Starting phenix.real_space_refine on Tue Sep 15 12:09:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.cif" model { file = "/net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hum_0281/09_2026/6hum_0281.map" } resolution = 3.34 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12130 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 168 5.16 5 C 19508 2.51 5 N 4758 2.21 5 O 5075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29521 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2718 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3706 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 23, 'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "E" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 769 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "B" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3541 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 52 Chain: "G" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1262 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1278 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain: "P" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3153 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 370} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 180} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1594 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 184} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "F" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4717 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1160 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 11, 'TRANS': 135} Chain: "M" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "S" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "Q" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 293 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18481 SG CYS I 103 47.382 91.207 38.473 1.00 26.35 S ATOM 18525 SG CYS I 109 44.242 93.994 33.933 1.00 28.75 S ATOM 18234 SG CYS I 73 46.157 97.062 39.909 1.00 28.05 S ATOM 18506 SG CYS I 106 41.768 93.980 39.802 1.00 27.85 S ATOM 18181 SG CYS I 66 44.541 103.300 28.434 1.00 32.87 S ATOM 18203 SG CYS I 69 46.002 99.047 31.191 1.00 30.30 S ATOM 18162 SG CYS I 63 49.829 100.629 25.719 1.00 35.29 S ATOM 18559 SG CYS I 113 43.654 97.644 26.474 1.00 31.80 S ATOM 20268 SG CYS K 148 45.749 88.119 47.073 1.00 27.27 S ATOM 19544 SG CYS K 53 46.363 82.991 50.147 1.00 29.75 S ATOM 19538 SG CYS K 52 41.606 84.909 50.781 1.00 30.22 S ATOM 20042 SG CYS K 117 46.734 89.806 50.339 1.00 26.68 S Time building chain proxies: 5.99, per 1000 atoms: 0.20 Number of scatterers: 29521 At special positions: 0 Unit cell: (97.2, 137.7, 243, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 168 16.00 O 5075 8.00 N 4758 7.00 C 19508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 103 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 106 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 73 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 109 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 113 " pdb=" SF4 K 501 " pdb="FE4 SF4 K 501 " - pdb=" SG CYS K 117 " pdb="FE3 SF4 K 501 " - pdb=" SG CYS K 52 " pdb="FE2 SF4 K 501 " - pdb=" SG CYS K 53 " pdb="FE1 SF4 K 501 " - pdb=" SG CYS K 148 " Number of angles added : 36 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6994 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 16 sheets defined 60.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 removed outlier: 3.927A pdb=" N LEU A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 30 through 59 removed outlier: 3.614A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.647A pdb=" N PHE A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 100' Processing helix chain 'A' and resid 101 through 113 Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.615A pdb=" N GLY A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.928A pdb=" N GLY A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.642A pdb=" N GLN A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 169' Processing helix chain 'A' and resid 173 through 187 removed outlier: 3.776A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.547A pdb=" N GLN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.967A pdb=" N THR A 247 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 277 Processing helix chain 'A' and resid 300 through 330 removed outlier: 3.776A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 347 through 366 removed outlier: 3.617A pdb=" N VAL A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 31 through 42 removed outlier: 3.801A pdb=" N SER C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 89 removed outlier: 3.859A pdb=" N ALA C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 4.835A pdb=" N HIS C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 removed outlier: 3.876A pdb=" N ILE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 32 through 53 removed outlier: 4.181A pdb=" N TRP D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 104 removed outlier: 3.941A pdb=" N THR D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 removed outlier: 3.947A pdb=" N LEU D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 146 through 156 Processing helix chain 'D' and resid 161 through 176 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.864A pdb=" N VAL D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 207 through 223 removed outlier: 3.702A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 4.247A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.793A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 267 Processing helix chain 'D' and resid 270 through 299 removed outlier: 3.724A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.902A pdb=" N ILE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 327 through 358 removed outlier: 3.698A pdb=" N LEU D 341 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.601A pdb=" N LYS D 371 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 removed outlier: 3.529A pdb=" N MET D 378 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 408 removed outlier: 3.612A pdb=" N VAL D 396 " --> pdb=" O MET D 392 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 424 removed outlier: 3.605A pdb=" N PHE D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.909A pdb=" N ILE D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Proline residue: D 431 - end of helix Processing helix chain 'D' and resid 460 through 480 removed outlier: 3.653A pdb=" N VAL D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 466 " --> pdb=" O ARG D 462 " (cutoff:3.500A) Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 486 Processing helix chain 'D' and resid 488 through 502 Processing helix chain 'E' and resid 2 through 24 Processing helix chain 'E' and resid 28 through 52 removed outlier: 3.919A pdb=" N MET E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 88 removed outlier: 3.798A pdb=" N PHE E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.530A pdb=" N PHE E 96 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 38 removed outlier: 3.945A pdb=" N GLN B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 59 removed outlier: 4.119A pdb=" N ALA B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 103 removed outlier: 5.493A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 127 removed outlier: 3.589A pdb=" N ALA B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.845A pdb=" N GLY B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 187 removed outlier: 3.622A pdb=" N ASN B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.601A pdb=" N LEU B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 224 removed outlier: 4.018A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 removed outlier: 4.478A pdb=" N ASP B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 264 removed outlier: 3.903A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 293 removed outlier: 3.575A pdb=" N ASN B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 318 Processing helix chain 'B' and resid 324 through 354 removed outlier: 3.715A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.950A pdb=" N ALA B 363 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.458A pdb=" N LYS B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.513A pdb=" N THR B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.712A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 removed outlier: 4.464A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 429 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.809A pdb=" N MET B 440 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.234A pdb=" N ASN B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 474 removed outlier: 3.721A pdb=" N ALA B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.651A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 29 removed outlier: 3.807A pdb=" N GLN G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 53 removed outlier: 3.884A pdb=" N SER G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 52 " --> pdb=" O GLY G 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'G' and resid 69 through 80 removed outlier: 3.981A pdb=" N MET G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 116 removed outlier: 3.920A pdb=" N GLN G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 3.685A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 163 removed outlier: 3.979A pdb=" N PHE G 147 " --> pdb=" O PHE G 143 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 163 " --> pdb=" O ILE G 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 removed outlier: 3.685A pdb=" N SER J 21 " --> pdb=" O ARG J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 56 Processing helix chain 'J' and resid 116 through 129 removed outlier: 4.006A pdb=" N GLN J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.621A pdb=" N GLN J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 26 removed outlier: 4.474A pdb=" N ILE P 8 " --> pdb=" O SER P 4 " (cutoff:3.500A) Proline residue: P 14 - end of helix removed outlier: 3.899A pdb=" N THR P 25 " --> pdb=" O LEU P 21 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG P 26 " --> pdb=" O PHE P 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 55 Processing helix chain 'H' and resid 59 through 68 Proline residue: H 65 - end of helix removed outlier: 4.012A pdb=" N SER H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 90 Proline residue: H 86 - end of helix removed outlier: 3.973A pdb=" N LEU H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 124 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 128 through 135 removed outlier: 3.630A pdb=" N PHE H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 149 removed outlier: 4.360A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR H 142 " --> pdb=" O ARG H 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 172 through 194 removed outlier: 3.889A pdb=" N LEU H 184 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.715A pdb=" N ASP H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 202 Processing helix chain 'H' and resid 213 through 218 removed outlier: 3.816A pdb=" N TRP H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 227 Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 257 through 281 removed outlier: 3.749A pdb=" N VAL H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG H 270 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 removed outlier: 3.854A pdb=" N GLU H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 310 removed outlier: 3.790A pdb=" N GLY H 306 " --> pdb=" O GLU H 303 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE H 307 " --> pdb=" O TRP H 304 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP H 308 " --> pdb=" O ASN H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 365 removed outlier: 4.061A pdb=" N ASN H 361 " --> pdb=" O PRO H 357 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL H 365 " --> pdb=" O ASN H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 383 removed outlier: 3.784A pdb=" N ILE H 381 " --> pdb=" O ASP H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 393 removed outlier: 3.616A pdb=" N ASP H 393 " --> pdb=" O GLY H 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 32 removed outlier: 3.838A pdb=" N GLY I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 73 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 137 through 141 removed outlier: 3.658A pdb=" N MET I 141 " --> pdb=" O SER I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 163 removed outlier: 4.028A pdb=" N LEU I 163 " --> pdb=" O PHE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 193 Processing helix chain 'K' and resid 25 through 41 removed outlier: 3.630A pdb=" N LEU K 31 " --> pdb=" O ILE K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 62 removed outlier: 3.657A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 103 removed outlier: 4.301A pdb=" N LEU K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.812A pdb=" N SER K 126 " --> pdb=" O MET K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.603A pdb=" N LYS K 137 " --> pdb=" O GLY K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 167 removed outlier: 3.576A pdb=" N ILE K 155 " --> pdb=" O ARG K 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET K 156 " --> pdb=" O PRO K 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 178 removed outlier: 3.717A pdb=" N GLU K 173 " --> pdb=" O HIS K 170 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG K 174 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY K 175 " --> pdb=" O ASN K 172 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA K 178 " --> pdb=" O GLY K 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 Processing helix chain 'L' and resid 23 through 35 removed outlier: 3.608A pdb=" N ARG L 35 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 54 removed outlier: 3.691A pdb=" N ALA L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 59 removed outlier: 3.532A pdb=" N LEU L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 4.036A pdb=" N VAL F 13 " --> pdb=" O TRP F 9 " (cutoff:3.500A) Proline residue: F 15 - end of helix Processing helix chain 'F' and resid 29 through 36 Processing helix chain 'F' and resid 37 through 65 Processing helix chain 'F' and resid 90 through 115 removed outlier: 3.774A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 140 removed outlier: 3.541A pdb=" N PHE F 124 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE F 125 " --> pdb=" O TYR F 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 163 removed outlier: 3.805A pdb=" N PHE F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY F 155 " --> pdb=" O TRP F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 200 removed outlier: 3.878A pdb=" N ASN F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 218 removed outlier: 3.589A pdb=" N LEU F 212 " --> pdb=" O MET F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.510A pdb=" N LEU F 232 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 248 through 253 removed outlier: 4.043A pdb=" N ASP F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 264 Processing helix chain 'F' and resid 269 through 279 removed outlier: 4.235A pdb=" N GLY F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 Processing helix chain 'F' and resid 287 through 312 removed outlier: 3.958A pdb=" N MET F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR F 292 " --> pdb=" O PRO F 288 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR F 311 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 336 removed outlier: 3.882A pdb=" N TYR F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 366 removed outlier: 3.666A pdb=" N HIS F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR F 351 " --> pdb=" O MET F 347 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE F 352 " --> pdb=" O THR F 348 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 353 " --> pdb=" O HIS F 349 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 384 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.513A pdb=" N ILE F 405 " --> pdb=" O GLY F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 427 removed outlier: 3.911A pdb=" N TRP F 415 " --> pdb=" O PHE F 411 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU F 419 " --> pdb=" O TRP F 415 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 452 removed outlier: 3.779A pdb=" N PHE F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR F 450 " --> pdb=" O MET F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 500 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 504 Processing helix chain 'F' and resid 510 through 515 Processing helix chain 'F' and resid 533 through 556 removed outlier: 4.283A pdb=" N SER F 539 " --> pdb=" O ILE F 535 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER F 540 " --> pdb=" O LEU F 536 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 541 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET F 554 " --> pdb=" O VAL F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 590 Processing helix chain 'F' and resid 590 through 607 removed outlier: 3.524A pdb=" N ARG F 595 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG F 599 " --> pdb=" O ARG F 595 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL F 604 " --> pdb=" O GLN F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 628 removed outlier: 3.961A pdb=" N VAL F 613 " --> pdb=" O VAL F 609 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR F 616 " --> pdb=" O VAL F 612 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY F 617 " --> pdb=" O VAL F 613 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY F 624 " --> pdb=" O THR F 620 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 628 " --> pdb=" O GLY F 624 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 631 No H-bonds generated for 'chain 'F' and resid 629 through 631' Processing helix chain 'F' and resid 634 through 644 removed outlier: 4.124A pdb=" N LEU F 643 " --> pdb=" O ALA F 639 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 17 Processing helix chain 'N' and resid 30 through 39 removed outlier: 3.578A pdb=" N GLN N 34 " --> pdb=" O GLU N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 122 removed outlier: 4.299A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR N 122 " --> pdb=" O GLN N 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 58 removed outlier: 3.635A pdb=" N ALA M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 88 removed outlier: 3.592A pdb=" N LEU M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'Q' and resid 16 through 40 removed outlier: 3.981A pdb=" N LEU Q 26 " --> pdb=" O ILE Q 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 67 through 68 removed outlier: 3.737A pdb=" N VAL D 82 " --> pdb=" O GLU D 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 30 through 31 removed outlier: 3.853A pdb=" N GLY J 30 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU J 37 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS J 97 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE J 39 " --> pdb=" O LYS J 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 107 through 108 removed outlier: 6.917A pdb=" N VAL J 107 " --> pdb=" O GLU J 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 14 removed outlier: 3.624A pdb=" N ASP H 39 " --> pdb=" O THR H 31 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 160 Processing sheet with id=AA6, first strand: chain 'H' and resid 327 through 332 Processing sheet with id=AA7, first strand: chain 'I' and resid 79 through 82 removed outlier: 6.527A pdb=" N VAL I 79 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR I 96 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP I 81 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 83 through 87 removed outlier: 3.533A pdb=" N LEU K 145 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 182 through 184 removed outlier: 4.331A pdb=" N ARG K 182 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE K 184 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU M 31 " --> pdb=" O PHE K 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 74 through 77 removed outlier: 6.877A pdb=" N ILE F 83 " --> pdb=" O TRP F 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 21 removed outlier: 7.228A pdb=" N LEU N 102 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'M' and resid 39 through 40 removed outlier: 4.052A pdb=" N GLY M 91 " --> pdb=" O GLU M 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 86 through 91 removed outlier: 3.778A pdb=" N LYS S 86 " --> pdb=" O PHE S 79 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG S 69 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU S 78 " --> pdb=" O VAL S 67 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL S 67 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 11 Processing sheet with id=AB7, first strand: chain 'O' and resid 40 through 44 removed outlier: 3.897A pdb=" N ASP O 42 " --> pdb=" O GLN O 49 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR O 47 " --> pdb=" O ARG O 44 " (cutoff:3.500A) 1485 hydrogen bonds defined for protein. 4356 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: 7.78 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 12575 1.42 - 1.64: 17395 1.64 - 1.85: 281 1.85 - 2.07: 0 2.07 - 2.28: 37 Bond restraints: 30288 Sorted by residual: bond pdb=" C ILE D 24 " pdb=" N PRO D 25 " ideal model delta sigma weight residual 1.334 2.241 -0.907 2.34e-02 1.83e+03 1.50e+03 bond pdb=" C GLN F 570 " pdb=" N PRO F 571 " ideal model delta sigma weight residual 1.332 1.365 -0.033 8.90e-03 1.26e+04 1.35e+01 bond pdb=" C LYS O 51 " pdb=" N PHE O 52 " ideal model delta sigma weight residual 1.331 1.394 -0.063 2.07e-02 2.33e+03 9.33e+00 bond pdb=" C GLN L 70 " pdb=" N PRO L 71 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.27e-02 6.20e+03 7.66e+00 bond pdb=" C PRO J 91 " pdb=" N PRO J 92 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 7.27e+00 ... (remaining 30283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.67: 41271 21.67 - 43.35: 0 43.35 - 65.02: 0 65.02 - 86.69: 0 86.69 - 108.37: 1 Bond angle restraints: 41272 Sorted by residual: angle pdb=" O ILE D 24 " pdb=" C ILE D 24 " pdb=" N PRO D 25 " ideal model delta sigma weight residual 121.10 12.73 108.37 1.14e+00 7.69e-01 9.04e+03 angle pdb=" C ALA O 22 " pdb=" N LEU O 23 " pdb=" CA LEU O 23 " ideal model delta sigma weight residual 120.63 140.45 -19.82 1.61e+00 3.86e-01 1.52e+02 angle pdb=" O PHE D 23 " pdb=" C PHE D 23 " pdb=" N ILE D 24 " ideal model delta sigma weight residual 122.59 109.25 13.34 1.33e+00 5.65e-01 1.01e+02 angle pdb=" C TYR O 47 " pdb=" N ALA O 48 " pdb=" CA ALA O 48 " ideal model delta sigma weight residual 122.94 134.62 -11.68 1.50e+00 4.44e-01 6.07e+01 angle pdb=" N ASP J 32 " pdb=" CA ASP J 32 " pdb=" C ASP J 32 " ideal model delta sigma weight residual 112.26 121.64 -9.38 1.32e+00 5.74e-01 5.05e+01 ... (remaining 41267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 17167 23.82 - 47.64: 439 47.64 - 71.46: 30 71.46 - 95.28: 15 95.28 - 119.11: 1 Dihedral angle restraints: 17652 sinusoidal: 6725 harmonic: 10927 Sorted by residual: dihedral pdb=" CA CYS K 148 " pdb=" C CYS K 148 " pdb=" N PRO K 149 " pdb=" CA PRO K 149 " ideal model delta harmonic sigma weight residual -180.00 -116.41 -63.59 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA PRO B 387 " pdb=" C PRO B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -117.52 -62.48 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA LEU C 16 " pdb=" C LEU C 16 " pdb=" N SER C 17 " pdb=" CA SER C 17 " ideal model delta harmonic sigma weight residual -180.00 -142.51 -37.49 0 5.00e+00 4.00e-02 5.62e+01 ... (remaining 17649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 4755 0.348 - 0.696: 18 0.696 - 1.044: 0 1.044 - 1.392: 1 1.392 - 1.740: 10 Chirality restraints: 4784 Sorted by residual: chirality pdb=" CG LEU O 33 " pdb=" CB LEU O 33 " pdb=" CD1 LEU O 33 " pdb=" CD2 LEU O 33 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.57e+01 chirality pdb=" CG LEU M 29 " pdb=" CB LEU M 29 " pdb=" CD1 LEU M 29 " pdb=" CD2 LEU M 29 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 chirality pdb=" CG LEU J 75 " pdb=" CB LEU J 75 " pdb=" CD1 LEU J 75 " pdb=" CD2 LEU J 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 ... (remaining 4781 not shown) Planarity restraints: 5110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 601 " -0.503 2.00e-02 2.50e+03 3.29e-01 1.36e+03 pdb=" C11 BCR D 601 " 0.387 2.00e-02 2.50e+03 pdb=" C34 BCR D 601 " 0.079 2.00e-02 2.50e+03 pdb=" C8 BCR D 601 " 0.276 2.00e-02 2.50e+03 pdb=" C9 BCR D 601 " -0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 601 " 0.229 2.00e-02 2.50e+03 2.00e-01 4.98e+02 pdb=" C17 BCR D 601 " -0.362 2.00e-02 2.50e+03 pdb=" C18 BCR D 601 " 0.024 2.00e-02 2.50e+03 pdb=" C19 BCR D 601 " 0.124 2.00e-02 2.50e+03 pdb=" C36 BCR D 601 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BCR D 601 " 0.161 2.00e-02 2.50e+03 1.81e-01 3.28e+02 pdb=" C23 BCR D 601 " -0.115 2.00e-02 2.50e+03 pdb=" C24 BCR D 601 " -0.236 2.00e-02 2.50e+03 pdb=" C25 BCR D 601 " 0.190 2.00e-02 2.50e+03 ... (remaining 5107 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 11 2.02 - 2.74: 3054 2.74 - 3.46: 44447 3.46 - 4.18: 69585 4.18 - 4.90: 128226 Nonbonded interactions: 245323 Sorted by model distance: nonbonded pdb=" CG ARG D 356 " pdb=" CB LEU D 456 " model vdw 1.302 3.840 nonbonded pdb=" CE1 PHE H 153 " pdb=" OE2 GLU K 56 " model vdw 1.460 3.340 nonbonded pdb=" OG1 THR M 7 " pdb=" OE2 GLU M 78 " model vdw 1.508 3.040 nonbonded pdb=" CG2 THR D 233 " pdb=" OD1 ASP F 610 " model vdw 1.684 3.460 nonbonded pdb=" OD2 ASP J 32 " pdb=" NH1 ARG J 95 " model vdw 1.731 3.120 ... (remaining 245318 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.100 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.009 0.907 30300 Z= 0.383 Angle : 1.339 108.368 41308 Z= 0.739 Chirality : 0.098 1.740 4784 Planarity : 0.010 0.329 5110 Dihedral : 10.915 119.106 10658 Min Nonbonded Distance : 1.302 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.67 % Allowed : 11.47 % Favored : 87.86 % Rotamer: Outliers : 0.33 % Allowed : 4.54 % Favored : 95.13 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.11 % 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: -4.32 (0.12), residues: 3739 helix: -2.07 (0.10), residues: 2105 sheet: -3.97 (0.34), residues: 152 loop : -3.89 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 39 TYR 0.033 0.003 TYR A 258 PHE 0.045 0.003 PHE B 125 TRP 0.027 0.002 TRP B 274 HIS 0.020 0.002 HIS D 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.38 (30288) covalent geometry : angle 1.20370 / 0.74 (41272) hydrogen bonds : bond 0.15490 / 10.37 ( 1485) hydrogen bonds : angle 6.69340 / 4.66 ( 4356) metal coordination : bond 0.01091 / 0.66 ( 12) metal coordination : angle 19.86861 / 13.16 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 773 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 SER cc_start: 0.8581 (t) cc_final: 0.8059 (m) REVERT: C 72 VAL cc_start: 0.8612 (t) cc_final: 0.8288 (t) REVERT: D 228 ILE cc_start: 0.7750 (mm) cc_final: 0.7284 (mm) REVERT: D 446 GLU cc_start: 0.6094 (tp30) cc_final: 0.5497 (tp30) REVERT: B 222 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8665 (mmmt) REVERT: J 138 LEU cc_start: 0.8421 (tm) cc_final: 0.8205 (tp) REVERT: J 139 LYS cc_start: 0.7864 (mttp) cc_final: 0.7574 (mtpp) REVERT: H 305 ASN cc_start: 0.7515 (t0) cc_final: 0.7187 (t0) REVERT: K 24 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6191 (tm-30) REVERT: F 136 LEU cc_start: 0.8677 (mt) cc_final: 0.8422 (mt) REVERT: F 177 LYS cc_start: 0.8456 (tttt) cc_final: 0.8193 (ttpt) REVERT: F 243 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7953 (mm-40) REVERT: F 280 MET cc_start: 0.7726 (mmm) cc_final: 0.7501 (mmm) REVERT: F 348 THR cc_start: 0.8833 (m) cc_final: 0.8524 (p) REVERT: F 452 MET cc_start: 0.7724 (ttm) cc_final: 0.7404 (ttm) REVERT: F 555 TYR cc_start: 0.7922 (m-80) cc_final: 0.7114 (m-80) REVERT: F 563 GLN cc_start: 0.7269 (pm20) cc_final: 0.7047 (mt0) REVERT: F 596 ARG cc_start: 0.6454 (tmt-80) cc_final: 0.6148 (ptt90) REVERT: N 45 LEU cc_start: 0.8177 (pp) cc_final: 0.7781 (pp) REVERT: M 4 LYS cc_start: 0.8686 (pmtt) cc_final: 0.8297 (pttm) REVERT: M 19 ASP cc_start: 0.7714 (p0) cc_final: 0.7380 (p0) REVERT: O 35 GLU cc_start: 0.7119 (pt0) cc_final: 0.6831 (pt0) REVERT: O 49 GLN cc_start: 0.8488 (tt0) cc_final: 0.8199 (tt0) outliers start: 10 outliers final: 8 residues processed: 781 average time/residue: 0.2000 time to fit residues: 249.5565 Evaluate side-chains 569 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 561 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 157 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS C 100 GLN D 326 ASN B 273 GLN B 290 ASN B 340 ASN B 479 ASN G 71 ASN G 121 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN H 205 GLN I 16 GLN I 85 ASN K 76 ASN K 104 GLN F 146 GLN F 313 ASN F 509 ASN M 32 ASN M 59 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.146518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.125705 restraints weight = 36978.394| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.47 r_work: 0.3219 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30300 Z= 0.179 Angle : 0.943 48.065 41308 Z= 0.395 Chirality : 0.047 0.258 4784 Planarity : 0.006 0.070 5110 Dihedral : 7.855 100.941 4159 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.84 % Favored : 89.95 % Rotamer: Outliers : 2.58 % Allowed : 10.22 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.13), residues: 3741 helix: -0.73 (0.11), residues: 2131 sheet: -3.71 (0.33), residues: 173 loop : -3.49 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 35 TYR 0.028 0.002 TYR L 13 PHE 0.031 0.002 PHE E 62 TRP 0.040 0.002 TRP F 436 HIS 0.008 0.001 HIS D 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (30288) covalent geometry : angle 0.79568 / 0.39 (41272) hydrogen bonds : bond 0.04753 / 3.20 ( 1485) hydrogen bonds : angle 4.83016 / 3.39 ( 4356) metal coordination : bond 0.00961 / 0.49 ( 12) metal coordination : angle 17.17059 / 11.61 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 663 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8332 (tt) REVERT: A 169 SER cc_start: 0.8968 (t) cc_final: 0.8545 (m) REVERT: A 170 ILE cc_start: 0.8814 (tt) cc_final: 0.8563 (tt) REVERT: A 248 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8491 (mm-30) REVERT: A 286 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7571 (tp) REVERT: C 60 MET cc_start: 0.8115 (mmm) cc_final: 0.7883 (mmm) REVERT: C 72 VAL cc_start: 0.8628 (t) cc_final: 0.8349 (t) REVERT: C 108 GLU cc_start: 0.7289 (tp30) cc_final: 0.6734 (tp30) REVERT: C 124 TRP cc_start: 0.7242 (t60) cc_final: 0.6547 (t60) REVERT: D 57 TYR cc_start: 0.7222 (t80) cc_final: 0.6434 (t80) REVERT: D 58 ASP cc_start: 0.6350 (p0) cc_final: 0.6143 (p0) REVERT: D 123 MET cc_start: 0.8334 (ptm) cc_final: 0.7908 (ttp) REVERT: D 178 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8430 (tt) REVERT: D 222 TYR cc_start: 0.8994 (m-80) cc_final: 0.8599 (m-80) REVERT: D 228 ILE cc_start: 0.7673 (mm) cc_final: 0.7281 (mm) REVERT: D 446 GLU cc_start: 0.6768 (tp30) cc_final: 0.6402 (tp30) REVERT: D 484 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8407 (tm) REVERT: E 78 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 42 TRP cc_start: 0.4310 (p90) cc_final: 0.4102 (p90) REVERT: G 83 LYS cc_start: 0.7176 (mtpt) cc_final: 0.6889 (mtpt) REVERT: J 106 ARG cc_start: 0.7322 (pmt170) cc_final: 0.6650 (ptp90) REVERT: J 138 LEU cc_start: 0.8625 (tm) cc_final: 0.8354 (tp) REVERT: J 139 LYS cc_start: 0.8223 (mttp) cc_final: 0.7722 (mtpp) REVERT: H 157 ASN cc_start: 0.9003 (p0) cc_final: 0.8587 (p0) REVERT: H 243 TYR cc_start: 0.7590 (m-10) cc_final: 0.7270 (m-10) REVERT: I 136 TYR cc_start: 0.8931 (m-10) cc_final: 0.8585 (m-80) REVERT: K 24 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6372 (tm-30) REVERT: L 60 LEU cc_start: 0.8503 (mt) cc_final: 0.8274 (mt) REVERT: F 332 MET cc_start: 0.7802 (ttm) cc_final: 0.7565 (ttp) REVERT: F 452 MET cc_start: 0.8476 (ttm) cc_final: 0.8204 (ttm) REVERT: F 455 GLU cc_start: 0.7960 (tp30) cc_final: 0.7584 (mm-30) REVERT: F 535 ILE cc_start: 0.8824 (mt) cc_final: 0.8522 (mm) REVERT: F 545 LEU cc_start: 0.7138 (tp) cc_final: 0.6918 (tp) REVERT: F 563 GLN cc_start: 0.7750 (pm20) cc_final: 0.7461 (mt0) REVERT: F 596 ARG cc_start: 0.6434 (tmt-80) cc_final: 0.5507 (ppt170) REVERT: M 4 LYS cc_start: 0.8940 (pmtt) cc_final: 0.8605 (pttm) REVERT: M 19 ASP cc_start: 0.8144 (p0) cc_final: 0.7698 (p0) outliers start: 79 outliers final: 33 residues processed: 698 average time/residue: 0.1819 time to fit residues: 208.0464 Evaluate side-chains 599 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 561 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain M residue 85 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 164 optimal weight: 1.9990 chunk 197 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 326 ASN D 358 HIS E 50 ASN J 20 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN K 104 GLN K 203 ASN F 146 GLN ** F 247 HIS ** 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 = 0.3501 r_free = 0.3501 target = 0.141562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119681 restraints weight = 37396.732| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.56 r_work: 0.3149 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30300 Z= 0.161 Angle : 0.837 33.386 41308 Z= 0.363 Chirality : 0.045 0.250 4784 Planarity : 0.006 0.069 5110 Dihedral : 7.092 88.182 4148 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.44 % Favored : 90.35 % Rotamer: Outliers : 3.36 % Allowed : 12.61 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.14), residues: 3741 helix: -0.12 (0.11), residues: 2155 sheet: -3.38 (0.34), residues: 174 loop : -3.22 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 99 TYR 0.026 0.002 TYR L 13 PHE 0.033 0.002 PHE B 318 TRP 0.027 0.001 TRP F 436 HIS 0.008 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (30288) covalent geometry : angle 0.72794 / 0.36 (41272) hydrogen bonds : bond 0.04340 / 2.92 ( 1485) hydrogen bonds : angle 4.48765 / 3.15 ( 4356) metal coordination : bond 0.00874 / 0.50 ( 12) metal coordination : angle 14.00304 / 9.07 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 632 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8854 (tp) REVERT: A 160 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 170 ILE cc_start: 0.8873 (tt) cc_final: 0.8614 (tt) REVERT: C 60 MET cc_start: 0.8119 (mmm) cc_final: 0.7893 (mmm) REVERT: C 72 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8328 (t) REVERT: C 124 TRP cc_start: 0.7093 (t60) cc_final: 0.6416 (t60) REVERT: D 123 MET cc_start: 0.8332 (ptm) cc_final: 0.8087 (ttp) REVERT: D 228 ILE cc_start: 0.7530 (mm) cc_final: 0.7181 (mm) REVERT: D 326 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8603 (t0) REVERT: E 78 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8578 (mt) REVERT: B 142 LEU cc_start: 0.8910 (tt) cc_final: 0.8700 (tp) REVERT: B 199 GLN cc_start: 0.7897 (tt0) cc_final: 0.7586 (tm-30) REVERT: B 269 SER cc_start: 0.7429 (OUTLIER) cc_final: 0.6990 (m) REVERT: B 369 ASP cc_start: 0.7817 (t0) cc_final: 0.7546 (t0) REVERT: B 439 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8436 (mt-10) REVERT: J 138 LEU cc_start: 0.8753 (tm) cc_final: 0.8505 (tp) REVERT: J 139 LYS cc_start: 0.8260 (mttp) cc_final: 0.7889 (mtpp) REVERT: J 160 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: H 157 ASN cc_start: 0.8805 (p0) cc_final: 0.8510 (p0) REVERT: H 182 TYR cc_start: 0.8636 (t80) cc_final: 0.8409 (t80) REVERT: H 210 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8537 (mp) REVERT: H 243 TYR cc_start: 0.7593 (m-10) cc_final: 0.6020 (m-80) REVERT: H 326 GLU cc_start: 0.8217 (pt0) cc_final: 0.7762 (pt0) REVERT: H 389 MET cc_start: 0.8392 (mmm) cc_final: 0.8184 (mmm) REVERT: I 136 TYR cc_start: 0.9080 (m-10) cc_final: 0.8790 (m-80) REVERT: K 22 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6996 (mm) REVERT: K 24 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6310 (tm-30) REVERT: K 90 ILE cc_start: 0.9360 (mm) cc_final: 0.8892 (mm) REVERT: K 177 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8738 (tt) REVERT: F 31 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7537 (pm20) REVERT: F 48 MET cc_start: 0.8495 (tpp) cc_final: 0.8003 (tpp) REVERT: F 96 MET cc_start: 0.8637 (mmm) cc_final: 0.8427 (mmm) REVERT: F 127 TYR cc_start: 0.8910 (m-10) cc_final: 0.8007 (m-10) REVERT: F 156 MET cc_start: 0.9204 (tmm) cc_final: 0.8936 (tmm) REVERT: F 332 MET cc_start: 0.7909 (ttm) cc_final: 0.7653 (ttm) REVERT: F 452 MET cc_start: 0.8704 (ttm) cc_final: 0.8344 (ttm) REVERT: F 455 GLU cc_start: 0.8133 (tp30) cc_final: 0.7764 (mm-30) REVERT: F 545 LEU cc_start: 0.7177 (tp) cc_final: 0.6975 (tp) REVERT: F 563 GLN cc_start: 0.7726 (pm20) cc_final: 0.7418 (mt0) REVERT: F 596 ARG cc_start: 0.6430 (tmt-80) cc_final: 0.5216 (ppt170) REVERT: F 600 GLN cc_start: 0.6309 (tt0) cc_final: 0.5214 (mm-40) REVERT: M 4 LYS cc_start: 0.9004 (pmtt) cc_final: 0.8613 (pttm) REVERT: M 19 ASP cc_start: 0.8120 (p0) cc_final: 0.7595 (p0) outliers start: 103 outliers final: 51 residues processed: 692 average time/residue: 0.1869 time to fit residues: 209.9453 Evaluate side-chains 641 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 580 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 66 ASN Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 284 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 364 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 278 optimal weight: 0.0370 chunk 368 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS C 100 GLN D 65 GLN D 358 HIS E 55 GLN E 87 ASN B 191 HIS B 193 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN H 157 ASN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS F 146 GLN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 ASN N 87 HIS ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.132694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.111120 restraints weight = 38254.283| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.54 r_work: 0.3030 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30300 Z= 0.209 Angle : 0.863 33.170 41308 Z= 0.376 Chirality : 0.047 0.277 4784 Planarity : 0.006 0.073 5110 Dihedral : 6.982 89.912 4148 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.32 % Favored : 89.47 % Rotamer: Outliers : 4.28 % Allowed : 13.85 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.06 % 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: -1.83 (0.14), residues: 3741 helix: 0.10 (0.11), residues: 2148 sheet: -3.34 (0.35), residues: 172 loop : -3.04 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 96 TYR 0.026 0.002 TYR L 13 PHE 0.026 0.002 PHE K 70 TRP 0.018 0.002 TRP F 436 HIS 0.015 0.001 HIS D 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (30288) covalent geometry : angle 0.75412 / 0.37 (41272) hydrogen bonds : bond 0.04571 / 3.07 ( 1485) hydrogen bonds : angle 4.44181 / 3.12 ( 4356) metal coordination : bond 0.01568 / 0.96 ( 12) metal coordination : angle 14.21514 / 9.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 649 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8478 (mp10) cc_final: 0.7687 (mp10) REVERT: A 101 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8956 (tp) REVERT: A 160 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8210 (tp) REVERT: A 170 ILE cc_start: 0.8980 (tt) cc_final: 0.8699 (tt) REVERT: C 20 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7064 (pt0) REVERT: C 85 ASP cc_start: 0.8820 (t70) cc_final: 0.8588 (t0) REVERT: C 124 TRP cc_start: 0.7425 (t60) cc_final: 0.6383 (t60) REVERT: D 123 MET cc_start: 0.8343 (ptm) cc_final: 0.8103 (ttp) REVERT: D 228 ILE cc_start: 0.7789 (mm) cc_final: 0.7377 (mm) REVERT: D 400 MET cc_start: 0.8728 (mtm) cc_final: 0.8281 (mtp) REVERT: E 25 ARG cc_start: 0.8820 (mmm-85) cc_final: 0.8482 (mmm-85) REVERT: E 78 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8449 (mt) REVERT: E 99 LEU cc_start: 0.1837 (OUTLIER) cc_final: 0.1329 (tt) REVERT: B 124 MET cc_start: 0.9258 (mtm) cc_final: 0.9052 (mtm) REVERT: B 349 LEU cc_start: 0.8852 (tp) cc_final: 0.8574 (tp) REVERT: B 439 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 440 MET cc_start: 0.8381 (mtt) cc_final: 0.8134 (mtp) REVERT: G 83 LYS cc_start: 0.7198 (mtpt) cc_final: 0.6940 (mtpt) REVERT: G 166 ARG cc_start: 0.8126 (ttp-170) cc_final: 0.7844 (ttm170) REVERT: J 138 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8684 (tp) REVERT: J 139 LYS cc_start: 0.8299 (mttp) cc_final: 0.7934 (mtpp) REVERT: J 154 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8877 (mmmm) REVERT: J 160 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: P 6 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7779 (mttp) REVERT: H 139 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8369 (mm-30) REVERT: H 210 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8551 (mp) REVERT: H 231 LYS cc_start: 0.8291 (mmmt) cc_final: 0.8076 (tptt) REVERT: H 389 MET cc_start: 0.8701 (mmm) cc_final: 0.8426 (mmm) REVERT: I 30 ASP cc_start: 0.8346 (t70) cc_final: 0.8144 (t70) REVERT: K 22 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7028 (mm) REVERT: K 24 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6356 (tm-30) REVERT: K 90 ILE cc_start: 0.9302 (mm) cc_final: 0.9021 (mm) REVERT: K 200 GLN cc_start: 0.8259 (tp40) cc_final: 0.7204 (mm-40) REVERT: L 32 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8239 (mt) REVERT: L 61 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8288 (pp) REVERT: F 31 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7441 (pm20) REVERT: F 48 MET cc_start: 0.8628 (tpp) cc_final: 0.8254 (tpp) REVERT: F 92 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8219 (tt) REVERT: F 332 MET cc_start: 0.8164 (ttm) cc_final: 0.7874 (ttm) REVERT: F 382 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7622 (ptt180) REVERT: F 436 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7956 (t60) REVERT: F 455 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: F 563 GLN cc_start: 0.7816 (pm20) cc_final: 0.7323 (mt0) REVERT: F 596 ARG cc_start: 0.6604 (tmt-80) cc_final: 0.5310 (ptt90) REVERT: F 600 GLN cc_start: 0.6118 (tt0) cc_final: 0.5079 (mm-40) REVERT: F 632 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8000 (p0) REVERT: M 1 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6800 (pp-130) REVERT: M 4 LYS cc_start: 0.9114 (pmtt) cc_final: 0.8733 (pttm) REVERT: M 19 ASP cc_start: 0.8156 (p0) cc_final: 0.7615 (p0) REVERT: M 37 ASN cc_start: 0.9066 (m-40) cc_final: 0.8816 (m-40) outliers start: 131 outliers final: 69 residues processed: 735 average time/residue: 0.1878 time to fit residues: 225.0563 Evaluate side-chains 668 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 582 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 148 CYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 436 TRP Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 455 GLU Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 632 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 294 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 280 optimal weight: 0.6980 chunk 286 optimal weight: 0.5980 chunk 204 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS C 100 GLN D 358 HIS G 117 GLN J 20 GLN H 18 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 247 HIS F 312 GLN F 632 ASN ** M 95 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 = 0.3409 r_free = 0.3409 target = 0.133777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112467 restraints weight = 38304.844| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.49 r_work: 0.3050 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30300 Z= 0.159 Angle : 0.818 31.770 41308 Z= 0.353 Chirality : 0.045 0.225 4784 Planarity : 0.005 0.071 5110 Dihedral : 6.786 89.455 4148 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.68 % Favored : 90.11 % Rotamer: Outliers : 4.57 % Allowed : 15.32 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3741 helix: 0.37 (0.12), residues: 2138 sheet: -3.25 (0.36), residues: 172 loop : -2.96 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 36 TYR 0.024 0.002 TYR L 13 PHE 0.022 0.002 PHE B 46 TRP 0.021 0.001 TRP F 436 HIS 0.011 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (30288) covalent geometry : angle 0.71025 / 0.35 (41272) hydrogen bonds : bond 0.04207 / 2.82 ( 1485) hydrogen bonds : angle 4.30797 / 3.02 ( 4356) metal coordination : bond 0.00984 / 0.59 ( 12) metal coordination : angle 13.74420 / 8.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 622 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8419 (mp10) cc_final: 0.7810 (mp10) REVERT: A 101 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8940 (tp) REVERT: A 160 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 170 ILE cc_start: 0.8956 (tt) cc_final: 0.8647 (tt) REVERT: A 309 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8700 (tm) REVERT: C 85 ASP cc_start: 0.8788 (t70) cc_final: 0.8588 (t0) REVERT: C 124 TRP cc_start: 0.7485 (t60) cc_final: 0.6400 (t60) REVERT: D 134 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8184 (mm-40) REVERT: D 228 ILE cc_start: 0.7720 (mm) cc_final: 0.7472 (mm) REVERT: D 392 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7331 (mtt) REVERT: D 400 MET cc_start: 0.8686 (mtm) cc_final: 0.7990 (mtp) REVERT: E 58 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8711 (mtpt) REVERT: E 78 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8461 (mt) REVERT: E 99 LEU cc_start: 0.2408 (OUTLIER) cc_final: 0.1922 (tt) REVERT: B 20 ILE cc_start: 0.8358 (mp) cc_final: 0.8133 (mp) REVERT: B 97 MET cc_start: 0.8136 (mtp) cc_final: 0.7834 (mtp) REVERT: B 124 MET cc_start: 0.9312 (mtm) cc_final: 0.9100 (mtm) REVERT: B 224 SER cc_start: 0.9234 (m) cc_final: 0.8833 (t) REVERT: B 357 ASP cc_start: 0.4934 (t0) cc_final: 0.4636 (t0) REVERT: B 422 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8752 (tp) REVERT: B 439 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8388 (mt-10) REVERT: J 83 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8034 (mmtt) REVERT: J 138 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8653 (tp) REVERT: J 154 LYS cc_start: 0.9271 (mmtt) cc_final: 0.9015 (mmmt) REVERT: J 160 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: P 6 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7830 (mttp) REVERT: P 30 TYR cc_start: 0.8407 (m-80) cc_final: 0.7685 (m-80) REVERT: H 52 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8187 (mt-10) REVERT: H 210 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8548 (mp) REVERT: H 238 ASP cc_start: 0.8099 (t0) cc_final: 0.7828 (t0) REVERT: H 249 ASP cc_start: 0.6181 (m-30) cc_final: 0.5277 (m-30) REVERT: I 136 TYR cc_start: 0.9138 (m-10) cc_final: 0.8858 (m-80) REVERT: I 168 MET cc_start: 0.8734 (mmt) cc_final: 0.8257 (mmt) REVERT: K 22 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6930 (mm) REVERT: K 24 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6367 (tm-30) REVERT: K 200 GLN cc_start: 0.8077 (tp40) cc_final: 0.7189 (mm-40) REVERT: L 32 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8218 (mt) REVERT: L 61 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8254 (pp) REVERT: F 31 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7440 (pm20) REVERT: F 332 MET cc_start: 0.8008 (ttm) cc_final: 0.7610 (ttm) REVERT: F 367 MET cc_start: 0.8090 (mmm) cc_final: 0.7510 (ttt) REVERT: F 382 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7745 (ptt180) REVERT: F 436 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7706 (t60) REVERT: F 455 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: F 496 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8289 (Cg_endo) REVERT: F 563 GLN cc_start: 0.7893 (pm20) cc_final: 0.7373 (mt0) REVERT: F 596 ARG cc_start: 0.6545 (tmt-80) cc_final: 0.5315 (ptt90) REVERT: F 600 GLN cc_start: 0.6088 (tt0) cc_final: 0.5105 (mm-40) REVERT: F 632 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8065 (p0) REVERT: N 100 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7603 (tp) REVERT: M 1 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6897 (pp-130) REVERT: M 4 LYS cc_start: 0.9090 (pmtt) cc_final: 0.8833 (pttm) REVERT: M 19 ASP cc_start: 0.7923 (p0) cc_final: 0.7384 (p0) REVERT: M 37 ASN cc_start: 0.9059 (m-40) cc_final: 0.8851 (m-40) outliers start: 140 outliers final: 81 residues processed: 706 average time/residue: 0.1883 time to fit residues: 218.6275 Evaluate side-chains 683 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 582 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 480 TYR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 242 CYS Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 66 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 436 TRP Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 455 GLU Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 632 ASN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 54 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 270 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 149 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 326 ASN D 358 HIS E 55 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 247 HIS F 632 ASN ** M 95 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 = 0.3419 r_free = 0.3419 target = 0.134544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113356 restraints weight = 38003.558| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.47 r_work: 0.3057 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30300 Z= 0.147 Angle : 0.798 29.380 41308 Z= 0.344 Chirality : 0.045 0.297 4784 Planarity : 0.005 0.071 5110 Dihedral : 6.627 89.058 4148 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.73 % Favored : 90.06 % Rotamer: Outliers : 4.60 % Allowed : 15.81 % Favored : 79.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3741 helix: 0.53 (0.12), residues: 2139 sheet: -3.10 (0.36), residues: 170 loop : -2.87 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 88 TYR 0.023 0.001 TYR L 13 PHE 0.021 0.001 PHE B 46 TRP 0.022 0.001 TRP F 436 HIS 0.012 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (30288) covalent geometry : angle 0.69574 / 0.34 (41272) hydrogen bonds : bond 0.04020 / 2.69 ( 1485) hydrogen bonds : angle 4.21334 / 2.95 ( 4356) metal coordination : bond 0.00846 / 0.47 ( 12) metal coordination : angle 13.26469 / 8.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 607 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8415 (mp10) cc_final: 0.7968 (mp10) REVERT: A 160 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8268 (tp) REVERT: A 170 ILE cc_start: 0.8947 (tt) cc_final: 0.8632 (tt) REVERT: A 309 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8695 (tm) REVERT: C 124 TRP cc_start: 0.7482 (t60) cc_final: 0.6398 (t60) REVERT: D 201 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8309 (tt) REVERT: D 392 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7312 (mtt) REVERT: D 400 MET cc_start: 0.8683 (mtm) cc_final: 0.7977 (mtp) REVERT: E 58 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8690 (mtpt) REVERT: E 78 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8411 (mt) REVERT: E 99 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.1878 (tt) REVERT: B 224 SER cc_start: 0.9250 (m) cc_final: 0.8806 (t) REVERT: B 357 ASP cc_start: 0.4968 (t0) cc_final: 0.4673 (t0) REVERT: B 439 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8276 (mt-10) REVERT: J 19 LEU cc_start: 0.8185 (pp) cc_final: 0.7898 (pt) REVERT: J 83 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7976 (mmtt) REVERT: J 138 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8654 (tp) REVERT: J 139 LYS cc_start: 0.8207 (mttp) cc_final: 0.7877 (mtpp) REVERT: J 154 LYS cc_start: 0.9269 (mmtt) cc_final: 0.8996 (mmmt) REVERT: J 160 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: P 6 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7840 (mttp) REVERT: P 30 TYR cc_start: 0.8397 (m-80) cc_final: 0.7606 (m-80) REVERT: H 210 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8542 (mp) REVERT: H 238 ASP cc_start: 0.8102 (t0) cc_final: 0.7812 (t0) REVERT: I 136 TYR cc_start: 0.9150 (m-10) cc_final: 0.8884 (m-80) REVERT: I 168 MET cc_start: 0.8690 (mmt) cc_final: 0.8179 (mmt) REVERT: K 22 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6756 (mm) REVERT: K 24 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6335 (tm-30) REVERT: L 32 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8186 (mt) REVERT: L 61 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8266 (pp) REVERT: F 31 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7452 (pm20) REVERT: F 332 MET cc_start: 0.8132 (ttm) cc_final: 0.7804 (ttm) REVERT: F 367 MET cc_start: 0.8030 (mmm) cc_final: 0.7426 (ttt) REVERT: F 436 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7737 (t60) REVERT: F 455 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: F 496 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8330 (Cg_endo) REVERT: F 563 GLN cc_start: 0.7898 (pm20) cc_final: 0.7361 (mt0) REVERT: F 574 GLN cc_start: 0.7346 (mm-40) cc_final: 0.7056 (tt0) REVERT: F 596 ARG cc_start: 0.6459 (tmt-80) cc_final: 0.5306 (ptt90) REVERT: F 600 GLN cc_start: 0.6031 (tt0) cc_final: 0.5040 (mm-40) REVERT: N 100 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7626 (tp) REVERT: M 1 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6907 (pp-130) REVERT: M 4 LYS cc_start: 0.9068 (pmtt) cc_final: 0.8777 (pttm) REVERT: M 19 ASP cc_start: 0.7884 (p0) cc_final: 0.7326 (p0) REVERT: M 29 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8528 (mp) REVERT: M 55 GLU cc_start: 0.8670 (pp20) cc_final: 0.7860 (tp30) outliers start: 141 outliers final: 80 residues processed: 696 average time/residue: 0.1812 time to fit residues: 208.0332 Evaluate side-chains 690 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 591 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 66 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 436 TRP Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 455 GLU Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 284 optimal weight: 3.9990 chunk 361 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 279 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 300 optimal weight: 0.7980 chunk 311 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 326 ASN D 358 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 247 HIS F 632 ASN M 37 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110637 restraints weight = 38587.479| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.53 r_work: 0.3020 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30300 Z= 0.167 Angle : 0.807 29.467 41308 Z= 0.350 Chirality : 0.045 0.260 4784 Planarity : 0.005 0.072 5110 Dihedral : 6.588 89.793 4148 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.94 % Favored : 89.87 % Rotamer: Outliers : 4.64 % Allowed : 16.62 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3741 helix: 0.57 (0.12), residues: 2152 sheet: -3.02 (0.37), residues: 171 loop : -2.76 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 498 TYR 0.023 0.002 TYR L 13 PHE 0.021 0.002 PHE B 46 TRP 0.021 0.001 TRP F 436 HIS 0.012 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (30288) covalent geometry : angle 0.70722 / 0.35 (41272) hydrogen bonds : bond 0.04106 / 2.75 ( 1485) hydrogen bonds : angle 4.22171 / 2.95 ( 4356) metal coordination : bond 0.01117 / 0.66 ( 12) metal coordination : angle 13.17373 / 8.59 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 612 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8449 (mp10) cc_final: 0.8218 (mp10) REVERT: A 36 MET cc_start: 0.8427 (tpp) cc_final: 0.8163 (tpp) REVERT: A 101 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8947 (tp) REVERT: A 160 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8280 (tp) REVERT: A 170 ILE cc_start: 0.8979 (tt) cc_final: 0.8667 (tt) REVERT: A 309 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8739 (tm) REVERT: C 124 TRP cc_start: 0.7634 (t60) cc_final: 0.6486 (t60) REVERT: D 127 GLN cc_start: 0.8936 (mt0) cc_final: 0.8647 (mt0) REVERT: D 392 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7513 (mtt) REVERT: E 58 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8690 (mtpt) REVERT: E 78 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8390 (mt) REVERT: E 99 LEU cc_start: 0.2470 (OUTLIER) cc_final: 0.1956 (tt) REVERT: B 224 SER cc_start: 0.9197 (m) cc_final: 0.8794 (t) REVERT: B 349 LEU cc_start: 0.8826 (tp) cc_final: 0.8580 (tp) REVERT: B 357 ASP cc_start: 0.4475 (OUTLIER) cc_final: 0.4222 (t70) REVERT: B 439 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8281 (mt-10) REVERT: J 19 LEU cc_start: 0.8225 (pp) cc_final: 0.7927 (pt) REVERT: J 83 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7927 (mmtt) REVERT: J 138 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8728 (tp) REVERT: J 139 LYS cc_start: 0.8221 (mttp) cc_final: 0.7919 (mtpp) REVERT: J 154 LYS cc_start: 0.9268 (mmtt) cc_final: 0.8979 (mmmt) REVERT: J 160 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: P 6 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7848 (mttp) REVERT: H 210 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8582 (mp) REVERT: H 231 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7982 (tptt) REVERT: H 238 ASP cc_start: 0.8284 (t0) cc_final: 0.7930 (t0) REVERT: I 136 TYR cc_start: 0.9183 (m-10) cc_final: 0.8908 (m-80) REVERT: I 173 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8094 (mp) REVERT: K 22 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6789 (mm) REVERT: K 24 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6429 (tm-30) REVERT: L 32 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8141 (mt) REVERT: L 61 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8428 (pp) REVERT: F 31 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7472 (pm20) REVERT: F 208 MET cc_start: 0.8448 (mtt) cc_final: 0.8243 (ttm) REVERT: F 332 MET cc_start: 0.8151 (ttm) cc_final: 0.7852 (ttm) REVERT: F 367 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7479 (ttt) REVERT: F 382 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7753 (ptt180) REVERT: F 436 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.7742 (t60) REVERT: F 455 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: F 496 PRO cc_start: 0.8683 (Cg_exo) cc_final: 0.8436 (Cg_endo) REVERT: F 563 GLN cc_start: 0.7931 (pm20) cc_final: 0.7344 (mt0) REVERT: F 596 ARG cc_start: 0.6505 (tmt-80) cc_final: 0.5547 (ptt90) REVERT: F 600 GLN cc_start: 0.6018 (tt0) cc_final: 0.5581 (mm-40) REVERT: N 100 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7740 (tp) REVERT: M 1 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6970 (pp-130) REVERT: M 4 LYS cc_start: 0.9079 (pmtt) cc_final: 0.8774 (pttm) REVERT: M 19 ASP cc_start: 0.7827 (p0) cc_final: 0.7325 (p0) REVERT: M 29 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8575 (mp) REVERT: M 55 GLU cc_start: 0.8731 (pp20) cc_final: 0.7914 (tp30) outliers start: 142 outliers final: 90 residues processed: 699 average time/residue: 0.1759 time to fit residues: 203.1640 Evaluate side-chains 707 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 595 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 242 CYS Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 66 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 436 TRP Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 455 GLU Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 283 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 300 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 129 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 204 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 326 ASN D 358 HIS E 39 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS F 632 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.133704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111743 restraints weight = 38417.996| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.63 r_work: 0.3036 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30300 Z= 0.146 Angle : 0.799 29.848 41308 Z= 0.344 Chirality : 0.045 0.346 4784 Planarity : 0.005 0.100 5110 Dihedral : 6.333 86.738 4143 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.49 % Favored : 90.35 % Rotamer: Outliers : 4.64 % Allowed : 17.11 % Favored : 78.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3741 helix: 0.70 (0.12), residues: 2148 sheet: -2.93 (0.38), residues: 170 loop : -2.72 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 498 TYR 0.023 0.001 TYR L 13 PHE 0.022 0.001 PHE B 46 TRP 0.023 0.001 TRP F 436 HIS 0.012 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (30288) covalent geometry : angle 0.69762 / 0.34 (41272) hydrogen bonds : bond 0.03936 / 2.63 ( 1485) hydrogen bonds : angle 4.16646 / 2.91 ( 4356) metal coordination : bond 0.01046 / 0.56 ( 12) metal coordination : angle 13.19952 / 8.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 611 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8465 (tpp) cc_final: 0.8206 (tpp) REVERT: A 101 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8929 (tp) REVERT: A 160 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8285 (tp) REVERT: A 170 ILE cc_start: 0.8940 (tt) cc_final: 0.8633 (tt) REVERT: A 309 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8725 (tm) REVERT: C 20 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6064 (pm20) REVERT: C 124 TRP cc_start: 0.7627 (t60) cc_final: 0.6497 (t60) REVERT: D 127 GLN cc_start: 0.8871 (mt0) cc_final: 0.8602 (mt0) REVERT: D 269 MET cc_start: 0.8518 (mtt) cc_final: 0.8285 (mtt) REVERT: D 392 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7411 (mtt) REVERT: E 58 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8749 (mtpt) REVERT: E 78 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8408 (mt) REVERT: E 99 LEU cc_start: 0.2383 (OUTLIER) cc_final: 0.1901 (tt) REVERT: B 57 THR cc_start: 0.8844 (p) cc_final: 0.8584 (t) REVERT: B 224 SER cc_start: 0.9132 (m) cc_final: 0.8775 (t) REVERT: B 357 ASP cc_start: 0.4410 (OUTLIER) cc_final: 0.4155 (t70) REVERT: B 439 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8141 (mt-10) REVERT: G 137 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8557 (mm110) REVERT: J 19 LEU cc_start: 0.8225 (pp) cc_final: 0.7900 (pt) REVERT: J 83 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7897 (mmtt) REVERT: J 138 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8718 (tp) REVERT: J 154 LYS cc_start: 0.9283 (mmtt) cc_final: 0.8979 (mmmt) REVERT: J 160 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: P 6 LYS cc_start: 0.8351 (mtpp) cc_final: 0.7860 (mttp) REVERT: H 67 VAL cc_start: 0.9310 (t) cc_final: 0.9105 (t) REVERT: H 78 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.7966 (p0) REVERT: H 210 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8615 (mp) REVERT: H 231 LYS cc_start: 0.8312 (mmmt) cc_final: 0.8094 (tptt) REVERT: H 238 ASP cc_start: 0.8188 (t0) cc_final: 0.7886 (t0) REVERT: H 243 TYR cc_start: 0.8116 (m-10) cc_final: 0.7414 (m-10) REVERT: I 136 TYR cc_start: 0.9160 (m-10) cc_final: 0.8862 (m-80) REVERT: I 173 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8061 (mp) REVERT: K 22 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6680 (mm) REVERT: K 24 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6435 (tm-30) REVERT: K 90 ILE cc_start: 0.8961 (mm) cc_final: 0.8616 (mm) REVERT: L 32 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8089 (mt) REVERT: L 61 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8407 (pp) REVERT: F 31 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7501 (pm20) REVERT: F 254 MET cc_start: 0.8188 (mmp) cc_final: 0.7984 (mmp) REVERT: F 332 MET cc_start: 0.8127 (ttm) cc_final: 0.7805 (ttm) REVERT: F 367 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7688 (ttt) REVERT: F 382 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7783 (ptt180) REVERT: F 436 TRP cc_start: 0.8169 (OUTLIER) cc_final: 0.7597 (t60) REVERT: F 455 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: F 496 PRO cc_start: 0.8694 (Cg_exo) cc_final: 0.8463 (Cg_endo) REVERT: F 563 GLN cc_start: 0.7934 (pm20) cc_final: 0.7345 (mt0) REVERT: F 596 ARG cc_start: 0.6492 (tmt-80) cc_final: 0.5539 (ptt90) REVERT: F 600 GLN cc_start: 0.5977 (tt0) cc_final: 0.5641 (mm-40) REVERT: F 603 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7364 (mm-30) REVERT: N 100 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7698 (tp) REVERT: M 1 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6976 (pp-130) REVERT: M 4 LYS cc_start: 0.9064 (pmtt) cc_final: 0.8778 (pttm) REVERT: M 19 ASP cc_start: 0.7889 (p0) cc_final: 0.7363 (p0) REVERT: M 55 GLU cc_start: 0.8712 (pp20) cc_final: 0.7959 (tp30) outliers start: 142 outliers final: 95 residues processed: 689 average time/residue: 0.1858 time to fit residues: 211.1783 Evaluate side-chains 707 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 589 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 242 CYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 66 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 436 TRP Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 455 GLU Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 497 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 613 VAL Chi-restraints excluded: chain F residue 643 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 212 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 155 optimal weight: 0.0370 chunk 296 optimal weight: 1.9990 chunk 359 optimal weight: 0.0770 chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 344 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 326 ASN D 358 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 247 HIS F 632 ASN ** M 95 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 = 0.3433 r_free = 0.3433 target = 0.135974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.114145 restraints weight = 38182.989| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.61 r_work: 0.3067 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30300 Z= 0.132 Angle : 0.779 27.876 41308 Z= 0.336 Chirality : 0.044 0.289 4784 Planarity : 0.005 0.103 5110 Dihedral : 6.157 84.823 4143 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.01 % Favored : 90.83 % Rotamer: Outliers : 4.28 % Allowed : 17.73 % Favored : 77.99 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3741 helix: 0.83 (0.12), residues: 2146 sheet: -2.90 (0.39), residues: 160 loop : -2.65 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 498 TYR 0.023 0.001 TYR L 13 PHE 0.023 0.001 PHE B 46 TRP 0.024 0.001 TRP F 436 HIS 0.013 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (30288) covalent geometry : angle 0.68237 / 0.33 (41272) hydrogen bonds : bond 0.03754 / 2.50 ( 1485) hydrogen bonds : angle 4.10611 / 2.86 ( 4356) metal coordination : bond 0.00848 / 0.43 ( 12) metal coordination : angle 12.73086 / 8.13 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 628 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8551 (mtt) REVERT: A 36 MET cc_start: 0.8530 (tpp) cc_final: 0.8293 (tpp) REVERT: A 101 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8888 (tp) REVERT: A 160 LEU cc_start: 0.8546 (tt) cc_final: 0.8310 (tp) REVERT: A 170 ILE cc_start: 0.8939 (tt) cc_final: 0.8644 (tt) REVERT: A 185 MET cc_start: 0.8978 (tpp) cc_final: 0.8774 (tpp) REVERT: A 309 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8721 (tm) REVERT: C 20 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.5608 (pm20) REVERT: C 124 TRP cc_start: 0.7665 (t60) cc_final: 0.6566 (t60) REVERT: D 23 PHE cc_start: 0.8012 (p90) cc_final: 0.7533 (p90) REVERT: D 127 GLN cc_start: 0.8792 (mt0) cc_final: 0.8537 (mt0) REVERT: D 269 MET cc_start: 0.8647 (mtt) cc_final: 0.8392 (mtt) REVERT: D 392 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7266 (mtt) REVERT: D 400 MET cc_start: 0.8728 (mtm) cc_final: 0.8033 (mtp) REVERT: E 25 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8576 (tpt-90) REVERT: E 58 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8663 (mtpt) REVERT: E 78 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8423 (mt) REVERT: E 99 LEU cc_start: 0.2280 (OUTLIER) cc_final: 0.1748 (tt) REVERT: B 57 THR cc_start: 0.8856 (p) cc_final: 0.8611 (t) REVERT: B 224 SER cc_start: 0.9082 (m) cc_final: 0.8720 (t) REVERT: B 276 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8010 (tp) REVERT: B 357 ASP cc_start: 0.4395 (OUTLIER) cc_final: 0.4142 (t70) REVERT: B 368 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7055 (mttm) REVERT: B 439 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8249 (mt-10) REVERT: G 137 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8518 (mm110) REVERT: J 58 PHE cc_start: 0.7798 (m-10) cc_final: 0.7398 (m-80) REVERT: J 138 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8697 (tp) REVERT: J 154 LYS cc_start: 0.9297 (mmtt) cc_final: 0.8983 (mmmt) REVERT: J 160 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: P 6 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7870 (mttp) REVERT: H 67 VAL cc_start: 0.9338 (t) cc_final: 0.9088 (t) REVERT: H 78 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.7921 (p0) REVERT: H 139 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: H 186 LYS cc_start: 0.7202 (mttm) cc_final: 0.6712 (mttm) REVERT: H 210 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8610 (mp) REVERT: H 231 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7976 (tptt) REVERT: H 238 ASP cc_start: 0.8162 (t0) cc_final: 0.7905 (t0) REVERT: H 243 TYR cc_start: 0.8267 (m-10) cc_final: 0.7556 (m-10) REVERT: H 373 MET cc_start: 0.7444 (mmt) cc_final: 0.7233 (mmm) REVERT: I 136 TYR cc_start: 0.9155 (m-10) cc_final: 0.8864 (m-80) REVERT: I 173 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8004 (mp) REVERT: K 22 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6548 (mm) REVERT: K 24 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6346 (tm-30) REVERT: K 90 ILE cc_start: 0.9078 (mm) cc_final: 0.8786 (mm) REVERT: F 31 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7505 (pm20) REVERT: F 208 MET cc_start: 0.8241 (mtt) cc_final: 0.7851 (ttm) REVERT: F 332 MET cc_start: 0.8106 (ttm) cc_final: 0.7680 (ttm) REVERT: F 367 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7664 (ttt) REVERT: F 436 TRP cc_start: 0.8102 (OUTLIER) cc_final: 0.7610 (t60) REVERT: F 496 PRO cc_start: 0.8683 (Cg_exo) cc_final: 0.8472 (Cg_endo) REVERT: F 563 GLN cc_start: 0.7924 (pm20) cc_final: 0.7353 (mt0) REVERT: F 574 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7140 (tt0) REVERT: F 596 ARG cc_start: 0.6481 (tmt-80) cc_final: 0.5355 (ppt170) REVERT: F 600 GLN cc_start: 0.6063 (tt0) cc_final: 0.5203 (mm-40) REVERT: N 100 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7701 (tp) REVERT: M 1 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6992 (pp-130) REVERT: M 4 LYS cc_start: 0.9031 (pmtt) cc_final: 0.8740 (pttm) REVERT: M 19 ASP cc_start: 0.7924 (p0) cc_final: 0.7264 (p0) REVERT: M 29 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8473 (mp) REVERT: M 55 GLU cc_start: 0.8677 (pp20) cc_final: 0.8200 (pt0) REVERT: S 69 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8559 (ttm110) outliers start: 131 outliers final: 86 residues processed: 705 average time/residue: 0.1817 time to fit residues: 211.1156 Evaluate side-chains 709 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 601 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 242 CYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 66 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 436 TRP Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 497 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 613 VAL Chi-restraints excluded: chain F residue 643 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 122 optimal weight: 0.0050 chunk 58 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 295 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 162 optimal weight: 3.9990 chunk 294 optimal weight: 0.0670 chunk 286 optimal weight: 0.9980 chunk 368 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 overall best weight: 0.3532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 326 ASN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS F 632 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114580 restraints weight = 38076.405| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.58 r_work: 0.3078 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30300 Z= 0.130 Angle : 0.783 27.923 41308 Z= 0.337 Chirality : 0.044 0.278 4784 Planarity : 0.005 0.104 5110 Dihedral : 6.073 83.456 4143 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.01 % Favored : 90.88 % Rotamer: Outliers : 3.92 % Allowed : 18.58 % Favored : 77.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3741 helix: 0.91 (0.12), residues: 2140 sheet: -2.70 (0.40), residues: 155 loop : -2.62 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 498 TYR 0.024 0.001 TYR L 13 PHE 0.023 0.001 PHE B 46 TRP 0.022 0.001 TRP F 436 HIS 0.013 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (30288) covalent geometry : angle 0.68741 / 0.34 (41272) hydrogen bonds : bond 0.03726 / 2.49 ( 1485) hydrogen bonds : angle 4.11458 / 2.87 ( 4356) metal coordination : bond 0.00849 / 0.41 ( 12) metal coordination : angle 12.72533 / 8.13 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 622 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8599 (mp10) cc_final: 0.8231 (mp10) REVERT: A 34 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8521 (mtt) REVERT: A 36 MET cc_start: 0.8527 (tpp) cc_final: 0.8283 (tpp) REVERT: A 101 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8860 (tp) REVERT: A 170 ILE cc_start: 0.8848 (tt) cc_final: 0.8569 (tt) REVERT: A 185 MET cc_start: 0.8974 (tpp) cc_final: 0.8759 (tpp) REVERT: A 309 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8695 (tm) REVERT: C 20 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5554 (pm20) REVERT: C 124 TRP cc_start: 0.7614 (t60) cc_final: 0.6517 (t60) REVERT: D 23 PHE cc_start: 0.7996 (p90) cc_final: 0.7489 (p90) REVERT: D 269 MET cc_start: 0.8646 (mtt) cc_final: 0.8373 (mtt) REVERT: D 392 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7253 (mtt) REVERT: D 400 MET cc_start: 0.8707 (mtm) cc_final: 0.8036 (mtp) REVERT: E 25 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8590 (tpt-90) REVERT: E 58 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8600 (mtpt) REVERT: E 78 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8411 (mt) REVERT: E 99 LEU cc_start: 0.2473 (OUTLIER) cc_final: 0.1996 (tt) REVERT: B 57 THR cc_start: 0.8944 (p) cc_final: 0.8718 (t) REVERT: B 224 SER cc_start: 0.9107 (m) cc_final: 0.8723 (t) REVERT: B 276 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7993 (tp) REVERT: B 357 ASP cc_start: 0.4343 (OUTLIER) cc_final: 0.4094 (t70) REVERT: B 368 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7288 (mttm) REVERT: B 439 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8195 (mt-10) REVERT: G 137 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8626 (mm110) REVERT: J 133 GLU cc_start: 0.8880 (mp0) cc_final: 0.8491 (mt-10) REVERT: J 139 LYS cc_start: 0.8204 (mttp) cc_final: 0.7881 (mtpp) REVERT: J 154 LYS cc_start: 0.9288 (mmtt) cc_final: 0.8991 (mmmt) REVERT: J 160 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: H 67 VAL cc_start: 0.9330 (t) cc_final: 0.9055 (t) REVERT: H 78 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.7878 (p0) REVERT: H 139 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8086 (mm-30) REVERT: H 186 LYS cc_start: 0.7204 (mttm) cc_final: 0.6877 (mttm) REVERT: H 243 TYR cc_start: 0.8145 (m-10) cc_final: 0.7431 (m-10) REVERT: H 326 GLU cc_start: 0.8295 (pt0) cc_final: 0.7880 (pt0) REVERT: I 136 TYR cc_start: 0.9154 (m-10) cc_final: 0.8851 (m-80) REVERT: I 173 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7962 (mp) REVERT: K 24 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6304 (tm-30) REVERT: K 90 ILE cc_start: 0.9088 (mm) cc_final: 0.8796 (mm) REVERT: F 31 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7467 (pm20) REVERT: F 208 MET cc_start: 0.8287 (mtt) cc_final: 0.7998 (ttm) REVERT: F 265 HIS cc_start: 0.7746 (m90) cc_final: 0.7398 (m-70) REVERT: F 332 MET cc_start: 0.8032 (ttm) cc_final: 0.7689 (ttm) REVERT: F 367 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7245 (ttt) REVERT: F 436 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7497 (t60) REVERT: F 563 GLN cc_start: 0.7921 (pm20) cc_final: 0.7334 (mt0) REVERT: F 574 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7101 (tt0) REVERT: F 596 ARG cc_start: 0.6404 (tmt-80) cc_final: 0.5442 (ppt170) REVERT: F 600 GLN cc_start: 0.5982 (tt0) cc_final: 0.5715 (mm-40) REVERT: N 100 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7680 (tp) REVERT: M 1 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6940 (pp-130) REVERT: M 4 LYS cc_start: 0.9027 (pmtt) cc_final: 0.8746 (pttm) REVERT: M 19 ASP cc_start: 0.7903 (p0) cc_final: 0.7286 (p0) REVERT: M 29 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8565 (mt) REVERT: M 55 GLU cc_start: 0.8687 (pp20) cc_final: 0.8203 (pt0) REVERT: S 69 ARG cc_start: 0.8782 (ttm110) cc_final: 0.8552 (ttm110) outliers start: 120 outliers final: 83 residues processed: 696 average time/residue: 0.1756 time to fit residues: 200.6576 Evaluate side-chains 712 residues out of total 3122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 610 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 242 CYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 66 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 390 TYR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 436 TRP Chi-restraints excluded: chain F residue 484 TRP Chi-restraints excluded: chain F residue 497 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 613 VAL Chi-restraints excluded: chain F residue 643 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain O residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 72 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 302 optimal weight: 0.8980 chunk 266 optimal weight: 0.3980 chunk 357 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 0.0980 chunk 162 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 326 ASN B 130 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 ASN K 181 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS F 632 ASN ** M 95 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 = 0.3435 r_free = 0.3435 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114055 restraints weight = 38458.347| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.59 r_work: 0.3072 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30300 Z= 0.138 Angle : 0.794 27.684 41308 Z= 0.343 Chirality : 0.044 0.272 4784 Planarity : 0.005 0.104 5110 Dihedral : 6.057 82.295 4143 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.17 % Favored : 90.72 % Rotamer: Outliers : 3.76 % Allowed : 19.01 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3741 helix: 0.89 (0.12), residues: 2146 sheet: -2.65 (0.41), residues: 155 loop : -2.61 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 498 TYR 0.024 0.001 TYR L 13 PHE 0.023 0.001 PHE B 46 TRP 0.022 0.001 TRP F 436 HIS 0.013 0.001 HIS F 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (30288) covalent geometry : angle 0.70027 / 0.34 (41272) hydrogen bonds : bond 0.03763 / 2.51 ( 1485) hydrogen bonds : angle 4.13051 / 2.87 ( 4356) metal coordination : bond 0.00940 / 0.49 ( 12) metal coordination : angle 12.72178 / 8.09 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8257.50 seconds wall clock time: 141 minutes 45.90 seconds (8505.90 seconds total)