Starting phenix.real_space_refine on Mon Aug 10 04:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x3r_66507/08_2026/9x3r_66507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x3r_66507/08_2026/9x3r_66507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x3r_66507/08_2026/9x3r_66507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x3r_66507/08_2026/9x3r_66507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x3r_66507/08_2026/9x3r_66507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x3r_66507/08_2026/9x3r_66507.map" } resolution = 3.8 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= 0.000 sd= 0.008 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 119 5.16 5 C 26316 2.51 5 N 6978 2.21 5 O 8319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41732 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2674 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 305} Chain: "B" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2658 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 303} Chain: "C" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3940 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 25, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2165 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "E" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2174 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain: "F" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "G" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4667 Classifications: {'peptide': 601} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain: "H" Number of atoms: 4675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4675 Classifications: {'peptide': 602} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 574} Chain: "I" Number of atoms: 4675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4675 Classifications: {'peptide': 602} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 574} Chain: "J" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1665 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "K" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1665 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "L" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1665 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "M" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2314 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain: "N" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2314 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain: "O" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2314 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Time building chain proxies: 9.40, per 1000 atoms: 0.23 Number of scatterers: 41732 At special positions: 0 Unit cell: (245.7, 188.37, 181.818, 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 119 16.00 O 8319 8.00 N 6978 7.00 C 26316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS I 555 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS H 331 " - pdb=" SG CYS H 342 " distance=2.03 Simple disulfide: pdb=" SG CYS I 331 " - pdb=" SG CYS I 342 " distance=2.03 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9862 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 113 sheets defined 12.6% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 removed outlier: 3.926A pdb=" N ARG A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.529A pdb=" N VAL A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 195 through 201 Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.517A pdb=" N GLU A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'B' and resid 13 through 28 removed outlier: 3.699A pdb=" N ARG B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 28 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.938A pdb=" N THR B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 149 through 156 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 237 through 243 Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.639A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.556A pdb=" N ARG C 189 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 190 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 190' Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.807A pdb=" N ARG C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 Processing helix chain 'C' and resid 459 through 463 Processing helix chain 'C' and resid 966 through 973 removed outlier: 3.864A pdb=" N ASN C 970 " --> pdb=" O PRO C 966 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 971 " --> pdb=" O ASP C 967 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 973 " --> pdb=" O TYR C 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 42 Processing helix chain 'D' and resid 44 through 49 removed outlier: 3.555A pdb=" N LYS D 47 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.653A pdb=" N ALA D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 42 removed outlier: 3.727A pdb=" N PHE E 42 " --> pdb=" O ILE E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.799A pdb=" N MET E 48 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA E 49 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 4.130A pdb=" N THR E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 41 Processing helix chain 'F' and resid 44 through 48 Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.943A pdb=" N THR F 77 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 38 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 269 through 271 No H-bonds generated for 'chain 'G' and resid 269 through 271' Processing helix chain 'G' and resid 284 through 288 removed outlier: 3.746A pdb=" N THR G 287 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 Processing helix chain 'G' and resid 305 through 307 No H-bonds generated for 'chain 'G' and resid 305 through 307' Processing helix chain 'G' and resid 338 through 345 removed outlier: 3.566A pdb=" N LEU G 345 " --> pdb=" O GLU G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 407 removed outlier: 3.721A pdb=" N ILE G 399 " --> pdb=" O THR G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 433 Processing helix chain 'G' and resid 445 through 454 removed outlier: 3.560A pdb=" N ILE G 449 " --> pdb=" O ALA G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 473 removed outlier: 3.654A pdb=" N TYR G 472 " --> pdb=" O ASN G 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 37 removed outlier: 5.300A pdb=" N TYR H 34 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 160 No H-bonds generated for 'chain 'H' and resid 158 through 160' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 284 through 288 removed outlier: 3.794A pdb=" N THR H 287 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 297 removed outlier: 3.788A pdb=" N GLY H 297 " --> pdb=" O SER H 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 294 through 297' Processing helix chain 'H' and resid 338 through 346 Processing helix chain 'H' and resid 395 through 405 removed outlier: 3.752A pdb=" N ASP H 401 " --> pdb=" O ASP H 397 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN H 405 " --> pdb=" O ASP H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 454 removed outlier: 3.537A pdb=" N ILE H 449 " --> pdb=" O ALA H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 473 removed outlier: 3.735A pdb=" N TYR H 472 " --> pdb=" O ASN H 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 38 removed outlier: 3.644A pdb=" N LEU I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.868A pdb=" N TYR I 89 " --> pdb=" O VAL I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 297 Processing helix chain 'I' and resid 305 through 309 removed outlier: 4.061A pdb=" N LEU I 309 " --> pdb=" O PRO I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 346 removed outlier: 3.642A pdb=" N GLY I 346 " --> pdb=" O CYS I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 405 removed outlier: 3.855A pdb=" N ILE I 399 " --> pdb=" O THR I 395 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP I 401 " --> pdb=" O ASP I 397 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN I 405 " --> pdb=" O ASP I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 454 removed outlier: 3.625A pdb=" N ILE I 449 " --> pdb=" O ALA I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 577 through 581 removed outlier: 3.825A pdb=" N HIS I 580 " --> pdb=" O ASN I 577 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR I 581 " --> pdb=" O SER I 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 577 through 581' Processing helix chain 'J' and resid 3 through 9 removed outlier: 4.036A pdb=" N GLY J 9 " --> pdb=" O ASN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.658A pdb=" N LEU J 18 " --> pdb=" O ALA J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 45 Processing helix chain 'J' and resid 51 through 64 Processing helix chain 'J' and resid 121 through 139 removed outlier: 3.621A pdb=" N VAL J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 14 through 18 removed outlier: 3.910A pdb=" N LEU K 18 " --> pdb=" O ALA K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 45 Processing helix chain 'K' and resid 51 through 64 Processing helix chain 'K' and resid 121 through 139 removed outlier: 3.591A pdb=" N VAL K 131 " --> pdb=" O ALA K 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 8 Processing helix chain 'L' and resid 14 through 18 removed outlier: 3.698A pdb=" N LEU L 18 " --> pdb=" O ALA L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 46 Processing helix chain 'L' and resid 51 through 64 Processing helix chain 'L' and resid 121 through 139 removed outlier: 3.539A pdb=" N VAL L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 45 Processing helix chain 'M' and resid 83 through 85 No H-bonds generated for 'chain 'M' and resid 83 through 85' Processing helix chain 'N' and resid 37 through 45 Processing helix chain 'N' and resid 83 through 85 No H-bonds generated for 'chain 'N' and resid 83 through 85' Processing helix chain 'O' and resid 37 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 4.885A pdb=" N ILE A 37 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 204 removed outlier: 4.507A pdb=" N ALA A 88 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 246 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 114 removed outlier: 4.524A pdb=" N PHE A 192 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG A 132 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR A 190 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.807A pdb=" N MET A 141 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 161 " --> pdb=" O MET A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 254 removed outlier: 3.514A pdb=" N ILE A 328 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 326 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 12.543A pdb=" N ILE C 913 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N ASN C1009 " --> pdb=" O ILE C 913 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS C 915 " --> pdb=" O LEU C1007 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C1007 " --> pdb=" O LYS C 915 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.914A pdb=" N ILE A 274 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B 6 " --> pdb=" O VAL C1028 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 75 through 80 removed outlier: 4.142A pdb=" N GLY B 77 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 274 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 310 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 210 removed outlier: 4.346A pdb=" N ALA B 88 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 246 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 249 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 330 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.559A pdb=" N VAL B 130 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 192 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG B 132 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR B 190 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB2, first strand: chain 'B' and resid 269 through 271 removed outlier: 5.381A pdb=" N ARG B 270 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 174 through 175 removed outlier: 3.652A pdb=" N ARG C 523 " --> pdb=" O VAL C 535 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 193 through 194 removed outlier: 3.733A pdb=" N LYS C 210 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 240 removed outlier: 7.216A pdb=" N ILE C 253 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.726A pdb=" N ALA C 310 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 321 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 365 through 371 removed outlier: 6.084A pdb=" N LYS C 367 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU C 378 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C 375 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 414 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 382 through 383 removed outlier: 3.688A pdb=" N GLU C 382 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 444 through 445 removed outlier: 4.761A pdb=" N ALA C 489 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 502 " --> pdb=" O ILE C 491 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 933 through 934 Processing sheet with id=AC2, first strand: chain 'D' and resid 84 through 86 removed outlier: 6.474A pdb=" N HIS D 85 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 165 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 159 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER D 129 " --> pdb=" O TRP D 160 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR D 162 " --> pdb=" O SER D 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 86 removed outlier: 6.474A pdb=" N HIS D 85 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 165 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 159 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 10.571A pdb=" N GLY F 169 " --> pdb=" O TRP D 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR D 162 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LYS F 171 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE D 164 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 96 through 97 removed outlier: 6.823A pdb=" N VAL D 96 " --> pdb=" O GLN D 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 171 removed outlier: 3.741A pdb=" N GLY D 169 " --> pdb=" O TYR E 162 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER E 166 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL E 159 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 169 through 171 removed outlier: 3.741A pdb=" N GLY D 169 " --> pdb=" O TYR E 162 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER E 166 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER E 129 " --> pdb=" O TRP E 160 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N TYR E 162 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 179 through 180 removed outlier: 7.320A pdb=" N LYS D 201 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR D 281 " --> pdb=" O MET D 199 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET D 199 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE D 221 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 204 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 214 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG D 239 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR D 216 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL D 237 " --> pdb=" O THR D 216 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU D 218 " --> pdb=" O TYR D 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 186 through 193 removed outlier: 4.869A pdb=" N VAL D 261 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.745A pdb=" N GLN E 125 " --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 171 removed outlier: 3.823A pdb=" N SER F 166 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 179 through 180 removed outlier: 6.834A pdb=" N LYS E 201 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR E 281 " --> pdb=" O MET E 199 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET E 199 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN E 220 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 179 through 180 removed outlier: 6.834A pdb=" N LYS E 201 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR E 281 " --> pdb=" O MET E 199 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET E 199 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 186 through 190 removed outlier: 3.542A pdb=" N SER E 255 " --> pdb=" O THR E 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 94 through 97 removed outlier: 3.528A pdb=" N THR F 123 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 150 through 153 Processing sheet with id=AD7, first strand: chain 'F' and resid 178 through 179 removed outlier: 5.312A pdb=" N ALA F 274 " --> pdb=" O GLN F 207 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLN F 207 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL F 276 " --> pdb=" O THR F 205 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N THR F 205 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL F 278 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU F 203 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 214 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG F 239 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR F 216 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL F 237 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR F 235 " --> pdb=" O GLU F 218 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP F 224 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU F 229 " --> pdb=" O ASP F 224 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 186 through 193 removed outlier: 5.579A pdb=" N ASP F 188 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE F 265 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA F 263 " --> pdb=" O PRO F 190 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE F 192 " --> pdb=" O VAL F 261 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 50 through 53 removed outlier: 6.233A pdb=" N LYS G 50 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN G 71 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR G 52 " --> pdb=" O ASN G 71 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 59 through 61 removed outlier: 6.038A pdb=" N ILE G 79 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 160 through 168 removed outlier: 3.634A pdb=" N LYS G 165 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE G 244 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 242 " --> pdb=" O PHE G 167 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 174 through 177 removed outlier: 5.429A pdb=" N THR G 175 " --> pdb=" O LEU G 232 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 280 through 283 removed outlier: 3.590A pdb=" N THR G 259 " --> pdb=" O TRP G 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP G 385 " --> pdb=" O THR G 259 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 263 " --> pdb=" O ILE G 381 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 316 " --> pdb=" O PHE G 313 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 290 through 292 removed outlier: 4.020A pdb=" N ILE G 368 " --> pdb=" O GLU G 359 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 359 " --> pdb=" O ILE G 368 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 329 through 332 removed outlier: 3.511A pdb=" N HIS G 330 " --> pdb=" O GLU G 350 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU G 350 " --> pdb=" O HIS G 330 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 414 through 416 removed outlier: 3.761A pdb=" N ILE G 416 " --> pdb=" O TYR G 439 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 459 through 462 Processing sheet with id=AE9, first strand: chain 'G' and resid 478 through 480 removed outlier: 3.674A pdb=" N GLY H 520 " --> pdb=" O TYR G 592 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 486 through 488 removed outlier: 3.504A pdb=" N ILE I 593 " --> pdb=" O VAL G 486 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 502 through 506 removed outlier: 4.001A pdb=" N SER G 513 " --> pdb=" O ASN G 502 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 524 through 525 Processing sheet with id=AF4, first strand: chain 'G' and resid 535 through 536 Processing sheet with id=AF5, first strand: chain 'G' and resid 543 through 544 removed outlier: 3.510A pdb=" N ILE G 543 " --> pdb=" O ARG I 570 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR I 567 " --> pdb=" O VAL G 552 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL G 552 " --> pdb=" O THR I 567 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 541 through 544 Processing sheet with id=AF7, first strand: chain 'G' and resid 575 through 576 Processing sheet with id=AF8, first strand: chain 'H' and resid 50 through 52 removed outlier: 7.060A pdb=" N TYR H 68 " --> pdb=" O ARG H 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 59 through 60 removed outlier: 5.899A pdb=" N LEU H 60 " --> pdb=" O ASN H 80 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE H 79 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 136 through 137 Processing sheet with id=AG2, first strand: chain 'H' and resid 162 through 167 removed outlier: 4.214A pdb=" N VAL H 242 " --> pdb=" O PHE H 167 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 177 through 178 Processing sheet with id=AG4, first strand: chain 'H' and resid 280 through 283 removed outlier: 7.516A pdb=" N TYR H 281 " --> pdb=" O GLN H 262 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG H 264 " --> pdb=" O TYR H 281 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR H 283 " --> pdb=" O ARG H 264 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU H 266 " --> pdb=" O THR H 283 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 259 " --> pdb=" O TRP H 385 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP H 385 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG H 261 " --> pdb=" O ILE H 383 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL H 311 " --> pdb=" O GLN H 318 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.794A pdb=" N ILE H 368 " --> pdb=" O GLU H 359 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 329 through 332 removed outlier: 3.542A pdb=" N HIS H 330 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU H 350 " --> pdb=" O HIS H 330 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 392 through 393 removed outlier: 6.411A pdb=" N THR H 392 " --> pdb=" O LEU I 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'H' and resid 414 through 416 Processing sheet with id=AG9, first strand: chain 'H' and resid 420 through 422 Processing sheet with id=AH1, first strand: chain 'H' and resid 459 through 462 Processing sheet with id=AH2, first strand: chain 'H' and resid 477 through 480 removed outlier: 7.442A pdb=" N SER H 477 " --> pdb=" O ILE H 601 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY I 520 " --> pdb=" O TYR H 592 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 502 through 506 removed outlier: 6.715A pdb=" N ASP H 505 " --> pdb=" O SER H 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 513 " --> pdb=" O ASP H 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'H' and resid 524 through 525 Processing sheet with id=AH5, first strand: chain 'H' and resid 556 through 557 removed outlier: 3.573A pdb=" N TYR H 557 " --> pdb=" O CYS I 555 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS I 555 " --> pdb=" O TYR H 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'I' and resid 541 through 544 removed outlier: 3.577A pdb=" N THR H 567 " --> pdb=" O VAL I 552 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 575 through 576 Processing sheet with id=AH8, first strand: chain 'I' and resid 50 through 51 removed outlier: 6.853A pdb=" N LYS I 50 " --> pdb=" O ALA I 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.430A pdb=" N LEU I 60 " --> pdb=" O ASN I 80 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AI2, first strand: chain 'I' and resid 163 through 168 removed outlier: 3.953A pdb=" N ALA I 163 " --> pdb=" O THR I 246 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 246 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 174 through 177 removed outlier: 3.890A pdb=" N GLN I 174 " --> pdb=" O CYS I 236 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP I 176 " --> pdb=" O GLN I 234 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N GLN I 234 " --> pdb=" O ASP I 176 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 280 through 283 removed outlier: 7.814A pdb=" N TYR I 281 " --> pdb=" O GLN I 262 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG I 264 " --> pdb=" O TYR I 281 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR I 283 " --> pdb=" O ARG I 264 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU I 266 " --> pdb=" O THR I 283 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL I 311 " --> pdb=" O GLN I 318 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 290 through 292 removed outlier: 3.647A pdb=" N ILE I 368 " --> pdb=" O GLU I 359 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 331 through 332 Processing sheet with id=AI7, first strand: chain 'I' and resid 414 through 416 Processing sheet with id=AI8, first strand: chain 'I' and resid 420 through 422 Processing sheet with id=AI9, first strand: chain 'I' and resid 459 through 460 Processing sheet with id=AJ1, first strand: chain 'I' and resid 502 through 506 removed outlier: 3.796A pdb=" N SER I 513 " --> pdb=" O ASN I 502 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 524 through 525 Processing sheet with id=AJ3, first strand: chain 'J' and resid 193 through 201 removed outlier: 5.378A pdb=" N LEU J 195 " --> pdb=" O GLU J 216 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU J 216 " --> pdb=" O LEU J 195 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY J 197 " --> pdb=" O HIS J 214 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN J 73 " --> pdb=" O TYR J 213 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE J 70 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N THR L 72 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR J 72 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 11.820A pdb=" N ILE L 70 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N THR K 72 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR L 72 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR K 69 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG K 217 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS K 214 " --> pdb=" O GLY K 197 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY K 197 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU K 216 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU K 195 " --> pdb=" O GLU K 216 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 193 through 201 removed outlier: 5.378A pdb=" N LEU J 195 " --> pdb=" O GLU J 216 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU J 216 " --> pdb=" O LEU J 195 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY J 197 " --> pdb=" O HIS J 214 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN J 73 " --> pdb=" O TYR J 213 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE J 70 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N THR L 72 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR J 72 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR L 69 " --> pdb=" O ARG L 217 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG L 217 " --> pdb=" O THR L 69 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN L 73 " --> pdb=" O TYR L 213 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY L 197 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU L 216 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU L 195 " --> pdb=" O GLU L 216 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'J' and resid 145 through 148 removed outlier: 3.581A pdb=" N SER J 145 " --> pdb=" O THR J 159 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU J 156 " --> pdb=" O TRP J 88 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'J' and resid 104 through 109 Processing sheet with id=AJ7, first strand: chain 'K' and resid 145 through 148 removed outlier: 3.541A pdb=" N SER K 145 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 104 through 109 Processing sheet with id=AJ9, first strand: chain 'L' and resid 145 through 148 removed outlier: 3.763A pdb=" N SER L 145 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU L 156 " --> pdb=" O TRP L 88 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR L 85 " --> pdb=" O ILE L 183 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR L 173 " --> pdb=" O ILE L 176 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 104 through 109 Processing sheet with id=AK2, first strand: chain 'M' and resid 8 through 9 removed outlier: 6.731A pdb=" N PHE M 8 " --> pdb=" O ASP N 15 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY N 17 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE O 21 " --> pdb=" O LEU N 14 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA N 16 " --> pdb=" O ILE O 21 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN O 23 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'N' and resid 21 through 24 removed outlier: 4.677A pdb=" N ILE N 21 " --> pdb=" O LEU M 14 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA M 16 " --> pdb=" O ILE N 21 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN N 23 " --> pdb=" O ALA M 16 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'M' and resid 21 through 22 removed outlier: 4.476A pdb=" N ILE M 21 " --> pdb=" O GLY N 35 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'M' and resid 61 through 64 Processing sheet with id=AK6, first strand: chain 'M' and resid 96 through 99 removed outlier: 3.504A pdb=" N SER M 184 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'M' and resid 96 through 99 Processing sheet with id=AK8, first strand: chain 'M' and resid 102 through 105 removed outlier: 3.598A pdb=" N THR M 123 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE M 122 " --> pdb=" O LEU M 151 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL M 153 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE M 124 " --> pdb=" O VAL M 153 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'M' and resid 199 through 202 removed outlier: 7.044A pdb=" N SER M 264 " --> pdb=" O TRP M 292 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU M 294 " --> pdb=" O SER M 264 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'M' and resid 208 through 209 removed outlier: 5.921A pdb=" N VAL M 228 " --> pdb=" O THR M 257 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR M 254 " --> pdb=" O GLY M 275 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'N' and resid 8 through 9 removed outlier: 6.359A pdb=" N PHE N 8 " --> pdb=" O ASP O 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'N' and resid 61 through 64 Processing sheet with id=AL4, first strand: chain 'N' and resid 97 through 99 removed outlier: 6.065A pdb=" N ILE N 97 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'N' and resid 97 through 99 removed outlier: 6.065A pdb=" N ILE N 97 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'N' and resid 102 through 105 removed outlier: 3.678A pdb=" N THR N 123 " --> pdb=" O GLY N 102 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'N' and resid 159 through 160 Processing sheet with id=AL8, first strand: chain 'N' and resid 200 through 202 removed outlier: 6.753A pdb=" N ILE N 216 " --> pdb=" O VAL N 243 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER N 264 " --> pdb=" O TRP N 292 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU N 294 " --> pdb=" O SER N 264 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'N' and resid 208 through 209 removed outlier: 7.290A pdb=" N TYR N 208 " --> pdb=" O LYS N 229 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'O' and resid 62 through 64 Processing sheet with id=AM2, first strand: chain 'O' and resid 96 through 99 removed outlier: 6.070A pdb=" N ILE O 97 " --> pdb=" O SER O 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE O 112 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN O 178 " --> pdb=" O ALA O 193 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET O 190 " --> pdb=" O VAL O 160 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'O' and resid 102 through 105 removed outlier: 4.005A pdb=" N THR O 123 " --> pdb=" O GLY O 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR O 125 " --> pdb=" O TYR O 104 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'O' and resid 200 through 202 removed outlier: 5.642A pdb=" N ILE O 200 " --> pdb=" O VAL O 217 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE O 242 " --> pdb=" O GLY O 281 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY O 281 " --> pdb=" O PHE O 242 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER O 264 " --> pdb=" O TRP O 292 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU O 294 " --> pdb=" O SER O 264 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'O' and resid 208 through 209 removed outlier: 6.935A pdb=" N TYR O 208 " --> pdb=" O LYS O 229 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE O 226 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR O 257 " --> pdb=" O ILE O 226 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL O 228 " --> pdb=" O THR O 257 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR O 254 " --> pdb=" O GLY O 275 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 2796 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: 12.31 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13884 1.34 - 1.46: 9579 1.46 - 1.58: 18975 1.58 - 1.70: 0 1.70 - 1.82: 199 Bond restraints: 42637 Sorted by residual: bond pdb=" CA VAL C 237 " pdb=" C VAL C 237 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.27e-02 6.20e+03 4.21e+00 bond pdb=" C THR K 39 " pdb=" N ILE K 40 " ideal model delta sigma weight residual 1.335 1.318 0.017 1.21e-02 6.83e+03 2.04e+00 bond pdb=" CB PRO H 224 " pdb=" CG PRO H 224 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.03e+00 bond pdb=" N VAL C 237 " pdb=" CA VAL C 237 " ideal model delta sigma weight residual 1.456 1.443 0.013 1.09e-02 8.42e+03 1.43e+00 bond pdb=" CA VAL C 237 " pdb=" CB VAL C 237 " ideal model delta sigma weight residual 1.541 1.528 0.012 1.05e-02 9.07e+03 1.36e+00 ... (remaining 42632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 57354 1.90 - 3.81: 631 3.81 - 5.71: 67 5.71 - 7.62: 10 7.62 - 9.52: 2 Bond angle restraints: 58064 Sorted by residual: angle pdb=" N GLN C 240 " pdb=" CA GLN C 240 " pdb=" C GLN C 240 " ideal model delta sigma weight residual 109.24 116.10 -6.86 1.51e+00 4.39e-01 2.06e+01 angle pdb=" N MET G 473 " pdb=" CA MET G 473 " pdb=" C MET G 473 " ideal model delta sigma weight residual 114.56 108.83 5.73 1.27e+00 6.20e-01 2.03e+01 angle pdb=" N VAL C 237 " pdb=" CA VAL C 237 " pdb=" C VAL C 237 " ideal model delta sigma weight residual 111.88 107.70 4.18 1.06e+00 8.90e-01 1.55e+01 angle pdb=" N GLY A 185 " pdb=" CA GLY A 185 " pdb=" C GLY A 185 " ideal model delta sigma weight residual 113.58 109.64 3.94 1.07e+00 8.73e-01 1.36e+01 angle pdb=" CA PRO H 224 " pdb=" N PRO H 224 " pdb=" CD PRO H 224 " ideal model delta sigma weight residual 112.00 107.09 4.91 1.40e+00 5.10e-01 1.23e+01 ... (remaining 58059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 22958 17.74 - 35.47: 1956 35.47 - 53.21: 297 53.21 - 70.95: 47 70.95 - 88.68: 28 Dihedral angle restraints: 25286 sinusoidal: 9864 harmonic: 15422 Sorted by residual: dihedral pdb=" CA GLN H 253 " pdb=" C GLN H 253 " pdb=" N TRP H 254 " pdb=" CA TRP H 254 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR I 472 " pdb=" C TYR I 472 " pdb=" N MET I 473 " pdb=" CA MET I 473 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA VAL J 10 " pdb=" C VAL J 10 " pdb=" N ILE J 11 " pdb=" CA ILE J 11 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 25283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5419 0.059 - 0.118: 1015 0.118 - 0.177: 86 0.177 - 0.236: 0 0.236 - 0.295: 3 Chirality restraints: 6523 Sorted by residual: chirality pdb=" CB ILE G 117 " pdb=" CA ILE G 117 " pdb=" CG1 ILE G 117 " pdb=" CG2 ILE G 117 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB ILE L 176 " pdb=" CA ILE L 176 " pdb=" CG1 ILE L 176 " pdb=" CG2 ILE L 176 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE C 977 " pdb=" CA ILE C 977 " pdb=" CG1 ILE C 977 " pdb=" CG2 ILE C 977 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 6520 not shown) Planarity restraints: 7606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 230 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO M 231 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO M 231 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO M 231 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 223 " -0.056 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO H 224 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO H 224 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 224 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 208 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO L 209 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO L 209 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 209 " 0.035 5.00e-02 4.00e+02 ... (remaining 7603 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4543 2.75 - 3.29: 41301 3.29 - 3.83: 67750 3.83 - 4.36: 78140 4.36 - 4.90: 136795 Nonbonded interactions: 328529 Sorted by model distance: nonbonded pdb=" O CYS C 313 " pdb=" OG SER C 370 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 272 " pdb=" O THR E 20 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLN L 33 " pdb=" OG SER L 37 " model vdw 2.230 3.040 nonbonded pdb=" ND2 ASN I 462 " pdb=" OH TYR I 472 " model vdw 2.231 3.120 nonbonded pdb=" NE2 GLN J 33 " pdb=" OD1 ASP K 162 " model vdw 2.234 3.120 ... (remaining 328524 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' and resid 3 through 334) selection = chain 'B' } ncs_group { reference = (chain 'D' and resid 2 through 287) selection = (chain 'E' and resid 2 through 287) selection = (chain 'F' and resid 2 through 287) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 2 through 602) selection = (chain 'I' and resid 2 through 602) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 41.100 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.071 42643 Z= 0.119 Angle : 0.516 9.524 58076 Z= 0.276 Chirality : 0.045 0.295 6523 Planarity : 0.004 0.084 7606 Dihedral : 13.353 88.685 15406 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.11), residues: 5323 helix: 0.11 (0.23), residues: 575 sheet: -0.30 (0.15), residues: 1351 loop : -0.98 (0.10), residues: 3397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 204 TYR 0.025 0.001 TYR J 160 PHE 0.012 0.001 PHE B 249 TRP 0.030 0.001 TRP J 193 HIS 0.005 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (42637) covalent geometry : angle 0.51603 / 0.28 (58064) SS BOND : bond 0.00133 / 0.06 ( 6) SS BOND : angle 0.52517 / 0.27 ( 12) hydrogen bonds : bond 0.25121 / 16.62 ( 1021) hydrogen bonds : angle 9.24329 / 6.50 ( 2796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1238 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 MET cc_start: 0.5841 (ptt) cc_final: 0.4207 (mtp) REVERT: B 155 LYS cc_start: 0.6303 (tttt) cc_final: 0.5900 (tttt) REVERT: B 180 ILE cc_start: 0.7481 (mp) cc_final: 0.7261 (mt) REVERT: B 192 PHE cc_start: 0.8542 (p90) cc_final: 0.8224 (p90) REVERT: B 234 ASP cc_start: 0.5238 (p0) cc_final: 0.4613 (p0) REVERT: B 236 PHE cc_start: 0.6699 (m-10) cc_final: 0.6422 (m-10) REVERT: B 263 LEU cc_start: 0.6143 (tp) cc_final: 0.5578 (tp) REVERT: C 172 GLU cc_start: 0.6754 (mp0) cc_final: 0.6186 (tp30) REVERT: C 194 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6422 (tm-30) REVERT: C 338 PHE cc_start: 0.6378 (m-80) cc_final: 0.6169 (m-80) REVERT: C 378 LEU cc_start: 0.8052 (tp) cc_final: 0.7786 (tp) REVERT: C 396 ILE cc_start: 0.7633 (pt) cc_final: 0.7400 (tt) REVERT: C 411 LYS cc_start: 0.6890 (mmtt) cc_final: 0.6429 (mtmm) REVERT: C 424 ARG cc_start: 0.6690 (mtm-85) cc_final: 0.6486 (mtm180) REVERT: C 449 LYS cc_start: 0.7300 (pttt) cc_final: 0.6751 (tppt) REVERT: C 923 SER cc_start: 0.8319 (m) cc_final: 0.7991 (p) REVERT: C 1028 VAL cc_start: 0.9214 (p) cc_final: 0.8996 (m) REVERT: D 1 MET cc_start: 0.5865 (mtp) cc_final: 0.5071 (mtm) REVERT: D 32 ASN cc_start: 0.8167 (m-40) cc_final: 0.7911 (m-40) REVERT: D 99 GLU cc_start: 0.6860 (tt0) cc_final: 0.6523 (tt0) REVERT: D 199 MET cc_start: 0.8406 (tmm) cc_final: 0.8144 (tmm) REVERT: D 238 MET cc_start: 0.8099 (mtt) cc_final: 0.7895 (mtt) REVERT: D 273 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7860 (mmt90) REVERT: E 100 ARG cc_start: 0.8603 (ptp-170) cc_final: 0.8316 (ptp-170) REVERT: E 112 SER cc_start: 0.8465 (m) cc_final: 0.8185 (m) REVERT: E 119 THR cc_start: 0.8156 (p) cc_final: 0.7743 (t) REVERT: F 32 ASN cc_start: 0.7625 (m-40) cc_final: 0.7220 (m-40) REVERT: F 44 ASP cc_start: 0.8249 (t0) cc_final: 0.7797 (t70) REVERT: F 46 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7729 (mtm110) REVERT: F 88 ASP cc_start: 0.7415 (p0) cc_final: 0.7202 (p0) REVERT: F 152 SER cc_start: 0.8535 (t) cc_final: 0.8004 (m) REVERT: F 199 MET cc_start: 0.8218 (tmm) cc_final: 0.7919 (ttp) REVERT: F 213 LYS cc_start: 0.9079 (mttt) cc_final: 0.8680 (mtpt) REVERT: G 96 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7418 (ttm-80) REVERT: G 144 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7449 (mm-30) REVERT: G 305 ASN cc_start: 0.7831 (t0) cc_final: 0.7265 (t0) REVERT: G 487 LEU cc_start: 0.8860 (tp) cc_final: 0.8646 (tp) REVERT: G 545 ASP cc_start: 0.7843 (t70) cc_final: 0.7453 (t0) REVERT: H 42 VAL cc_start: 0.8375 (p) cc_final: 0.8036 (m) REVERT: H 91 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8199 (mmtp) REVERT: H 285 LEU cc_start: 0.8624 (mm) cc_final: 0.8231 (mt) REVERT: H 294 SER cc_start: 0.8622 (p) cc_final: 0.8330 (t) REVERT: H 368 ILE cc_start: 0.8890 (mm) cc_final: 0.8560 (mm) REVERT: H 404 ASP cc_start: 0.7889 (t70) cc_final: 0.7374 (t0) REVERT: H 456 ILE cc_start: 0.8814 (mm) cc_final: 0.8453 (mm) REVERT: H 555 CYS cc_start: 0.7715 (p) cc_final: 0.6943 (p) REVERT: I 50 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7714 (mmpt) REVERT: I 71 ASN cc_start: 0.5833 (t0) cc_final: 0.5516 (t0) REVERT: I 144 GLU cc_start: 0.7236 (mt-10) cc_final: 0.7009 (pt0) REVERT: I 285 LEU cc_start: 0.8684 (mm) cc_final: 0.8326 (mp) REVERT: I 299 ILE cc_start: 0.7742 (mt) cc_final: 0.7524 (mm) REVERT: I 304 ILE cc_start: 0.8884 (mm) cc_final: 0.8644 (mm) REVERT: I 318 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7682 (mm-40) REVERT: I 428 ILE cc_start: 0.7583 (mm) cc_final: 0.7257 (mm) REVERT: J 16 ASP cc_start: 0.7756 (m-30) cc_final: 0.7338 (m-30) REVERT: J 77 VAL cc_start: 0.8007 (p) cc_final: 0.7740 (t) REVERT: J 186 SER cc_start: 0.7478 (m) cc_final: 0.7245 (p) REVERT: K 148 ASP cc_start: 0.7916 (m-30) cc_final: 0.7697 (p0) REVERT: L 6 ASN cc_start: 0.8102 (m-40) cc_final: 0.7833 (m-40) REVERT: L 134 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7157 (tp-100) REVERT: L 163 ASN cc_start: 0.8811 (p0) cc_final: 0.8602 (p0) REVERT: L 210 THR cc_start: 0.9098 (p) cc_final: 0.8847 (p) REVERT: M 173 THR cc_start: 0.7295 (p) cc_final: 0.7043 (m) REVERT: M 178 GLN cc_start: 0.7394 (mp10) cc_final: 0.7150 (mp10) REVERT: N 4 ILE cc_start: 0.7567 (mm) cc_final: 0.7117 (tt) REVERT: N 64 TYR cc_start: 0.8974 (t80) cc_final: 0.8545 (t80) REVERT: N 65 ASP cc_start: 0.6614 (t70) cc_final: 0.5754 (t70) REVERT: O 22 ILE cc_start: 0.8980 (pt) cc_final: 0.8599 (pt) REVERT: O 73 ASN cc_start: 0.8217 (m-40) cc_final: 0.7438 (p0) REVERT: O 139 GLN cc_start: 0.8030 (tp40) cc_final: 0.7824 (tp40) REVERT: O 213 ASN cc_start: 0.6181 (t0) cc_final: 0.5811 (t0) outliers start: 0 outliers final: 0 residues processed: 1238 average time/residue: 0.2420 time to fit residues: 495.4778 Evaluate side-chains 715 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 715 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 74 HIS B 228 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS C 213 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 68 GLN E 113 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN G 580 HIS H 80 ASN H 90 ASN H 150 GLN H 588 ASN I 103 ASN I 314 ASN I 318 GLN I 421 ASN J 166 HIS K 61 ASN K 134 GLN L 61 ASN L 206 GLN M 213 ASN M 235 ASN N 115 ASN N 120 ASN O 66 ASN O 174 HIS O 241 ASN O 249 ASN O 266 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.151835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144404 restraints weight = 57601.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132398 restraints weight = 117929.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.130404 restraints weight = 105779.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.131207 restraints weight = 95459.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131756 restraints weight = 68851.294| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42643 Z= 0.144 Angle : 0.578 9.993 58076 Z= 0.308 Chirality : 0.047 0.221 6523 Planarity : 0.004 0.055 7606 Dihedral : 4.337 42.821 5780 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.06 % Allowed : 11.16 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.11), residues: 5323 helix: 0.14 (0.23), residues: 562 sheet: -0.27 (0.14), residues: 1402 loop : -0.95 (0.10), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 204 TYR 0.023 0.002 TYR I 566 PHE 0.018 0.001 PHE H 475 TRP 0.020 0.001 TRP K 193 HIS 0.010 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (42637) covalent geometry : angle 0.57809 / 0.31 (58064) SS BOND : bond 0.00974 / 0.48 ( 6) SS BOND : angle 0.79323 / 0.46 ( 12) hydrogen bonds : bond 0.04100 / 2.70 ( 1021) hydrogen bonds : angle 6.56832 / 4.62 ( 2796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 756 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TRP cc_start: 0.8798 (t-100) cc_final: 0.7765 (t-100) REVERT: A 210 VAL cc_start: 0.9035 (t) cc_final: 0.8766 (m) REVERT: B 141 MET cc_start: 0.5047 (ptt) cc_final: 0.4166 (ptp) REVERT: B 155 LYS cc_start: 0.6416 (tttt) cc_final: 0.6051 (tttt) REVERT: B 175 ASP cc_start: 0.7864 (t70) cc_final: 0.7278 (m-30) REVERT: B 180 ILE cc_start: 0.7475 (mp) cc_final: 0.7231 (mt) REVERT: B 229 LEU cc_start: 0.7488 (mp) cc_final: 0.7133 (mp) REVERT: C 172 GLU cc_start: 0.6956 (mp0) cc_final: 0.6737 (tp30) REVERT: C 252 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8280 (ptpp) REVERT: C 268 ASP cc_start: 0.6902 (m-30) cc_final: 0.6546 (m-30) REVERT: C 397 ASP cc_start: 0.7184 (t0) cc_final: 0.6941 (t0) REVERT: C 411 LYS cc_start: 0.6879 (mmtt) cc_final: 0.6443 (mtmm) REVERT: C 424 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6475 (mtm180) REVERT: C 449 LYS cc_start: 0.7782 (pttt) cc_final: 0.6774 (tppt) REVERT: C 487 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6224 (mtm) REVERT: C 923 SER cc_start: 0.8105 (m) cc_final: 0.7777 (p) REVERT: D 1 MET cc_start: 0.5171 (mtp) cc_final: 0.4882 (mtm) REVERT: D 32 ASN cc_start: 0.8039 (m-40) cc_final: 0.7783 (m-40) REVERT: D 83 THR cc_start: 0.9374 (p) cc_final: 0.8838 (t) REVERT: D 136 ASN cc_start: 0.7616 (p0) cc_final: 0.7402 (p0) REVERT: D 167 MET cc_start: 0.8441 (ptm) cc_final: 0.8206 (ptm) REVERT: E 17 ASN cc_start: 0.6366 (t0) cc_final: 0.6143 (m-40) REVERT: E 245 GLU cc_start: 0.7614 (tp30) cc_final: 0.7143 (tm-30) REVERT: E 258 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6716 (pm20) REVERT: F 199 MET cc_start: 0.8285 (tmm) cc_final: 0.8040 (ttp) REVERT: F 265 ILE cc_start: 0.9191 (mm) cc_final: 0.8981 (mp) REVERT: G 96 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7920 (ttm-80) REVERT: G 109 LEU cc_start: 0.8451 (tt) cc_final: 0.8185 (mp) REVERT: G 167 PHE cc_start: 0.6580 (m-80) cc_final: 0.6375 (m-10) REVERT: G 545 ASP cc_start: 0.7890 (t70) cc_final: 0.7614 (t0) REVERT: H 91 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8099 (mmtp) REVERT: H 294 SER cc_start: 0.8549 (p) cc_final: 0.8249 (t) REVERT: H 368 ILE cc_start: 0.8973 (mm) cc_final: 0.8643 (mm) REVERT: H 372 ASP cc_start: 0.8007 (m-30) cc_final: 0.7768 (t0) REVERT: H 404 ASP cc_start: 0.7987 (t70) cc_final: 0.7587 (t0) REVERT: H 424 ASP cc_start: 0.6455 (t0) cc_final: 0.6209 (t0) REVERT: H 499 PHE cc_start: 0.8217 (m-10) cc_final: 0.8005 (m-80) REVERT: H 514 HIS cc_start: 0.7969 (t-170) cc_final: 0.7575 (t-170) REVERT: H 555 CYS cc_start: 0.8002 (p) cc_final: 0.7260 (p) REVERT: I 71 ASN cc_start: 0.6161 (t0) cc_final: 0.5878 (t0) REVERT: I 144 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6603 (pt0) REVERT: I 304 ILE cc_start: 0.8800 (mm) cc_final: 0.8485 (mm) REVERT: I 428 ILE cc_start: 0.7868 (mm) cc_final: 0.7456 (mm) REVERT: J 16 ASP cc_start: 0.7738 (m-30) cc_final: 0.7478 (m-30) REVERT: J 186 SER cc_start: 0.7489 (m) cc_final: 0.7181 (p) REVERT: K 27 ILE cc_start: 0.8286 (pt) cc_final: 0.8072 (pt) REVERT: K 148 ASP cc_start: 0.8072 (m-30) cc_final: 0.7759 (p0) REVERT: L 6 ASN cc_start: 0.8379 (m-40) cc_final: 0.7608 (m-40) REVERT: L 120 MET cc_start: 0.8042 (mtt) cc_final: 0.7814 (mtp) REVERT: L 134 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7221 (tp-100) REVERT: L 148 ASP cc_start: 0.6933 (t0) cc_final: 0.6509 (t0) REVERT: L 163 ASN cc_start: 0.8771 (p0) cc_final: 0.8497 (p0) REVERT: M 153 VAL cc_start: 0.8822 (t) cc_final: 0.8604 (p) REVERT: M 173 THR cc_start: 0.7627 (p) cc_final: 0.7372 (m) REVERT: M 284 MET cc_start: 0.6995 (ppp) cc_final: 0.6370 (ttm) REVERT: N 64 TYR cc_start: 0.8980 (t80) cc_final: 0.8298 (t80) REVERT: N 65 ASP cc_start: 0.6255 (t70) cc_final: 0.5573 (t70) REVERT: N 190 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7741 (mtp) REVERT: O 66 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8435 (m-40) REVERT: O 139 GLN cc_start: 0.8219 (tp40) cc_final: 0.7985 (tp40) REVERT: O 157 GLN cc_start: 0.7025 (mp10) cc_final: 0.6700 (mm-40) REVERT: O 196 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.7857 (p) REVERT: O 211 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6363 (mp10) REVERT: O 284 MET cc_start: 0.7099 (ttt) cc_final: 0.6883 (tmm) outliers start: 95 outliers final: 63 residues processed: 816 average time/residue: 0.2205 time to fit residues: 302.9508 Evaluate side-chains 688 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 621 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 535 THR Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 196 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 476 optimal weight: 3.9990 chunk 107 optimal weight: 0.0010 chunk 461 optimal weight: 6.9990 chunk 484 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 392 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 HIS D 161 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN G 580 HIS H 243 GLN H 588 ASN ** J 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN ** J 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 ASN M 157 GLN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN O 73 ASN O 120 ASN O 241 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132862 restraints weight = 57741.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.124068 restraints weight = 101237.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122968 restraints weight = 94827.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.123276 restraints weight = 86092.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123368 restraints weight = 71903.234| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 42643 Z= 0.184 Angle : 0.573 8.286 58076 Z= 0.305 Chirality : 0.047 0.200 6523 Planarity : 0.004 0.081 7606 Dihedral : 4.516 40.408 5780 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.16 % Allowed : 13.83 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.11), residues: 5323 helix: -0.03 (0.22), residues: 567 sheet: -0.39 (0.14), residues: 1390 loop : -1.03 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 204 TYR 0.027 0.002 TYR B 225 PHE 0.021 0.002 PHE M 162 TRP 0.031 0.002 TRP H 49 HIS 0.010 0.001 HIS I 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (42637) covalent geometry : angle 0.57330 / 0.30 (58064) SS BOND : bond 0.00270 / 0.14 ( 6) SS BOND : angle 0.88187 / 0.49 ( 12) hydrogen bonds : bond 0.03797 / 2.49 ( 1021) hydrogen bonds : angle 5.89690 / 4.13 ( 2796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 685 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8559 (m100) cc_final: 0.8253 (m100) REVERT: B 141 MET cc_start: 0.5656 (ptt) cc_final: 0.4375 (mtm) REVERT: B 155 LYS cc_start: 0.6588 (tttt) cc_final: 0.6289 (tttt) REVERT: B 180 ILE cc_start: 0.7497 (mp) cc_final: 0.7276 (mt) REVERT: B 188 TRP cc_start: 0.8204 (m100) cc_final: 0.8000 (m100) REVERT: C 172 GLU cc_start: 0.7340 (mp0) cc_final: 0.6730 (tp30) REVERT: C 231 TYR cc_start: 0.6482 (t80) cc_final: 0.6075 (t80) REVERT: C 250 TYR cc_start: 0.8366 (t80) cc_final: 0.8121 (t80) REVERT: C 268 ASP cc_start: 0.6916 (m-30) cc_final: 0.6605 (m-30) REVERT: C 323 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7156 (ttm110) REVERT: C 444 SER cc_start: 0.8723 (t) cc_final: 0.8282 (p) REVERT: C 449 LYS cc_start: 0.7902 (pttt) cc_final: 0.6898 (tppt) REVERT: C 923 SER cc_start: 0.8373 (m) cc_final: 0.7953 (p) REVERT: D 1 MET cc_start: 0.5405 (mtp) cc_final: 0.5098 (mtm) REVERT: D 83 THR cc_start: 0.9351 (p) cc_final: 0.8933 (t) REVERT: D 136 ASN cc_start: 0.7774 (p0) cc_final: 0.7475 (p0) REVERT: D 202 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8945 (pp) REVERT: D 272 MET cc_start: 0.8643 (tpp) cc_final: 0.8307 (mmm) REVERT: E 3 ILE cc_start: 0.8818 (tp) cc_final: 0.8455 (pt) REVERT: E 165 GLU cc_start: 0.8187 (pm20) cc_final: 0.7912 (pt0) REVERT: E 188 ASP cc_start: 0.7948 (p0) cc_final: 0.7739 (p0) REVERT: E 199 MET cc_start: 0.8514 (tmm) cc_final: 0.8164 (ttt) REVERT: F 199 MET cc_start: 0.8385 (tmm) cc_final: 0.8042 (ttp) REVERT: F 269 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8312 (t) REVERT: G 96 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8004 (ttm170) REVERT: G 397 ASP cc_start: 0.7472 (t0) cc_final: 0.7267 (t0) REVERT: G 545 ASP cc_start: 0.7854 (t70) cc_final: 0.7531 (t0) REVERT: H 18 TYR cc_start: 0.8350 (m-80) cc_final: 0.8111 (m-80) REVERT: H 91 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8077 (mmtp) REVERT: H 166 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6041 (tp30) REVERT: H 368 ILE cc_start: 0.9017 (mm) cc_final: 0.8676 (mm) REVERT: H 424 ASP cc_start: 0.6568 (t0) cc_final: 0.6362 (t0) REVERT: H 514 HIS cc_start: 0.8139 (t-170) cc_final: 0.7661 (t-170) REVERT: H 555 CYS cc_start: 0.8124 (p) cc_final: 0.7446 (p) REVERT: I 71 ASN cc_start: 0.6471 (t0) cc_final: 0.6197 (t0) REVERT: I 98 VAL cc_start: 0.7451 (t) cc_final: 0.7098 (m) REVERT: I 124 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7935 (m) REVERT: I 128 VAL cc_start: 0.8109 (p) cc_final: 0.7840 (t) REVERT: I 428 ILE cc_start: 0.8204 (mm) cc_final: 0.7692 (mm) REVERT: J 186 SER cc_start: 0.7560 (m) cc_final: 0.7206 (p) REVERT: K 27 ILE cc_start: 0.8630 (pt) cc_final: 0.8420 (pt) REVERT: K 87 TYR cc_start: 0.7300 (m-10) cc_final: 0.6495 (m-10) REVERT: K 157 GLU cc_start: 0.7369 (tt0) cc_final: 0.7007 (mt-10) REVERT: K 204 ASP cc_start: 0.6738 (p0) cc_final: 0.6445 (p0) REVERT: L 6 ASN cc_start: 0.8448 (m-40) cc_final: 0.7662 (m-40) REVERT: L 120 MET cc_start: 0.7835 (mtt) cc_final: 0.7555 (mtp) REVERT: L 134 GLN cc_start: 0.8689 (mm-40) cc_final: 0.7271 (tp-100) REVERT: M 153 VAL cc_start: 0.8757 (t) cc_final: 0.8511 (p) REVERT: M 173 THR cc_start: 0.7761 (p) cc_final: 0.7335 (m) REVERT: M 187 LEU cc_start: 0.7363 (mp) cc_final: 0.6378 (mp) REVERT: M 189 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7334 (mp10) REVERT: M 190 MET cc_start: 0.7377 (ttm) cc_final: 0.6997 (mmm) REVERT: M 284 MET cc_start: 0.6786 (ppp) cc_final: 0.6530 (ttm) REVERT: N 4 ILE cc_start: 0.7684 (mm) cc_final: 0.7484 (tt) REVERT: N 65 ASP cc_start: 0.6419 (t70) cc_final: 0.5789 (t70) REVERT: N 190 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7881 (mtp) REVERT: N 255 ILE cc_start: 0.6307 (mp) cc_final: 0.5994 (tp) REVERT: N 284 MET cc_start: 0.6951 (ttp) cc_final: 0.6357 (ttt) REVERT: O 157 GLN cc_start: 0.7517 (mp10) cc_final: 0.6938 (mm-40) REVERT: O 189 GLN cc_start: 0.8029 (mp10) cc_final: 0.6981 (mp10) REVERT: O 211 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6337 (mp10) outliers start: 146 outliers final: 104 residues processed: 780 average time/residue: 0.2289 time to fit residues: 302.0305 Evaluate side-chains 709 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 601 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 999 THR Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 507 ASP Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 535 THR Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 546 GLU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 241 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 297 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN C 527 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN G 448 ASN G 580 HIS I 353 HIS I 448 ASN ** J 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN O 66 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129695 restraints weight = 57733.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120658 restraints weight = 108056.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119022 restraints weight = 107121.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119431 restraints weight = 99497.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.119742 restraints weight = 78792.163| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 42643 Z= 0.184 Angle : 0.568 8.322 58076 Z= 0.301 Chirality : 0.047 0.182 6523 Planarity : 0.004 0.050 7606 Dihedral : 4.593 41.209 5780 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.07 % Allowed : 15.53 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.11), residues: 5323 helix: -0.17 (0.22), residues: 568 sheet: -0.47 (0.14), residues: 1373 loop : -1.08 (0.10), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 46 TYR 0.026 0.002 TYR H 201 PHE 0.017 0.002 PHE G 181 TRP 0.032 0.002 TRP H 254 HIS 0.011 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (42637) covalent geometry : angle 0.56788 / 0.30 (58064) SS BOND : bond 0.02298 / 1.14 ( 6) SS BOND : angle 1.24676 / 0.73 ( 12) hydrogen bonds : bond 0.03457 / 2.27 ( 1021) hydrogen bonds : angle 5.65012 / 3.96 ( 2796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 660 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.7793 (t80) cc_final: 0.7545 (t80) REVERT: A 221 THR cc_start: 0.8790 (m) cc_final: 0.8589 (t) REVERT: A 322 MET cc_start: 0.7589 (mmm) cc_final: 0.7386 (mmm) REVERT: B 47 TRP cc_start: 0.8609 (m100) cc_final: 0.8291 (m100) REVERT: B 141 MET cc_start: 0.5405 (ptt) cc_final: 0.4651 (mtm) REVERT: B 155 LYS cc_start: 0.6717 (tttt) cc_final: 0.6509 (tttt) REVERT: B 180 ILE cc_start: 0.7517 (mp) cc_final: 0.7275 (mt) REVERT: B 188 TRP cc_start: 0.8227 (m100) cc_final: 0.7654 (m-90) REVERT: B 300 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7077 (tp30) REVERT: C 172 GLU cc_start: 0.7181 (mp0) cc_final: 0.6429 (tp30) REVERT: C 231 TYR cc_start: 0.7338 (t80) cc_final: 0.6393 (t80) REVERT: C 250 TYR cc_start: 0.8600 (t80) cc_final: 0.8192 (t80) REVERT: C 252 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8359 (pttt) REVERT: C 268 ASP cc_start: 0.6794 (m-30) cc_final: 0.6471 (m-30) REVERT: C 323 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7182 (ttm110) REVERT: C 444 SER cc_start: 0.8730 (t) cc_final: 0.8323 (p) REVERT: C 927 THR cc_start: 0.8806 (p) cc_final: 0.8482 (m) REVERT: C 946 SER cc_start: 0.8423 (m) cc_final: 0.8217 (p) REVERT: C 952 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8310 (pt) REVERT: D 136 ASN cc_start: 0.8133 (p0) cc_final: 0.7847 (p0) REVERT: D 202 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9000 (pp) REVERT: D 235 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: D 272 MET cc_start: 0.8658 (tpp) cc_final: 0.8315 (mmm) REVERT: E 165 GLU cc_start: 0.8160 (pm20) cc_final: 0.7898 (pt0) REVERT: E 199 MET cc_start: 0.8572 (tmm) cc_final: 0.8276 (ttt) REVERT: E 245 GLU cc_start: 0.7798 (tp30) cc_final: 0.7221 (tm-30) REVERT: E 257 LYS cc_start: 0.7856 (mptt) cc_final: 0.7592 (mptt) REVERT: F 199 MET cc_start: 0.8360 (tmm) cc_final: 0.8157 (ttp) REVERT: F 269 THR cc_start: 0.8828 (p) cc_final: 0.8390 (t) REVERT: G 96 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8066 (ttm-80) REVERT: G 167 PHE cc_start: 0.6024 (m-10) cc_final: 0.5813 (m-80) REVERT: G 379 ASP cc_start: 0.7655 (m-30) cc_final: 0.7352 (m-30) REVERT: G 397 ASP cc_start: 0.7593 (t0) cc_final: 0.7249 (t0) REVERT: G 545 ASP cc_start: 0.7805 (t70) cc_final: 0.7518 (t0) REVERT: H 91 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8102 (mmtp) REVERT: H 368 ILE cc_start: 0.8983 (mm) cc_final: 0.8628 (mm) REVERT: H 514 HIS cc_start: 0.8255 (t-170) cc_final: 0.7841 (t-170) REVERT: H 546 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6969 (pp20) REVERT: H 555 CYS cc_start: 0.8120 (p) cc_final: 0.7516 (p) REVERT: I 71 ASN cc_start: 0.6444 (t0) cc_final: 0.6240 (t0) REVERT: I 124 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8051 (m) REVERT: I 428 ILE cc_start: 0.8347 (mm) cc_final: 0.7912 (mm) REVERT: J 49 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8024 (mm-30) REVERT: J 128 LYS cc_start: 0.6840 (mtmm) cc_final: 0.6595 (mtmm) REVERT: J 186 SER cc_start: 0.7587 (m) cc_final: 0.7209 (p) REVERT: K 87 TYR cc_start: 0.7374 (m-10) cc_final: 0.6646 (m-10) REVERT: K 204 ASP cc_start: 0.6930 (p0) cc_final: 0.6601 (p0) REVERT: L 6 ASN cc_start: 0.8395 (m-40) cc_final: 0.7979 (m-40) REVERT: L 134 GLN cc_start: 0.8808 (mm-40) cc_final: 0.7317 (tp-100) REVERT: M 153 VAL cc_start: 0.8769 (t) cc_final: 0.8520 (p) REVERT: M 173 THR cc_start: 0.7837 (p) cc_final: 0.7503 (m) REVERT: M 187 LEU cc_start: 0.7390 (mp) cc_final: 0.6349 (mp) REVERT: M 189 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7365 (mp10) REVERT: M 190 MET cc_start: 0.7504 (ttm) cc_final: 0.6896 (mmm) REVERT: M 284 MET cc_start: 0.7335 (ppp) cc_final: 0.6633 (ttm) REVERT: N 65 ASP cc_start: 0.6655 (t70) cc_final: 0.6189 (t70) REVERT: N 190 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7923 (mtp) REVERT: N 255 ILE cc_start: 0.6375 (mp) cc_final: 0.6030 (tp) REVERT: N 284 MET cc_start: 0.7055 (ttp) cc_final: 0.6325 (ttt) REVERT: O 157 GLN cc_start: 0.7586 (mp10) cc_final: 0.7052 (mm-40) REVERT: O 189 GLN cc_start: 0.8200 (mp10) cc_final: 0.7170 (mp10) REVERT: O 211 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6272 (mp10) outliers start: 188 outliers final: 130 residues processed: 792 average time/residue: 0.2109 time to fit residues: 284.9602 Evaluate side-chains 733 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 597 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 999 THR Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 293 PHE Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 507 ASP Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 535 THR Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain H residue 546 GLU Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 367 GLU Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 481 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 466 optimal weight: 6.9990 chunk 452 optimal weight: 2.9990 chunk 460 optimal weight: 7.9990 chunk 128 optimal weight: 0.0000 chunk 72 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 125 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 580 HIS J 5 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** 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 = 0.3504 r_free = 0.3504 target = 0.139526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.129018 restraints weight = 57529.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120650 restraints weight = 107520.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119226 restraints weight = 118792.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119649 restraints weight = 107378.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119902 restraints weight = 77694.761| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42643 Z= 0.157 Angle : 0.546 11.078 58076 Z= 0.287 Chirality : 0.046 0.206 6523 Planarity : 0.004 0.049 7606 Dihedral : 4.542 42.813 5780 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.85 % Allowed : 17.42 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.11), residues: 5323 helix: -0.18 (0.22), residues: 568 sheet: -0.47 (0.14), residues: 1342 loop : -1.08 (0.10), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 46 TYR 0.028 0.002 TYR H 201 PHE 0.015 0.001 PHE G 181 TRP 0.017 0.001 TRP H 49 HIS 0.010 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (42637) covalent geometry : angle 0.54598 / 0.29 (58064) SS BOND : bond 0.00707 / 0.34 ( 6) SS BOND : angle 0.64938 / 0.36 ( 12) hydrogen bonds : bond 0.03252 / 2.13 ( 1021) hydrogen bonds : angle 5.49013 / 3.84 ( 2796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 615 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8606 (m100) cc_final: 0.8304 (m100) REVERT: B 141 MET cc_start: 0.5427 (ptt) cc_final: 0.4649 (mtm) REVERT: B 155 LYS cc_start: 0.6867 (tttt) cc_final: 0.6552 (tttt) REVERT: B 188 TRP cc_start: 0.8260 (m100) cc_final: 0.7706 (m-90) REVERT: C 172 GLU cc_start: 0.7253 (mp0) cc_final: 0.6383 (tp30) REVERT: C 231 TYR cc_start: 0.7579 (t80) cc_final: 0.6593 (t80) REVERT: C 252 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8158 (pttt) REVERT: C 335 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7832 (pp) REVERT: C 444 SER cc_start: 0.8711 (t) cc_final: 0.8315 (p) REVERT: C 491 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8842 (mt) REVERT: C 927 THR cc_start: 0.8883 (p) cc_final: 0.8562 (m) REVERT: C 946 SER cc_start: 0.8422 (m) cc_final: 0.8176 (p) REVERT: C 952 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8314 (pt) REVERT: D 83 THR cc_start: 0.9512 (p) cc_final: 0.9122 (t) REVERT: D 136 ASN cc_start: 0.8168 (p0) cc_final: 0.7872 (p0) REVERT: D 202 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8913 (pp) REVERT: D 235 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: D 272 MET cc_start: 0.8626 (tpp) cc_final: 0.8274 (mmm) REVERT: E 165 GLU cc_start: 0.8321 (pm20) cc_final: 0.7894 (pt0) REVERT: E 199 MET cc_start: 0.8601 (tmm) cc_final: 0.8286 (ttt) REVERT: F 269 THR cc_start: 0.8854 (p) cc_final: 0.8409 (t) REVERT: G 96 ARG cc_start: 0.8510 (ttm170) cc_final: 0.8063 (ttm-80) REVERT: G 379 ASP cc_start: 0.7602 (m-30) cc_final: 0.7319 (m-30) REVERT: G 397 ASP cc_start: 0.7651 (t0) cc_final: 0.7290 (t0) REVERT: G 545 ASP cc_start: 0.7779 (t70) cc_final: 0.7492 (t0) REVERT: G 557 TYR cc_start: 0.5971 (t80) cc_final: 0.5449 (t80) REVERT: H 91 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8086 (mmtp) REVERT: H 248 MET cc_start: 0.6221 (mtt) cc_final: 0.5857 (mtt) REVERT: H 368 ILE cc_start: 0.8982 (mm) cc_final: 0.8654 (mm) REVERT: H 514 HIS cc_start: 0.8327 (t-170) cc_final: 0.7804 (t-170) REVERT: H 555 CYS cc_start: 0.8122 (p) cc_final: 0.7549 (p) REVERT: I 85 THR cc_start: 0.8633 (p) cc_final: 0.8394 (t) REVERT: I 124 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8093 (m) REVERT: I 151 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7090 (mt) REVERT: I 168 LEU cc_start: 0.6873 (mt) cc_final: 0.6336 (tt) REVERT: I 320 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8737 (tt) REVERT: I 365 ILE cc_start: 0.8853 (mm) cc_final: 0.8350 (pt) REVERT: I 428 ILE cc_start: 0.8383 (mm) cc_final: 0.7935 (mm) REVERT: I 461 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6825 (mt-10) REVERT: J 49 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8055 (mm-30) REVERT: J 128 LYS cc_start: 0.6853 (mtmm) cc_final: 0.6471 (mtmm) REVERT: J 186 SER cc_start: 0.7532 (m) cc_final: 0.7185 (p) REVERT: K 62 PHE cc_start: 0.8209 (m-10) cc_final: 0.7994 (m-80) REVERT: K 87 TYR cc_start: 0.7443 (m-10) cc_final: 0.6830 (m-10) REVERT: K 157 GLU cc_start: 0.7290 (tt0) cc_final: 0.6865 (mt-10) REVERT: L 6 ASN cc_start: 0.8410 (m-40) cc_final: 0.7893 (m-40) REVERT: L 128 LYS cc_start: 0.8502 (mmtt) cc_final: 0.7986 (mmmt) REVERT: L 134 GLN cc_start: 0.8789 (mm-40) cc_final: 0.7342 (tp-100) REVERT: M 101 SER cc_start: 0.9235 (t) cc_final: 0.8698 (m) REVERT: M 153 VAL cc_start: 0.8769 (t) cc_final: 0.8499 (p) REVERT: M 173 THR cc_start: 0.7821 (p) cc_final: 0.7566 (m) REVERT: M 189 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7339 (mp10) REVERT: M 284 MET cc_start: 0.7516 (ppp) cc_final: 0.6735 (ttm) REVERT: N 65 ASP cc_start: 0.7007 (t70) cc_final: 0.6479 (t70) REVERT: N 190 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7945 (mtp) REVERT: N 236 HIS cc_start: 0.7362 (t-90) cc_final: 0.7036 (t-90) REVERT: N 255 ILE cc_start: 0.6432 (mp) cc_final: 0.6086 (tp) REVERT: N 284 MET cc_start: 0.6884 (ttp) cc_final: 0.6545 (ttt) REVERT: O 171 LEU cc_start: 0.8165 (mm) cc_final: 0.7820 (mp) outliers start: 178 outliers final: 136 residues processed: 741 average time/residue: 0.2169 time to fit residues: 274.0655 Evaluate side-chains 745 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 600 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 293 PHE Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 507 ASP Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 535 THR Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 367 GLU Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 452 THR Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 179 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 292 optimal weight: 0.0070 chunk 53 optimal weight: 0.8980 chunk 275 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 351 optimal weight: 0.1980 chunk 218 optimal weight: 0.0000 chunk 69 optimal weight: 0.7980 chunk 328 optimal weight: 9.9990 chunk 516 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 125 GLN ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 580 HIS I 198 ASN J 31 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.145346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134994 restraints weight = 57203.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124129 restraints weight = 107475.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122792 restraints weight = 93562.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.123227 restraints weight = 91526.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.123538 restraints weight = 71157.142| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 42643 Z= 0.097 Angle : 0.510 9.253 58076 Z= 0.268 Chirality : 0.045 0.171 6523 Planarity : 0.003 0.046 7606 Dihedral : 4.297 41.717 5780 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.86 % Allowed : 18.76 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.11), residues: 5323 helix: 0.01 (0.22), residues: 567 sheet: -0.35 (0.15), residues: 1342 loop : -1.00 (0.10), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 323 TYR 0.023 0.001 TYR H 201 PHE 0.017 0.001 PHE N 233 TRP 0.015 0.001 TRP H 478 HIS 0.008 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (42637) covalent geometry : angle 0.50987 / 0.27 (58064) SS BOND : bond 0.00061 / 0.03 ( 6) SS BOND : angle 0.90946 / 0.54 ( 12) hydrogen bonds : bond 0.02915 / 1.91 ( 1021) hydrogen bonds : angle 5.24666 / 3.66 ( 2796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 648 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8592 (m100) cc_final: 0.8249 (m100) REVERT: B 141 MET cc_start: 0.5315 (ptt) cc_final: 0.4520 (mtm) REVERT: B 155 LYS cc_start: 0.6642 (tttt) cc_final: 0.6302 (tttt) REVERT: B 188 TRP cc_start: 0.8287 (m100) cc_final: 0.7811 (m-90) REVERT: B 201 ASN cc_start: 0.7727 (t0) cc_final: 0.6806 (m-40) REVERT: B 312 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8246 (mmt) REVERT: B 320 MET cc_start: 0.3896 (ptt) cc_final: 0.3381 (mmt) REVERT: C 172 GLU cc_start: 0.7228 (mp0) cc_final: 0.6381 (tp30) REVERT: C 252 LYS cc_start: 0.8597 (ptpp) cc_final: 0.8247 (pttm) REVERT: C 312 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8542 (p) REVERT: C 444 SER cc_start: 0.8653 (t) cc_final: 0.8207 (p) REVERT: C 946 SER cc_start: 0.8451 (m) cc_final: 0.8186 (p) REVERT: D 83 THR cc_start: 0.9465 (p) cc_final: 0.9056 (t) REVERT: D 136 ASN cc_start: 0.8087 (p0) cc_final: 0.7825 (p0) REVERT: D 202 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8944 (pp) REVERT: D 235 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: D 239 ARG cc_start: 0.8602 (ptt90) cc_final: 0.8394 (ptt90) REVERT: D 272 MET cc_start: 0.8631 (tpp) cc_final: 0.8351 (mmm) REVERT: E 22 ASP cc_start: 0.8001 (t0) cc_final: 0.7786 (t70) REVERT: E 154 ASP cc_start: 0.6198 (t0) cc_final: 0.5399 (m-30) REVERT: E 199 MET cc_start: 0.8553 (tmm) cc_final: 0.8301 (ttt) REVERT: E 238 MET cc_start: 0.8617 (mtm) cc_final: 0.8238 (mtm) REVERT: F 199 MET cc_start: 0.8278 (ttp) cc_final: 0.7858 (ttp) REVERT: F 269 THR cc_start: 0.8758 (p) cc_final: 0.8376 (t) REVERT: G 96 ARG cc_start: 0.8446 (ttm170) cc_final: 0.8001 (ttm-80) REVERT: G 151 ILE cc_start: 0.8445 (mm) cc_final: 0.8011 (mt) REVERT: G 288 MET cc_start: 0.8527 (tpt) cc_final: 0.8307 (tpt) REVERT: G 305 ASN cc_start: 0.8574 (t0) cc_final: 0.7656 (t0) REVERT: G 379 ASP cc_start: 0.7528 (m-30) cc_final: 0.7269 (m-30) REVERT: G 397 ASP cc_start: 0.7677 (t0) cc_final: 0.7307 (t0) REVERT: G 545 ASP cc_start: 0.7778 (t70) cc_final: 0.7546 (t0) REVERT: G 557 TYR cc_start: 0.5910 (t80) cc_final: 0.5492 (t80) REVERT: H 91 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8183 (mmtp) REVERT: H 248 MET cc_start: 0.6176 (mtt) cc_final: 0.5769 (mtt) REVERT: H 368 ILE cc_start: 0.8946 (mm) cc_final: 0.8620 (mm) REVERT: H 514 HIS cc_start: 0.8262 (t-170) cc_final: 0.7742 (t-170) REVERT: H 555 CYS cc_start: 0.8050 (p) cc_final: 0.7364 (p) REVERT: I 85 THR cc_start: 0.8566 (p) cc_final: 0.8334 (t) REVERT: I 124 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8031 (m) REVERT: I 129 ARG cc_start: 0.6683 (tpt90) cc_final: 0.6417 (tpt170) REVERT: I 168 LEU cc_start: 0.7140 (mt) cc_final: 0.6674 (tt) REVERT: I 320 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8694 (tt) REVERT: I 428 ILE cc_start: 0.8320 (mm) cc_final: 0.7878 (mm) REVERT: I 461 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6744 (mt-10) REVERT: J 49 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7998 (mm-30) REVERT: J 73 ASN cc_start: 0.8616 (p0) cc_final: 0.8000 (p0) REVERT: J 128 LYS cc_start: 0.6779 (mtmm) cc_final: 0.6218 (mtmm) REVERT: J 186 SER cc_start: 0.7448 (m) cc_final: 0.7152 (p) REVERT: K 87 TYR cc_start: 0.7230 (m-10) cc_final: 0.6680 (m-10) REVERT: L 6 ASN cc_start: 0.8387 (m-40) cc_final: 0.7857 (m-40) REVERT: L 128 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8048 (mmmt) REVERT: L 134 GLN cc_start: 0.8756 (mm-40) cc_final: 0.7485 (tp-100) REVERT: M 7 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: M 101 SER cc_start: 0.9205 (t) cc_final: 0.8711 (m) REVERT: M 153 VAL cc_start: 0.8764 (t) cc_final: 0.8558 (p) REVERT: M 173 THR cc_start: 0.7755 (p) cc_final: 0.7443 (m) REVERT: M 189 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7346 (mp10) REVERT: M 284 MET cc_start: 0.7540 (ppp) cc_final: 0.6822 (ttm) REVERT: N 65 ASP cc_start: 0.6979 (t70) cc_final: 0.6455 (t70) REVERT: N 190 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: N 255 ILE cc_start: 0.6249 (mp) cc_final: 0.5918 (tp) REVERT: N 284 MET cc_start: 0.6869 (ttp) cc_final: 0.6411 (ttt) outliers start: 132 outliers final: 95 residues processed: 738 average time/residue: 0.2142 time to fit residues: 267.8329 Evaluate side-chains 709 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 606 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 507 ASP Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 343 SER Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 452 THR Chi-restraints excluded: chain I residue 544 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 192 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 200 optimal weight: 7.9990 chunk 512 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 451 optimal weight: 6.9990 chunk 453 optimal weight: 2.9990 chunk 506 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 289 ASN A 324 GLN B 74 HIS B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 125 GLN F 111 ASN ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 580 HIS ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125947 restraints weight = 57737.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.117421 restraints weight = 106730.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.116342 restraints weight = 91809.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.116520 restraints weight = 87466.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.116574 restraints weight = 74563.656| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 42643 Z= 0.212 Angle : 0.599 9.214 58076 Z= 0.316 Chirality : 0.048 0.188 6523 Planarity : 0.004 0.063 7606 Dihedral : 4.672 45.173 5780 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.13 % Allowed : 18.35 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.11), residues: 5323 helix: -0.17 (0.22), residues: 566 sheet: -0.57 (0.14), residues: 1381 loop : -1.10 (0.10), residues: 3376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 323 TYR 0.032 0.002 TYR C 231 PHE 0.015 0.002 PHE N 233 TRP 0.021 0.002 TRP H 49 HIS 0.011 0.001 HIS I 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (42637) covalent geometry : angle 0.59872 / 0.32 (58064) SS BOND : bond 0.00406 / 0.21 ( 6) SS BOND : angle 0.84918 / 0.49 ( 12) hydrogen bonds : bond 0.03410 / 2.23 ( 1021) hydrogen bonds : angle 5.39990 / 3.78 ( 2796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 625 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7343 (tp30) cc_final: 0.6952 (tt0) REVERT: B 47 TRP cc_start: 0.8631 (m100) cc_final: 0.8336 (m100) REVERT: B 141 MET cc_start: 0.5657 (ptt) cc_final: 0.4697 (mtm) REVERT: B 155 LYS cc_start: 0.6909 (tttt) cc_final: 0.6652 (tttt) REVERT: B 160 TRP cc_start: 0.7842 (t-100) cc_final: 0.7640 (t-100) REVERT: B 166 SER cc_start: 0.7954 (t) cc_final: 0.7641 (p) REVERT: B 188 TRP cc_start: 0.8313 (m100) cc_final: 0.7773 (m-90) REVERT: B 229 LEU cc_start: 0.8729 (mt) cc_final: 0.8509 (mp) REVERT: B 238 LEU cc_start: 0.8318 (tp) cc_final: 0.8085 (tp) REVERT: B 240 TYR cc_start: 0.8185 (m-80) cc_final: 0.7794 (m-80) REVERT: B 312 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8297 (mmt) REVERT: C 172 GLU cc_start: 0.6990 (mp0) cc_final: 0.5682 (tp30) REVERT: C 231 TYR cc_start: 0.7936 (t80) cc_final: 0.6828 (t80) REVERT: C 252 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8167 (pttt) REVERT: C 444 SER cc_start: 0.8854 (t) cc_final: 0.8484 (p) REVERT: C 494 GLU cc_start: 0.7653 (tp30) cc_final: 0.7442 (tp30) REVERT: C 946 SER cc_start: 0.8411 (m) cc_final: 0.8142 (p) REVERT: C 952 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8345 (pt) REVERT: D 83 THR cc_start: 0.9528 (p) cc_final: 0.9189 (t) REVERT: D 136 ASN cc_start: 0.8111 (p0) cc_final: 0.7823 (p0) REVERT: D 202 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8882 (pp) REVERT: D 235 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: D 272 MET cc_start: 0.8728 (tpp) cc_final: 0.8344 (mmm) REVERT: F 269 THR cc_start: 0.8820 (p) cc_final: 0.8344 (t) REVERT: G 151 ILE cc_start: 0.8637 (mm) cc_final: 0.8388 (mt) REVERT: G 379 ASP cc_start: 0.7615 (m-30) cc_final: 0.7289 (m-30) REVERT: G 397 ASP cc_start: 0.7750 (t0) cc_final: 0.7445 (t0) REVERT: G 434 GLU cc_start: 0.7713 (pm20) cc_final: 0.7509 (pm20) REVERT: G 545 ASP cc_start: 0.7771 (t70) cc_final: 0.7449 (t0) REVERT: G 557 TYR cc_start: 0.6012 (t80) cc_final: 0.5804 (t80) REVERT: H 248 MET cc_start: 0.6553 (mtt) cc_final: 0.6245 (mtt) REVERT: H 368 ILE cc_start: 0.8980 (mm) cc_final: 0.8747 (mm) REVERT: H 555 CYS cc_start: 0.8192 (p) cc_final: 0.7790 (p) REVERT: I 151 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7168 (mt) REVERT: I 168 LEU cc_start: 0.7485 (mt) cc_final: 0.7143 (tt) REVERT: I 365 ILE cc_start: 0.8929 (mm) cc_final: 0.8402 (pt) REVERT: I 428 ILE cc_start: 0.8542 (mm) cc_final: 0.8085 (mm) REVERT: I 434 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: J 30 MET cc_start: 0.6825 (tpp) cc_final: 0.6468 (tpt) REVERT: J 49 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8063 (mm-30) REVERT: J 186 SER cc_start: 0.7578 (m) cc_final: 0.7209 (p) REVERT: L 6 ASN cc_start: 0.8424 (m-40) cc_final: 0.8070 (m-40) REVERT: L 134 GLN cc_start: 0.8845 (mm-40) cc_final: 0.7312 (tp-100) REVERT: M 7 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: M 101 SER cc_start: 0.9233 (t) cc_final: 0.8706 (m) REVERT: M 153 VAL cc_start: 0.8765 (t) cc_final: 0.8504 (p) REVERT: M 173 THR cc_start: 0.7927 (p) cc_final: 0.7710 (m) REVERT: M 189 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7423 (mp10) REVERT: M 284 MET cc_start: 0.7476 (ppp) cc_final: 0.6783 (ttm) REVERT: N 65 ASP cc_start: 0.7064 (t70) cc_final: 0.6532 (t70) REVERT: N 190 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7998 (mtp) REVERT: N 255 ILE cc_start: 0.6425 (mp) cc_final: 0.6096 (tp) REVERT: N 284 MET cc_start: 0.6908 (ttp) cc_final: 0.6363 (ttp) REVERT: O 157 GLN cc_start: 0.7660 (mp10) cc_final: 0.7135 (mm-40) REVERT: O 211 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6183 (mp10) outliers start: 191 outliers final: 148 residues processed: 764 average time/residue: 0.2175 time to fit residues: 282.6601 Evaluate side-chains 745 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 589 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 293 PHE Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 343 SER Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 421 ASN Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 452 THR Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 256 VAL Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 192 VAL Chi-restraints excluded: chain O residue 242 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 423 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 475 optimal weight: 1.9990 chunk 483 optimal weight: 5.9990 chunk 105 optimal weight: 0.0370 chunk 444 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 487 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 458 optimal weight: 4.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 74 HIS B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 111 ASN ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN G 307 ASN G 580 HIS I 148 ASN L 206 GLN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 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 = 0.3517 r_free = 0.3517 target = 0.140253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.129537 restraints weight = 57569.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121457 restraints weight = 99954.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.120584 restraints weight = 77249.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.120494 restraints weight = 77620.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121021 restraints weight = 65396.714| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 42643 Z= 0.108 Angle : 0.536 9.517 58076 Z= 0.282 Chirality : 0.046 0.224 6523 Planarity : 0.004 0.057 7606 Dihedral : 4.413 44.388 5780 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.99 % Allowed : 20.12 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.11), residues: 5323 helix: 0.01 (0.22), residues: 555 sheet: -0.48 (0.14), residues: 1381 loop : -1.01 (0.10), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 323 TYR 0.021 0.001 TYR A 296 PHE 0.016 0.001 PHE N 233 TRP 0.014 0.001 TRP H 478 HIS 0.008 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (42637) covalent geometry : angle 0.53647 / 0.28 (58064) SS BOND : bond 0.00329 / 0.16 ( 6) SS BOND : angle 0.63099 / 0.32 ( 12) hydrogen bonds : bond 0.02923 / 1.92 ( 1021) hydrogen bonds : angle 5.17108 / 3.61 ( 2796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 617 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8418 (tp) cc_final: 0.7627 (mt) REVERT: B 21 MET cc_start: 0.9135 (ttp) cc_final: 0.8709 (ptm) REVERT: B 47 TRP cc_start: 0.8609 (m100) cc_final: 0.8384 (m100) REVERT: B 141 MET cc_start: 0.5425 (ptt) cc_final: 0.4591 (mtm) REVERT: B 155 LYS cc_start: 0.6658 (tttt) cc_final: 0.6391 (tttt) REVERT: B 166 SER cc_start: 0.7515 (t) cc_final: 0.7285 (p) REVERT: B 188 TRP cc_start: 0.8365 (m100) cc_final: 0.7949 (m-90) REVERT: B 192 PHE cc_start: 0.8894 (p90) cc_final: 0.8563 (p90) REVERT: B 238 LEU cc_start: 0.8384 (tp) cc_final: 0.8134 (tp) REVERT: B 240 TYR cc_start: 0.8240 (m-80) cc_final: 0.7979 (m-80) REVERT: B 308 GLU cc_start: 0.7521 (tp30) cc_final: 0.7150 (tp30) REVERT: B 312 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8314 (mmt) REVERT: B 320 MET cc_start: 0.3718 (ptt) cc_final: 0.3193 (mmt) REVERT: C 172 GLU cc_start: 0.6954 (mp0) cc_final: 0.5654 (tp30) REVERT: C 231 TYR cc_start: 0.7705 (t80) cc_final: 0.6648 (t80) REVERT: C 252 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8193 (pttt) REVERT: C 312 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8583 (p) REVERT: C 444 SER cc_start: 0.8730 (t) cc_final: 0.8253 (p) REVERT: C 952 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8177 (pt) REVERT: D 83 THR cc_start: 0.9379 (p) cc_final: 0.8952 (t) REVERT: D 136 ASN cc_start: 0.8051 (p0) cc_final: 0.7765 (p0) REVERT: D 202 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8944 (pp) REVERT: D 235 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: D 272 MET cc_start: 0.8653 (tpp) cc_final: 0.8266 (mmm) REVERT: E 154 ASP cc_start: 0.6202 (t0) cc_final: 0.5247 (m-30) REVERT: E 199 MET cc_start: 0.8594 (tmm) cc_final: 0.8285 (ttt) REVERT: E 238 MET cc_start: 0.8665 (mtm) cc_final: 0.8327 (mtm) REVERT: F 269 THR cc_start: 0.8760 (p) cc_final: 0.8255 (t) REVERT: G 96 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7980 (ttm-80) REVERT: G 151 ILE cc_start: 0.8461 (mm) cc_final: 0.8190 (mt) REVERT: G 379 ASP cc_start: 0.7628 (m-30) cc_final: 0.7398 (m-30) REVERT: G 397 ASP cc_start: 0.7829 (t0) cc_final: 0.7349 (t0) REVERT: G 545 ASP cc_start: 0.7700 (t70) cc_final: 0.7428 (t0) REVERT: G 557 TYR cc_start: 0.5958 (t80) cc_final: 0.5561 (t80) REVERT: H 108 THR cc_start: 0.8485 (t) cc_final: 0.8232 (p) REVERT: H 248 MET cc_start: 0.6474 (mtt) cc_final: 0.6113 (mtt) REVERT: H 514 HIS cc_start: 0.7837 (t-170) cc_final: 0.7340 (t-170) REVERT: H 555 CYS cc_start: 0.8093 (p) cc_final: 0.7612 (p) REVERT: I 168 LEU cc_start: 0.7415 (mt) cc_final: 0.7060 (tt) REVERT: I 194 LYS cc_start: 0.5229 (mttt) cc_final: 0.4671 (mttp) REVERT: I 428 ILE cc_start: 0.8417 (mm) cc_final: 0.7991 (mm) REVERT: J 49 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8145 (mm-30) REVERT: J 74 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7924 (mtpt) REVERT: J 186 SER cc_start: 0.7426 (m) cc_final: 0.7166 (p) REVERT: K 199 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7583 (tm-30) REVERT: L 6 ASN cc_start: 0.8449 (m-40) cc_final: 0.7913 (m-40) REVERT: L 128 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8333 (mmmt) REVERT: L 134 GLN cc_start: 0.8729 (mm-40) cc_final: 0.7423 (tp-100) REVERT: L 203 LEU cc_start: 0.6755 (mt) cc_final: 0.6356 (mt) REVERT: M 7 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: M 101 SER cc_start: 0.9225 (t) cc_final: 0.8705 (m) REVERT: M 150 VAL cc_start: 0.8830 (t) cc_final: 0.8593 (m) REVERT: M 153 VAL cc_start: 0.8762 (t) cc_final: 0.8522 (p) REVERT: M 172 MET cc_start: 0.6845 (ptp) cc_final: 0.5979 (ptt) REVERT: M 189 GLN cc_start: 0.8499 (mm-40) cc_final: 0.7444 (mp10) REVERT: M 198 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6909 (mt-10) REVERT: M 284 MET cc_start: 0.7537 (ppp) cc_final: 0.6811 (ttm) REVERT: N 65 ASP cc_start: 0.7018 (t70) cc_final: 0.6501 (t70) REVERT: N 190 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7916 (mtp) REVERT: N 255 ILE cc_start: 0.6233 (mp) cc_final: 0.5883 (tp) REVERT: N 284 MET cc_start: 0.6792 (ttp) cc_final: 0.6183 (ttp) REVERT: N 293 ARG cc_start: 0.7329 (ptm160) cc_final: 0.7114 (ptm160) REVERT: O 59 ASP cc_start: 0.7648 (m-30) cc_final: 0.7229 (m-30) outliers start: 138 outliers final: 114 residues processed: 712 average time/residue: 0.2144 time to fit residues: 259.3698 Evaluate side-chains 700 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 579 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 293 PHE Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain H residue 581 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 343 SER Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 421 ASN Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 452 THR Chi-restraints excluded: chain I residue 544 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain O residue 192 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 361 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 442 optimal weight: 0.8980 chunk 366 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 365 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 449 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 74 HIS B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 ASN G 330 HIS G 580 HIS H 71 ASN I 148 ASN J 206 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.136784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125868 restraints weight = 57888.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117825 restraints weight = 106789.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.116387 restraints weight = 104192.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.116815 restraints weight = 97993.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.117113 restraints weight = 73865.815| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 42643 Z= 0.190 Angle : 0.582 10.207 58076 Z= 0.307 Chirality : 0.047 0.244 6523 Planarity : 0.004 0.055 7606 Dihedral : 4.582 45.784 5780 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.46 % Allowed : 20.03 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.11), residues: 5323 helix: -0.15 (0.22), residues: 566 sheet: -0.55 (0.14), residues: 1356 loop : -1.10 (0.10), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 186 TYR 0.026 0.002 TYR A 296 PHE 0.014 0.002 PHE O 8 TRP 0.022 0.002 TRP B 160 HIS 0.010 0.001 HIS I 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (42637) covalent geometry : angle 0.58225 / 0.31 (58064) SS BOND : bond 0.01070 / 0.53 ( 6) SS BOND : angle 1.02729 / 0.58 ( 12) hydrogen bonds : bond 0.03220 / 2.10 ( 1021) hydrogen bonds : angle 5.27803 / 3.69 ( 2796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 601 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8506 (tp) cc_final: 0.7703 (mt) REVERT: A 280 GLU cc_start: 0.7075 (tp30) cc_final: 0.6852 (tt0) REVERT: B 141 MET cc_start: 0.5286 (ptt) cc_final: 0.4220 (mtm) REVERT: B 155 LYS cc_start: 0.6964 (tttt) cc_final: 0.6676 (tttt) REVERT: B 166 SER cc_start: 0.7834 (t) cc_final: 0.7541 (p) REVERT: B 188 TRP cc_start: 0.8463 (m100) cc_final: 0.8017 (m-90) REVERT: B 192 PHE cc_start: 0.8864 (p90) cc_final: 0.8569 (p90) REVERT: B 238 LEU cc_start: 0.8473 (tp) cc_final: 0.8096 (tp) REVERT: B 240 TYR cc_start: 0.8258 (m-80) cc_final: 0.8008 (m-80) REVERT: B 308 GLU cc_start: 0.7632 (tp30) cc_final: 0.7170 (tp30) REVERT: B 312 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8355 (mmt) REVERT: B 320 MET cc_start: 0.3240 (ptt) cc_final: 0.2887 (mmt) REVERT: C 172 GLU cc_start: 0.7123 (mp0) cc_final: 0.5658 (tp30) REVERT: C 231 TYR cc_start: 0.8123 (t80) cc_final: 0.7157 (t80) REVERT: C 252 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8168 (pttt) REVERT: C 406 LEU cc_start: 0.7807 (tt) cc_final: 0.7375 (tt) REVERT: C 444 SER cc_start: 0.8839 (t) cc_final: 0.8447 (p) REVERT: D 83 THR cc_start: 0.9381 (p) cc_final: 0.9003 (t) REVERT: D 136 ASN cc_start: 0.8095 (p0) cc_final: 0.7881 (p0) REVERT: D 202 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8829 (pp) REVERT: D 235 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: E 199 MET cc_start: 0.8657 (tmm) cc_final: 0.8235 (ttt) REVERT: F 187 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8354 (p) REVERT: F 269 THR cc_start: 0.8812 (p) cc_final: 0.8302 (t) REVERT: G 96 ARG cc_start: 0.8378 (ttm170) cc_final: 0.8006 (ttm-80) REVERT: G 130 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8148 (p90) REVERT: G 342 CYS cc_start: 0.7315 (t) cc_final: 0.6966 (t) REVERT: G 379 ASP cc_start: 0.7568 (m-30) cc_final: 0.7250 (m-30) REVERT: G 397 ASP cc_start: 0.7896 (t0) cc_final: 0.7506 (t0) REVERT: G 506 LEU cc_start: 0.8048 (mt) cc_final: 0.7785 (mt) REVERT: G 545 ASP cc_start: 0.7706 (t70) cc_final: 0.7396 (t0) REVERT: G 557 TYR cc_start: 0.5803 (t80) cc_final: 0.5415 (t80) REVERT: H 108 THR cc_start: 0.8794 (t) cc_final: 0.8549 (p) REVERT: H 514 HIS cc_start: 0.8129 (t-170) cc_final: 0.7608 (t-170) REVERT: H 555 CYS cc_start: 0.8209 (p) cc_final: 0.7780 (p) REVERT: I 129 ARG cc_start: 0.7344 (tpt90) cc_final: 0.6887 (tpt170) REVERT: I 168 LEU cc_start: 0.7579 (mt) cc_final: 0.7254 (tt) REVERT: I 365 ILE cc_start: 0.8951 (mm) cc_final: 0.8408 (pt) REVERT: I 428 ILE cc_start: 0.8490 (mm) cc_final: 0.8064 (mm) REVERT: I 522 SER cc_start: 0.9144 (t) cc_final: 0.8654 (p) REVERT: J 49 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8178 (mm-30) REVERT: J 186 SER cc_start: 0.7528 (m) cc_final: 0.7211 (p) REVERT: K 199 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7656 (tm-30) REVERT: L 6 ASN cc_start: 0.8483 (m-40) cc_final: 0.8078 (m-40) REVERT: L 128 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8363 (mmmt) REVERT: L 134 GLN cc_start: 0.8819 (mm-40) cc_final: 0.7376 (tp-100) REVERT: M 7 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: M 101 SER cc_start: 0.9240 (t) cc_final: 0.8709 (m) REVERT: M 153 VAL cc_start: 0.8602 (t) cc_final: 0.8335 (p) REVERT: M 189 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7759 (mm-40) REVERT: M 284 MET cc_start: 0.7582 (ppp) cc_final: 0.6804 (ttm) REVERT: N 65 ASP cc_start: 0.7063 (t70) cc_final: 0.6556 (t70) REVERT: N 190 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: N 284 MET cc_start: 0.6926 (ttp) cc_final: 0.6556 (ttt) REVERT: O 59 ASP cc_start: 0.7695 (m-30) cc_final: 0.7283 (m-30) outliers start: 160 outliers final: 139 residues processed: 719 average time/residue: 0.2077 time to fit residues: 253.9484 Evaluate side-chains 733 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 587 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 130 PHE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 293 PHE Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain H residue 581 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 343 SER Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 421 ASN Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 452 THR Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 185 optimal weight: 0.0050 chunk 499 optimal weight: 8.9990 chunk 390 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 416 optimal weight: 0.9990 chunk 472 optimal weight: 6.9990 chunk 371 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 410 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 228 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 580 HIS I 148 ASN J 206 GLN L 206 GLN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.139240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128675 restraints weight = 57584.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120131 restraints weight = 104030.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.119039 restraints weight = 86069.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.119263 restraints weight = 91797.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119441 restraints weight = 77601.902| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42643 Z= 0.111 Angle : 0.546 12.203 58076 Z= 0.286 Chirality : 0.046 0.236 6523 Planarity : 0.004 0.055 7606 Dihedral : 4.421 45.024 5780 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.94 % Allowed : 20.66 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.11), residues: 5323 helix: 0.06 (0.22), residues: 553 sheet: -0.50 (0.14), residues: 1365 loop : -1.04 (0.10), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 186 TYR 0.022 0.001 TYR A 296 PHE 0.015 0.001 PHE N 233 TRP 0.035 0.001 TRP B 47 HIS 0.008 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (42637) covalent geometry : angle 0.54613 / 0.29 (58064) SS BOND : bond 0.00187 / 0.09 ( 6) SS BOND : angle 0.77006 / 0.42 ( 12) hydrogen bonds : bond 0.02923 / 1.91 ( 1021) hydrogen bonds : angle 5.14516 / 3.59 ( 2796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 600 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8463 (tp) cc_final: 0.7677 (mt) REVERT: A 294 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8118 (mttm) REVERT: B 141 MET cc_start: 0.5246 (ptt) cc_final: 0.4140 (mtm) REVERT: B 155 LYS cc_start: 0.6749 (tttt) cc_final: 0.6449 (tttt) REVERT: B 188 TRP cc_start: 0.8358 (m100) cc_final: 0.7944 (m-90) REVERT: B 192 PHE cc_start: 0.8888 (p90) cc_final: 0.8624 (p90) REVERT: B 238 LEU cc_start: 0.8364 (tp) cc_final: 0.8088 (tp) REVERT: B 308 GLU cc_start: 0.7547 (tp30) cc_final: 0.7093 (tp30) REVERT: B 312 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8338 (mmt) REVERT: B 320 MET cc_start: 0.3202 (ptt) cc_final: 0.2848 (mmt) REVERT: C 172 GLU cc_start: 0.7080 (mp0) cc_final: 0.5585 (tp30) REVERT: C 231 TYR cc_start: 0.7949 (t80) cc_final: 0.7185 (t80) REVERT: C 252 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8209 (pttt) REVERT: C 312 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 444 SER cc_start: 0.8744 (t) cc_final: 0.8274 (p) REVERT: D 136 ASN cc_start: 0.8118 (p0) cc_final: 0.7893 (p0) REVERT: D 202 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8957 (pp) REVERT: D 235 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: E 154 ASP cc_start: 0.6204 (t0) cc_final: 0.5263 (m-30) REVERT: E 199 MET cc_start: 0.8562 (tmm) cc_final: 0.8246 (ttt) REVERT: E 238 MET cc_start: 0.8725 (mtm) cc_final: 0.8291 (mtm) REVERT: F 187 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8323 (p) REVERT: F 269 THR cc_start: 0.8769 (p) cc_final: 0.8239 (t) REVERT: G 96 ARG cc_start: 0.8331 (ttm170) cc_final: 0.7672 (ttm-80) REVERT: G 132 ASP cc_start: 0.7651 (t0) cc_final: 0.7047 (t0) REVERT: G 342 CYS cc_start: 0.7304 (t) cc_final: 0.6963 (t) REVERT: G 379 ASP cc_start: 0.7674 (m-30) cc_final: 0.7417 (m-30) REVERT: G 397 ASP cc_start: 0.7836 (t0) cc_final: 0.7442 (t0) REVERT: G 545 ASP cc_start: 0.7676 (t70) cc_final: 0.7370 (t0) REVERT: G 557 TYR cc_start: 0.5966 (t80) cc_final: 0.5572 (t80) REVERT: H 108 THR cc_start: 0.8514 (t) cc_final: 0.8301 (p) REVERT: H 248 MET cc_start: 0.6542 (mtt) cc_final: 0.6186 (mtt) REVERT: H 514 HIS cc_start: 0.7860 (t-170) cc_final: 0.7320 (t-170) REVERT: H 519 THR cc_start: 0.8100 (p) cc_final: 0.7436 (t) REVERT: H 555 CYS cc_start: 0.8170 (p) cc_final: 0.7728 (p) REVERT: I 168 LEU cc_start: 0.7907 (mt) cc_final: 0.7421 (tt) REVERT: I 365 ILE cc_start: 0.8918 (mm) cc_final: 0.8388 (pt) REVERT: I 428 ILE cc_start: 0.8409 (mm) cc_final: 0.7984 (mm) REVERT: I 522 SER cc_start: 0.9104 (t) cc_final: 0.8645 (p) REVERT: J 42 GLN cc_start: 0.8309 (mt0) cc_final: 0.8004 (mt0) REVERT: J 49 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8206 (mm-30) REVERT: J 186 SER cc_start: 0.7431 (m) cc_final: 0.7164 (p) REVERT: L 128 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8327 (mmmt) REVERT: L 134 GLN cc_start: 0.8738 (mm-40) cc_final: 0.7438 (tp-100) REVERT: M 7 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: M 101 SER cc_start: 0.9217 (t) cc_final: 0.8696 (m) REVERT: M 150 VAL cc_start: 0.8885 (t) cc_final: 0.8683 (m) REVERT: M 153 VAL cc_start: 0.8580 (t) cc_final: 0.8326 (p) REVERT: M 172 MET cc_start: 0.6867 (ptp) cc_final: 0.6191 (ptt) REVERT: M 189 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7424 (mp10) REVERT: M 200 ILE cc_start: 0.7441 (mt) cc_final: 0.7174 (pt) REVERT: M 214 ASP cc_start: 0.7806 (t0) cc_final: 0.7368 (t0) REVERT: M 284 MET cc_start: 0.7605 (ppp) cc_final: 0.6869 (ttm) REVERT: N 65 ASP cc_start: 0.7040 (t70) cc_final: 0.6521 (t70) REVERT: N 190 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: N 255 ILE cc_start: 0.6088 (mp) cc_final: 0.5732 (tp) REVERT: N 284 MET cc_start: 0.6857 (ttp) cc_final: 0.6470 (ttt) REVERT: O 59 ASP cc_start: 0.7720 (m-30) cc_final: 0.7339 (m-30) REVERT: O 97 ILE cc_start: 0.7205 (mt) cc_final: 0.6480 (mm) outliers start: 136 outliers final: 124 residues processed: 698 average time/residue: 0.2057 time to fit residues: 245.6931 Evaluate side-chains 716 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 585 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 228 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 293 PHE Chi-restraints excluded: chain G residue 307 ASN Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 519 THR Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 415 ASP Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain H residue 581 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 LYS Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 343 SER Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 421 ASN Chi-restraints excluded: chain I residue 438 SER Chi-restraints excluded: chain I residue 452 THR Chi-restraints excluded: chain I residue 544 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 149 optimal weight: 1.9990 chunk 512 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 465 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 394 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 142 optimal weight: 0.3980 chunk 371 optimal weight: 2.9990 chunk 449 optimal weight: 2.9990 chunk 379 optimal weight: 0.6980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 580 HIS I 148 ASN L 206 GLN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127613 restraints weight = 58054.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.119305 restraints weight = 102381.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.118569 restraints weight = 81758.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.118645 restraints weight = 88103.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.118775 restraints weight = 73297.295| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42643 Z= 0.138 Angle : 0.553 12.229 58076 Z= 0.289 Chirality : 0.046 0.239 6523 Planarity : 0.004 0.053 7606 Dihedral : 4.430 44.876 5780 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.33 % Allowed : 20.42 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.11), residues: 5323 helix: 0.05 (0.22), residues: 554 sheet: -0.49 (0.14), residues: 1364 loop : -1.06 (0.10), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 293 TYR 0.022 0.001 TYR A 296 PHE 0.015 0.001 PHE B 236 TRP 0.049 0.001 TRP B 47 HIS 0.009 0.001 HIS F 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (42637) covalent geometry : angle 0.55288 / 0.29 (58064) SS BOND : bond 0.00204 / 0.11 ( 6) SS BOND : angle 0.72599 / 0.42 ( 12) hydrogen bonds : bond 0.02955 / 1.93 ( 1021) hydrogen bonds : angle 5.13065 / 3.58 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7827.79 seconds wall clock time: 135 minutes 51.32 seconds (8151.32 seconds total)