 (mm-40) REVERT: E 467 ARG cc_start: 0.7816 (mpt180) cc_final: 0.6997 (mmm160) REVERT: E 510 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8646 (p) REVERT: F 173 TYR cc_start: 0.8641 (t80) cc_final: 0.8435 (t80) REVERT: F 196 MET cc_start: 0.7654 (mtt) cc_final: 0.7441 (mtt) REVERT: F 250 ARG cc_start: 0.8399 (mtm110) cc_final: 0.8163 (ttp-110) REVERT: F 415 MET cc_start: 0.8640 (tmm) cc_final: 0.8380 (tpp) REVERT: G 70 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: G 164 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7424 (tpt) REVERT: H 53 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8636 (mp) REVERT: H 139 GLU cc_start: 0.8113 (tt0) cc_final: 0.7495 (tm-30) REVERT: H 198 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7237 (mp0) REVERT: I 100 ASP cc_start: 0.8281 (m-30) cc_final: 0.7789 (m-30) REVERT: I 169 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.5223 (t80) REVERT: I 320 MET cc_start: 0.8565 (mmt) cc_final: 0.8159 (pp-130) REVERT: I 323 ASN cc_start: 0.8260 (m-40) cc_final: 0.8059 (m110) REVERT: J 35 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5904 (tm) REVERT: J 50 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7896 (mp0) REVERT: J 326 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7629 (p) REVERT: J 331 SER cc_start: 0.9087 (p) cc_final: 0.8885 (t) outliers start: 109 outliers final: 68 residues processed: 287 average time/residue: 0.6012 time to fit residues: 200.5187 Evaluate side-chains 261 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 176 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 495 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 477 GLN Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 137 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 359 ASN B 359 ASN G 244 GLN H 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.111405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090331 restraints weight = 49024.595| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.70 r_work: 0.3412 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24636 Z= 0.113 Angle : 0.558 10.276 33431 Z= 0.279 Chirality : 0.043 0.187 3968 Planarity : 0.004 0.062 4248 Dihedral : 4.452 62.698 3384 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 3.69 % Allowed : 20.38 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 3080 helix: 1.77 (0.16), residues: 1190 sheet: -0.65 (0.26), residues: 414 loop : -0.42 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 46 TYR 0.025 0.001 TYR I 92 PHE 0.021 0.001 PHE G 100 TRP 0.007 0.001 TRP B 111 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00271 (24636) covalent geometry : angle 0.55762 (33431) hydrogen bonds : bond 0.02996 ( 973) hydrogen bonds : angle 3.63755 ( 2724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 192 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7775 (t-100) cc_final: 0.6667 (t60) REVERT: A 130 SER cc_start: 0.7071 (OUTLIER) cc_final: 0.6758 (t) REVERT: A 175 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: A 181 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8245 (ttp) REVERT: A 387 ASP cc_start: 0.8765 (m-30) cc_final: 0.8275 (t0) REVERT: B 152 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8574 (m-10) REVERT: B 305 MET cc_start: 0.7358 (tpt) cc_final: 0.7103 (tpp) REVERT: C 56 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: C 166 MET cc_start: 0.7815 (ttp) cc_final: 0.7566 (ttp) REVERT: C 203 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.7258 (tpp) REVERT: C 340 MET cc_start: 0.7639 (mtm) cc_final: 0.7187 (tpp) REVERT: D 58 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7483 (mtp) REVERT: D 64 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: D 213 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.5914 (tm-30) REVERT: E 192 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8751 (tt) REVERT: E 235 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8010 (mm-40) REVERT: E 467 ARG cc_start: 0.7834 (mpt180) cc_final: 0.7003 (mmm160) REVERT: F 250 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8164 (ttp-110) REVERT: F 415 MET cc_start: 0.8628 (tmm) cc_final: 0.8388 (tpp) REVERT: G 70 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: G 164 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7500 (tpt) REVERT: H 53 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8641 (mp) REVERT: H 139 GLU cc_start: 0.8141 (tt0) cc_final: 0.7534 (tm-30) REVERT: H 198 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7407 (mp0) REVERT: I 100 ASP cc_start: 0.8288 (m-30) cc_final: 0.7793 (m-30) REVERT: I 169 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.5274 (t80) REVERT: I 320 MET cc_start: 0.8551 (mmt) cc_final: 0.8157 (pp-130) REVERT: I 323 ASN cc_start: 0.8255 (m-40) cc_final: 0.7997 (m110) REVERT: J 35 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5952 (tm) REVERT: J 50 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7892 (mp0) REVERT: J 326 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7557 (p) REVERT: J 331 SER cc_start: 0.9074 (p) cc_final: 0.8839 (t) outliers start: 97 outliers final: 65 residues processed: 276 average time/residue: 0.5853 time to fit residues: 187.2755 Evaluate side-chains 259 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 495 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 477 GLN Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 54 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 359 ASN B 359 ASN G 244 GLN H 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.111406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090353 restraints weight = 48853.041| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.70 r_work: 0.3413 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24636 Z= 0.116 Angle : 0.564 10.954 33431 Z= 0.282 Chirality : 0.043 0.185 3968 Planarity : 0.004 0.063 4248 Dihedral : 4.416 61.678 3383 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.31 % Allowed : 20.65 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 3080 helix: 1.80 (0.16), residues: 1190 sheet: -0.63 (0.26), residues: 414 loop : -0.38 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 46 TYR 0.025 0.001 TYR I 92 PHE 0.021 0.001 PHE G 100 TRP 0.008 0.001 TRP J 37 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00279 (24636) covalent geometry : angle 0.56351 (33431) hydrogen bonds : bond 0.03007 ( 973) hydrogen bonds : angle 3.64475 ( 2724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 182 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7794 (t-100) cc_final: 0.6708 (t60) REVERT: A 130 SER cc_start: 0.7108 (OUTLIER) cc_final: 0.6776 (t) REVERT: A 181 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8221 (ttp) REVERT: A 387 ASP cc_start: 0.8745 (m-30) cc_final: 0.8304 (t0) REVERT: B 152 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8567 (m-10) REVERT: B 305 MET cc_start: 0.7370 (tpt) cc_final: 0.7118 (tpp) REVERT: C 56 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: C 166 MET cc_start: 0.7850 (ttp) cc_final: 0.7586 (ttp) REVERT: C 203 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7263 (tpp) REVERT: C 340 MET cc_start: 0.7638 (mtm) cc_final: 0.7185 (tpp) REVERT: D 58 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7506 (mtp) REVERT: D 64 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: D 213 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.5921 (tm-30) REVERT: E 192 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8760 (tt) REVERT: E 235 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7994 (mm-40) REVERT: E 467 ARG cc_start: 0.7840 (mpt180) cc_final: 0.6994 (mmm160) REVERT: F 415 MET cc_start: 0.8603 (tmm) cc_final: 0.8386 (tpp) REVERT: G 70 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: G 164 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7511 (tpt) REVERT: H 53 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8634 (mp) REVERT: H 139 GLU cc_start: 0.8146 (tt0) cc_final: 0.7519 (tm-30) REVERT: H 198 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7386 (mp0) REVERT: I 100 ASP cc_start: 0.8281 (m-30) cc_final: 0.7801 (m-30) REVERT: I 169 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5265 (t80) REVERT: I 320 MET cc_start: 0.8539 (mmt) cc_final: 0.8143 (pp-130) REVERT: I 323 ASN cc_start: 0.8195 (m-40) cc_final: 0.7935 (m110) REVERT: J 35 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5949 (tm) REVERT: J 50 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7913 (mp0) REVERT: J 321 GLU cc_start: 0.9152 (mp0) cc_final: 0.8872 (mp0) REVERT: J 326 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7566 (p) REVERT: J 331 SER cc_start: 0.9072 (p) cc_final: 0.8829 (t) outliers start: 87 outliers final: 65 residues processed: 257 average time/residue: 0.5737 time to fit residues: 171.9791 Evaluate side-chains 256 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 176 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 495 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 191 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 303 optimal weight: 0.0070 chunk 272 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 13 optimal weight: 0.0010 chunk 48 optimal weight: 0.1980 chunk 270 optimal weight: 9.9990 chunk 111 optimal weight: 0.0570 chunk 226 optimal weight: 0.4980 overall best weight: 0.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS B 359 ASN C 230 ASN F 430 HIS I 323 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.109628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088543 restraints weight = 48990.043| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.69 r_work: 0.3452 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24636 Z= 0.100 Angle : 0.552 10.520 33431 Z= 0.276 Chirality : 0.043 0.193 3968 Planarity : 0.004 0.063 4248 Dihedral : 4.251 56.619 3383 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 2.36 % Allowed : 21.75 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 3080 helix: 1.93 (0.16), residues: 1189 sheet: -0.40 (0.27), residues: 401 loop : -0.34 (0.17), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 250 TYR 0.024 0.001 TYR I 92 PHE 0.019 0.001 PHE G 100 TRP 0.008 0.001 TRP J 37 HIS 0.005 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00228 (24636) covalent geometry : angle 0.55215 (33431) hydrogen bonds : bond 0.02679 ( 973) hydrogen bonds : angle 3.56492 ( 2724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7439.35 seconds wall clock time: 127 minutes 30.08 seconds (7650.08 seconds total)