Starting phenix.real_space_refine on Thu Nov 20 11:31:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q9e_4481/11_2025/6q9e_4481.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q9e_4481/11_2025/6q9e_4481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6q9e_4481/11_2025/6q9e_4481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q9e_4481/11_2025/6q9e_4481.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q9e_4481/11_2025/6q9e_4481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q9e_4481/11_2025/6q9e_4481.map" } resolution = 3.9 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 14 5.49 5 S 164 5.16 5 C 20484 2.51 5 N 5441 2.21 5 O 5884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31997 Number of models: 1 Model: "" Number of chains: 26 Chain: "a1" Number of atoms: 3409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3409 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 1 Chain: "a2" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3126 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 399} Chain breaks: 1 Chain: "b1" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c1" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1909 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "f1" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "d1" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 886 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "q1" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 618 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "h1" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x1" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 164 Classifications: {'peptide': 33} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 32} Link IDs: {'TRANS': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "i1" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a3" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3447 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 18, 'TRANS': 425} Chain: "a4" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3122 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 1 Chain: "b2" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c2" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1903 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "f2" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "d2" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 888 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "q2" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 631 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "h2" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x2" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "i2" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "b1" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 260 Unusual residues: {'3PE': 1, 'CDL': 2, 'HEM': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 188 Planarities with less than four sites: {'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-4': 1} Unresolved non-hydrogen planarities: 60 Chain: "c1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "f1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "b2" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 189 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 31 Chain: "c2" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "f2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12558 SG CYSf1 139 40.810 64.146 134.722 1.00154.41 S ATOM 12694 SG CYSf1 158 42.886 67.388 135.383 1.00144.15 S ATOM 28222 SG CYSf2 139 105.183 57.153 121.799 1.00143.28 S ATOM 28358 SG CYSf2 158 103.339 53.723 121.745 1.00139.12 S Time building chain proxies: 7.80, per 1000 atoms: 0.24 Number of scatterers: 31997 At special positions: 0 Unit cell: (134.4, 151.2, 176.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 164 16.00 P 14 15.00 O 5884 8.00 N 5441 7.00 C 20484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYSf1 144 " - pdb=" SG CYSf1 160 " distance=2.03 Simple disulfide: pdb=" SG CYSh1 24 " - pdb=" SG CYSh1 68 " distance=2.03 Simple disulfide: pdb=" SG CYSh1 40 " - pdb=" SG CYSh1 54 " distance=2.03 Simple disulfide: pdb=" SG CYSf2 144 " - pdb=" SG CYSf2 160 " distance=2.04 Simple disulfide: pdb=" SG CYSh2 24 " - pdb=" SG CYSh2 68 " distance=2.02 Simple disulfide: pdb=" SG CYSh2 40 " - pdb=" SG CYSh2 54 " distance=2.04 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESf1 501 " pdb="FE1 FESf1 501 " - pdb=" SG CYSf1 139 " pdb="FE1 FESf1 501 " - pdb=" SG CYSf1 158 " pdb="FE2 FESf1 501 " - pdb=" ND1 HISf1 161 " pdb="FE2 FESf1 501 " - pdb=" ND1 HISf1 141 " pdb=" FESf2 202 " pdb="FE1 FESf2 202 " - pdb=" SG CYSf2 158 " pdb="FE1 FESf2 202 " - pdb=" SG CYSf2 139 " pdb="FE2 FESf2 202 " - pdb=" ND1 HISf2 141 " pdb="FE2 FESf2 202 " - pdb=" ND1 HISf2 161 " Number of angles added : 6 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7474 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 15 sheets defined 56.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'a1' and resid 3 through 10 Processing helix chain 'a1' and resid 54 through 63 Processing helix chain 'a1' and resid 73 through 83 Processing helix chain 'a1' and resid 102 through 104 No H-bonds generated for 'chain 'a1' and resid 102 through 104' Processing helix chain 'a1' and resid 105 through 119 Processing helix chain 'a1' and resid 123 through 142 Processing helix chain 'a1' and resid 144 through 158 removed outlier: 3.513A pdb=" N VALa1 148 " --> pdb=" O SERa1 144 " (cutoff:3.500A) Processing helix chain 'a1' and resid 161 through 165 Processing helix chain 'a1' and resid 178 through 190 removed outlier: 3.858A pdb=" N LEUa1 182 " --> pdb=" O SERa1 178 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYRa1 190 " --> pdb=" O LEUa1 186 " (cutoff:3.500A) Processing helix chain 'a1' and resid 204 through 216 Processing helix chain 'a1' and resid 265 through 277 Processing helix chain 'a1' and resid 292 through 301 Processing helix chain 'a1' and resid 330 through 348 Processing helix chain 'a1' and resid 350 through 369 removed outlier: 3.925A pdb=" N VALa1 354 " --> pdb=" O THRa1 350 " (cutoff:3.500A) Processing helix chain 'a1' and resid 372 through 385 Processing helix chain 'a1' and resid 391 through 401 removed outlier: 3.619A pdb=" N TRPa1 395 " --> pdb=" O PROa1 391 " (cutoff:3.500A) Processing helix chain 'a1' and resid 403 through 415 removed outlier: 3.512A pdb=" N VALa1 407 " --> pdb=" O ASPa1 403 " (cutoff:3.500A) Processing helix chain 'a1' and resid 433 through 442 removed outlier: 3.649A pdb=" N PHEa1 442 " --> pdb=" O ARGa1 438 " (cutoff:3.500A) Processing helix chain 'a2' and resid 54 through 58 removed outlier: 3.644A pdb=" N TYRa2 57 " --> pdb=" O GLYa2 54 " (cutoff:3.500A) Processing helix chain 'a2' and resid 64 through 71 Processing helix chain 'a2' and resid 81 through 93 Processing helix chain 'a2' and resid 115 through 129 removed outlier: 4.084A pdb=" N LEUa2 119 " --> pdb=" O ASPa2 115 " (cutoff:3.500A) Processing helix chain 'a2' and resid 133 through 152 Processing helix chain 'a2' and resid 154 through 167 removed outlier: 4.128A pdb=" N HISa2 158 " --> pdb=" O ASNa2 154 " (cutoff:3.500A) Processing helix chain 'a2' and resid 170 through 174 removed outlier: 3.854A pdb=" N ASNa2 174 " --> pdb=" O ALAa2 171 " (cutoff:3.500A) Processing helix chain 'a2' and resid 187 through 197 Processing helix chain 'a2' and resid 212 through 223 removed outlier: 3.516A pdb=" N LEUa2 216 " --> pdb=" O SERa2 212 " (cutoff:3.500A) Processing helix chain 'a2' and resid 266 through 280 Processing helix chain 'a2' and resid 293 through 303 removed outlier: 3.759A pdb=" N GLNa2 297 " --> pdb=" O SERa2 293 " (cutoff:3.500A) Processing helix chain 'a2' and resid 332 through 349 removed outlier: 3.594A pdb=" N VALa2 336 " --> pdb=" O SERa2 332 " (cutoff:3.500A) Processing helix chain 'a2' and resid 353 through 371 Processing helix chain 'a2' and resid 374 through 389 removed outlier: 4.002A pdb=" N ALAa2 389 " --> pdb=" O GLNa2 385 " (cutoff:3.500A) Processing helix chain 'a2' and resid 394 through 404 Processing helix chain 'a2' and resid 406 through 420 removed outlier: 3.658A pdb=" N VALa2 410 " --> pdb=" O ALAa2 406 " (cutoff:3.500A) Processing helix chain 'b1' and resid 8 through 19 removed outlier: 3.963A pdb=" N ILEb1 13 " --> pdb=" O PROb1 9 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILEb1 19 " --> pdb=" O ASNb1 15 " (cutoff:3.500A) Processing helix chain 'b1' and resid 28 through 31 Processing helix chain 'b1' and resid 32 through 54 Processing helix chain 'b1' and resid 61 through 72 Processing helix chain 'b1' and resid 75 through 104 Processing helix chain 'b1' and resid 105 through 109 removed outlier: 3.608A pdb=" N THRb1 108 " --> pdb=" O GLYb1 105 " (cutoff:3.500A) Processing helix chain 'b1' and resid 110 through 133 Processing helix chain 'b1' and resid 136 through 151 Processing helix chain 'b1' and resid 156 through 165 Processing helix chain 'b1' and resid 171 through 204 removed outlier: 3.611A pdb=" N LEUb1 175 " --> pdb=" O ASPb1 171 " (cutoff:3.500A) Proline residue: b1 186 - end of helix Processing helix chain 'b1' and resid 223 through 245 Processing helix chain 'b1' and resid 252 through 256 removed outlier: 3.828A pdb=" N ASNb1 255 " --> pdb=" O ASPb1 252 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYRb1 256 " --> pdb=" O PROb1 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'b1' and resid 252 through 256' Processing helix chain 'b1' and resid 271 through 273 No H-bonds generated for 'chain 'b1' and resid 271 through 273' Processing helix chain 'b1' and resid 274 through 282 removed outlier: 3.537A pdb=" N LEUb1 281 " --> pdb=" O ALAb1 277 " (cutoff:3.500A) Processing helix chain 'b1' and resid 286 through 304 Processing helix chain 'b1' and resid 305 through 308 removed outlier: 3.825A pdb=" N HISb1 308 " --> pdb=" O PROb1 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'b1' and resid 305 through 308' Processing helix chain 'b1' and resid 318 through 340 Processing helix chain 'b1' and resid 344 through 364 Processing helix chain 'b1' and resid 364 through 377 removed outlier: 3.507A pdb=" N LEUb1 377 " --> pdb=" O GLUb1 373 " (cutoff:3.500A) Processing helix chain 'c1' and resid 22 through 36 Processing helix chain 'c1' and resid 37 through 40 removed outlier: 3.675A pdb=" N CYSc1 40 " --> pdb=" O CYSc1 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'c1' and resid 37 through 40' Processing helix chain 'c1' and resid 47 through 52 removed outlier: 3.594A pdb=" N VALc1 52 " --> pdb=" O ARGc1 49 " (cutoff:3.500A) Processing helix chain 'c1' and resid 58 through 68 removed outlier: 3.988A pdb=" N VALc1 68 " --> pdb=" O LEUc1 64 " (cutoff:3.500A) Processing helix chain 'c1' and resid 97 through 103 Processing helix chain 'c1' and resid 115 through 120 removed outlier: 3.634A pdb=" N ARGc1 120 " --> pdb=" O ILEc1 116 " (cutoff:3.500A) Processing helix chain 'c1' and resid 123 through 133 removed outlier: 3.928A pdb=" N VALc1 127 " --> pdb=" O GLYc1 123 " (cutoff:3.500A) Processing helix chain 'c1' and resid 177 through 194 removed outlier: 3.917A pdb=" N VALc1 181 " --> pdb=" O THRc1 177 " (cutoff:3.500A) Processing helix chain 'c1' and resid 196 through 226 removed outlier: 4.026A pdb=" N LEUc1 215 " --> pdb=" O METc1 211 " (cutoff:3.500A) Proline residue: c1 216 - end of helix removed outlier: 3.871A pdb=" N TYRc1 219 " --> pdb=" O LEUc1 215 " (cutoff:3.500A) Processing helix chain 'f1' and resid 15 through 19 removed outlier: 3.829A pdb=" N LEUf1 19 " --> pdb=" O PROf1 16 " (cutoff:3.500A) Processing helix chain 'f1' and resid 28 through 62 removed outlier: 4.235A pdb=" N ARGf1 32 " --> pdb=" O SERf1 28 " (cutoff:3.500A) Processing helix chain 'f1' and resid 102 through 111 removed outlier: 3.629A pdb=" N ILEf1 106 " --> pdb=" O THRf1 102 " (cutoff:3.500A) Processing helix chain 'f1' and resid 122 through 127 removed outlier: 3.759A pdb=" N VALf1 127 " --> pdb=" O ASPf1 123 " (cutoff:3.500A) Processing helix chain 'd1' and resid 12 through 24 Processing helix chain 'd1' and resid 32 through 36 removed outlier: 3.643A pdb=" N ASPd1 35 " --> pdb=" O METd1 32 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THRd1 36 " --> pdb=" O ARGd1 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd1' and resid 32 through 36' Processing helix chain 'd1' and resid 40 through 49 Processing helix chain 'd1' and resid 51 through 72 Processing helix chain 'd1' and resid 76 through 80 removed outlier: 3.818A pdb=" N TRPd1 80 " --> pdb=" O LYSd1 77 " (cutoff:3.500A) Processing helix chain 'd1' and resid 82 through 86 removed outlier: 3.549A pdb=" N GLUd1 85 " --> pdb=" O LYSd1 82 " (cutoff:3.500A) Processing helix chain 'd1' and resid 90 through 110 Processing helix chain 'q1' and resid 32 through 43 Processing helix chain 'q1' and resid 44 through 71 Proline residue: q1 50 - end of helix removed outlier: 3.933A pdb=" N VALq1 54 " --> pdb=" O PROq1 50 " (cutoff:3.500A) Processing helix chain 'h1' and resid 15 through 25 removed outlier: 3.721A pdb=" N THRh1 19 " --> pdb=" O ASPh1 15 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLUh1 25 " --> pdb=" O ARGh1 21 " (cutoff:3.500A) Processing helix chain 'h1' and resid 27 through 47 Processing helix chain 'h1' and resid 55 through 72 removed outlier: 3.632A pdb=" N LYSh1 72 " --> pdb=" O CYSh1 68 " (cutoff:3.500A) Processing helix chain 'i1' and resid 6 through 14 removed outlier: 3.583A pdb=" N PHEi1 14 " --> pdb=" O TYRi1 10 " (cutoff:3.500A) Processing helix chain 'i1' and resid 17 through 44 Processing helix chain 'i1' and resid 51 through 58 removed outlier: 3.614A pdb=" N ILEi1 55 " --> pdb=" O LEUi1 51 " (cutoff:3.500A) Processing helix chain 'a3' and resid 3 through 10 removed outlier: 3.572A pdb=" N SERa3 10 " --> pdb=" O GLNa3 6 " (cutoff:3.500A) Processing helix chain 'a3' and resid 55 through 63 Processing helix chain 'a3' and resid 73 through 82 Processing helix chain 'a3' and resid 105 through 118 removed outlier: 3.790A pdb=" N ALAa3 109 " --> pdb=" O ASPa3 105 " (cutoff:3.500A) Processing helix chain 'a3' and resid 123 through 144 removed outlier: 3.931A pdb=" N THRa3 143 " --> pdb=" O GLNa3 139 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SERa3 144 " --> pdb=" O GLUa3 140 " (cutoff:3.500A) Processing helix chain 'a3' and resid 145 through 158 Processing helix chain 'a3' and resid 161 through 165 Processing helix chain 'a3' and resid 178 through 189 removed outlier: 3.738A pdb=" N LEUa3 182 " --> pdb=" O SERa3 178 " (cutoff:3.500A) Processing helix chain 'a3' and resid 191 through 193 No H-bonds generated for 'chain 'a3' and resid 191 through 193' Processing helix chain 'a3' and resid 205 through 216 Processing helix chain 'a3' and resid 265 through 277 Processing helix chain 'a3' and resid 292 through 301 Processing helix chain 'a3' and resid 330 through 348 Processing helix chain 'a3' and resid 350 through 369 removed outlier: 3.830A pdb=" N VALa3 354 " --> pdb=" O THRa3 350 " (cutoff:3.500A) Processing helix chain 'a3' and resid 371 through 385 Processing helix chain 'a3' and resid 391 through 401 Processing helix chain 'a3' and resid 403 through 415 Processing helix chain 'a3' and resid 433 through 442 removed outlier: 4.109A pdb=" N PHEa3 442 " --> pdb=" O ARGa3 438 " (cutoff:3.500A) Processing helix chain 'a4' and resid 64 through 72 Processing helix chain 'a4' and resid 73 through 75 No H-bonds generated for 'chain 'a4' and resid 73 through 75' Processing helix chain 'a4' and resid 81 through 92 Processing helix chain 'a4' and resid 115 through 129 Processing helix chain 'a4' and resid 133 through 152 Processing helix chain 'a4' and resid 154 through 168 removed outlier: 4.315A pdb=" N HISa4 158 " --> pdb=" O ASNa4 154 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYRa4 168 " --> pdb=" O HISa4 164 " (cutoff:3.500A) Processing helix chain 'a4' and resid 170 through 174 removed outlier: 3.613A pdb=" N ASNa4 174 " --> pdb=" O ALAa4 171 " (cutoff:3.500A) Processing helix chain 'a4' and resid 187 through 197 removed outlier: 4.079A pdb=" N LEUa4 191 " --> pdb=" O THRa4 187 " (cutoff:3.500A) Processing helix chain 'a4' and resid 200 through 202 No H-bonds generated for 'chain 'a4' and resid 200 through 202' Processing helix chain 'a4' and resid 212 through 224 removed outlier: 4.098A pdb=" N LEUa4 216 " --> pdb=" O SERa4 212 " (cutoff:3.500A) Processing helix chain 'a4' and resid 266 through 280 Processing helix chain 'a4' and resid 293 through 303 Processing helix chain 'a4' and resid 332 through 349 Processing helix chain 'a4' and resid 353 through 371 removed outlier: 3.841A pdb=" N VALa4 357 " --> pdb=" O SERa4 353 " (cutoff:3.500A) Processing helix chain 'a4' and resid 374 through 389 removed outlier: 3.578A pdb=" N ALAa4 389 " --> pdb=" O GLNa4 385 " (cutoff:3.500A) Processing helix chain 'a4' and resid 394 through 405 removed outlier: 4.237A pdb=" N VALa4 405 " --> pdb=" O GLNa4 401 " (cutoff:3.500A) Processing helix chain 'a4' and resid 406 through 420 removed outlier: 3.683A pdb=" N VALa4 410 " --> pdb=" O ALAa4 406 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLYa4 420 " --> pdb=" O LYSa4 416 " (cutoff:3.500A) Processing helix chain 'b2' and resid 3 through 7 Processing helix chain 'b2' and resid 8 through 19 removed outlier: 3.920A pdb=" N ILEb2 13 " --> pdb=" O PROb2 9 " (cutoff:3.500A) Processing helix chain 'b2' and resid 28 through 31 Processing helix chain 'b2' and resid 32 through 54 Processing helix chain 'b2' and resid 61 through 72 Processing helix chain 'b2' and resid 75 through 104 Processing helix chain 'b2' and resid 105 through 108 removed outlier: 3.652A pdb=" N THRb2 108 " --> pdb=" O GLYb2 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'b2' and resid 105 through 108' Processing helix chain 'b2' and resid 109 through 133 removed outlier: 3.662A pdb=" N TRPb2 113 " --> pdb=" O PHEb2 109 " (cutoff:3.500A) Processing helix chain 'b2' and resid 136 through 151 Processing helix chain 'b2' and resid 156 through 165 Processing helix chain 'b2' and resid 171 through 204 Proline residue: b2 186 - end of helix Processing helix chain 'b2' and resid 223 through 245 Processing helix chain 'b2' and resid 271 through 273 No H-bonds generated for 'chain 'b2' and resid 271 through 273' Processing helix chain 'b2' and resid 274 through 282 removed outlier: 3.606A pdb=" N ALAb2 279 " --> pdb=" O LEUb2 275 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILEb2 280 " --> pdb=" O PHEb2 276 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEUb2 281 " --> pdb=" O ALAb2 277 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARGb2 282 " --> pdb=" O TYRb2 278 " (cutoff:3.500A) Processing helix chain 'b2' and resid 286 through 303 Processing helix chain 'b2' and resid 304 through 308 removed outlier: 3.502A pdb=" N LEUb2 307 " --> pdb=" O METb2 304 " (cutoff:3.500A) Processing helix chain 'b2' and resid 318 through 340 Processing helix chain 'b2' and resid 344 through 364 Processing helix chain 'b2' and resid 364 through 377 removed outlier: 3.616A pdb=" N LEUb2 377 " --> pdb=" O GLUb2 373 " (cutoff:3.500A) Processing helix chain 'c2' and resid 22 through 36 Processing helix chain 'c2' and resid 47 through 53 removed outlier: 3.501A pdb=" N VALc2 52 " --> pdb=" O ARGc2 49 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLYc2 53 " --> pdb=" O HISc2 50 " (cutoff:3.500A) Processing helix chain 'c2' and resid 57 through 67 removed outlier: 3.718A pdb=" N ALAc2 61 " --> pdb=" O THRc2 57 " (cutoff:3.500A) Processing helix chain 'c2' and resid 97 through 105 Processing helix chain 'c2' and resid 116 through 120 removed outlier: 4.485A pdb=" N ARGc2 120 " --> pdb=" O VALc2 117 " (cutoff:3.500A) Processing helix chain 'c2' and resid 123 through 133 removed outlier: 4.079A pdb=" N VALc2 127 " --> pdb=" O GLYc2 123 " (cutoff:3.500A) Processing helix chain 'c2' and resid 178 through 194 Processing helix chain 'c2' and resid 196 through 214 Processing helix chain 'c2' and resid 214 through 226 Processing helix chain 'c2' and resid 226 through 231 removed outlier: 3.666A pdb=" N SERc2 231 " --> pdb=" O SERc2 227 " (cutoff:3.500A) Processing helix chain 'f2' and resid 29 through 62 Processing helix chain 'f2' and resid 102 through 112 Processing helix chain 'f2' and resid 122 through 127 Processing helix chain 'd2' and resid 10 through 25 removed outlier: 4.452A pdb=" N GLYd2 25 " --> pdb=" O TYRd2 21 " (cutoff:3.500A) Processing helix chain 'd2' and resid 26 through 30 removed outlier: 3.649A pdb=" N GLYd2 30 " --> pdb=" O ASNd2 27 " (cutoff:3.500A) Processing helix chain 'd2' and resid 32 through 36 removed outlier: 3.550A pdb=" N ASPd2 35 " --> pdb=" O METd2 32 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRd2 36 " --> pdb=" O ARGd2 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd2' and resid 32 through 36' Processing helix chain 'd2' and resid 40 through 49 Processing helix chain 'd2' and resid 51 through 71 removed outlier: 3.645A pdb=" N TYRd2 55 " --> pdb=" O PROd2 51 " (cutoff:3.500A) Processing helix chain 'd2' and resid 76 through 80 removed outlier: 3.557A pdb=" N TRPd2 80 " --> pdb=" O LYSd2 77 " (cutoff:3.500A) Processing helix chain 'd2' and resid 90 through 109 Processing helix chain 'q2' and resid 32 through 43 Processing helix chain 'q2' and resid 44 through 69 Proline residue: q2 50 - end of helix removed outlier: 4.084A pdb=" N VALq2 54 " --> pdb=" O PROq2 50 " (cutoff:3.500A) Processing helix chain 'h2' and resid 15 through 25 removed outlier: 3.868A pdb=" N THRh2 19 " --> pdb=" O ASPh2 15 " (cutoff:3.500A) Processing helix chain 'h2' and resid 28 through 46 Processing helix chain 'h2' and resid 55 through 71 Processing helix chain 'h2' and resid 73 through 77 removed outlier: 3.517A pdb=" N SERh2 76 " --> pdb=" O LEUh2 73 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEUh2 77 " --> pdb=" O PHEh2 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'h2' and resid 73 through 77' Processing helix chain 'i2' and resid 3 through 5 No H-bonds generated for 'chain 'i2' and resid 3 through 5' Processing helix chain 'i2' and resid 6 through 14 Processing helix chain 'i2' and resid 17 through 46 Processing helix chain 'i2' and resid 51 through 58 removed outlier: 3.965A pdb=" N ILEi2 55 " --> pdb=" O LEUi2 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a1' and resid 15 through 19 Processing sheet with id=AA2, first strand: chain 'a1' and resid 278 through 280 Processing sheet with id=AA3, first strand: chain 'a2' and resid 25 through 28 removed outlier: 6.319A pdb=" N VALa2 34 " --> pdb=" O LEUa2 206 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLYa2 208 " --> pdb=" O VALa2 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALAa2 36 " --> pdb=" O GLYa2 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a2' and resid 243 through 247 removed outlier: 6.348A pdb=" N ILEa2 244 " --> pdb=" O ALAa2 426 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLYa2 428 " --> pdb=" O ILEa2 244 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLUa2 246 " --> pdb=" O GLYa2 428 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b1' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'f1' and resid 74 through 77 Processing sheet with id=AA7, first strand: chain 'f1' and resid 85 through 91 Processing sheet with id=AA8, first strand: chain 'f1' and resid 157 through 158 removed outlier: 3.666A pdb=" N LYSf1 173 " --> pdb=" O HISf1 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a3' and resid 15 through 19 removed outlier: 6.250A pdb=" N ARGa3 24 " --> pdb=" O LEUa3 197 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ALAa3 199 " --> pdb=" O ARGa3 24 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALAa3 26 " --> pdb=" O ALAa3 199 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLYa3 201 " --> pdb=" O ALAa3 26 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLUa3 28 " --> pdb=" O GLYa3 201 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a3' and resid 278 through 280 removed outlier: 7.123A pdb=" N CYSa3 304 " --> pdb=" O ASPa3 327 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASPa3 327 " --> pdb=" O CYSa3 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a4' and resid 25 through 28 Processing sheet with id=AB3, first strand: chain 'a4' and resid 242 through 247 removed outlier: 6.519A pdb=" N GLYa4 242 " --> pdb=" O METa4 424 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALAa4 426 " --> pdb=" O GLYa4 242 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILEa4 244 " --> pdb=" O ALAa4 426 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLYa4 428 " --> pdb=" O ILEa4 244 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLUa4 246 " --> pdb=" O GLYa4 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f2' and resid 74 through 77 Processing sheet with id=AB5, first strand: chain 'f2' and resid 86 through 88 Processing sheet with id=AB6, first strand: chain 'f2' and resid 147 through 150 removed outlier: 4.981A pdb=" N GLYf2 155 " --> pdb=" O ASNf2 149 " (cutoff:3.500A) 1778 hydrogen bonds defined for protein. 5118 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: 5.98 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 12238 1.38 - 1.58: 20233 1.58 - 1.79: 89 1.79 - 1.99: 201 1.99 - 2.19: 24 Bond restraints: 32785 Sorted by residual: bond pdb=" C2D HECc2 501 " pdb=" C3D HECc2 501 " ideal model delta sigma weight residual 1.544 1.316 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2D HECc1 501 " pdb=" C3D HECc1 501 " ideal model delta sigma weight residual 1.544 1.317 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CAC HECc2 501 " pdb=" CBC HECc2 501 " ideal model delta sigma weight residual 1.544 1.362 0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" CAC HECc1 501 " pdb=" CBC HECc1 501 " ideal model delta sigma weight residual 1.544 1.363 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C4 U10b1 406 " pdb=" O4 U10b1 406 " ideal model delta sigma weight residual 1.230 1.410 -0.180 2.00e-02 2.50e+03 8.14e+01 ... (remaining 32780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 43605 3.10 - 6.21: 800 6.21 - 9.31: 105 9.31 - 12.42: 16 12.42 - 15.52: 12 Bond angle restraints: 44538 Sorted by residual: angle pdb=" S1 FESf1 501 " pdb="FE2 FESf1 501 " pdb=" S2 FESf1 501 " ideal model delta sigma weight residual 104.33 90.01 14.32 1.14e+00 7.69e-01 1.58e+02 angle pdb="FE1 FESf1 501 " pdb=" S2 FESf1 501 " pdb="FE2 FESf1 501 " ideal model delta sigma weight residual 75.66 89.80 -14.14 1.14e+00 7.69e-01 1.54e+02 angle pdb=" S1 FESf2 202 " pdb="FE2 FESf2 202 " pdb=" S2 FESf2 202 " ideal model delta sigma weight residual 104.33 90.27 14.06 1.14e+00 7.69e-01 1.52e+02 angle pdb="FE1 FESf1 501 " pdb=" S1 FESf1 501 " pdb="FE2 FESf1 501 " ideal model delta sigma weight residual 75.66 90.17 -14.51 1.20e+00 6.94e-01 1.46e+02 angle pdb="FE1 FESf2 202 " pdb=" S2 FESf2 202 " pdb="FE2 FESf2 202 " ideal model delta sigma weight residual 75.66 89.44 -13.78 1.14e+00 7.69e-01 1.46e+02 ... (remaining 44533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 19218 35.88 - 71.76: 263 71.76 - 107.65: 43 107.65 - 143.53: 2 143.53 - 179.41: 3 Dihedral angle restraints: 19529 sinusoidal: 7931 harmonic: 11598 Sorted by residual: dihedral pdb=" CA ARGq1 11 " pdb=" C ARGq1 11 " pdb=" N HISq1 12 " pdb=" CA HISq1 12 " ideal model delta harmonic sigma weight residual -180.00 -115.42 -64.58 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CB CYSh1 24 " pdb=" SG CYSh1 24 " pdb=" SG CYSh1 68 " pdb=" CB CYSh1 68 " ideal model delta sinusoidal sigma weight residual 93.00 179.42 -86.42 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYSh2 24 " pdb=" SG CYSh2 24 " pdb=" SG CYSh2 68 " pdb=" CB CYSh2 68 " ideal model delta sinusoidal sigma weight residual -86.00 -168.77 82.77 1 1.00e+01 1.00e-02 8.39e+01 ... (remaining 19526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4558 0.111 - 0.221: 269 0.221 - 0.332: 6 0.332 - 0.443: 2 0.443 - 0.553: 2 Chirality restraints: 4837 Sorted by residual: chirality pdb=" CB4 CDLc2 502 " pdb=" CB3 CDLc2 502 " pdb=" CB6 CDLc2 502 " pdb=" OB6 CDLc2 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.02 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CB ILEq2 34 " pdb=" CA ILEq2 34 " pdb=" CG1 ILEq2 34 " pdb=" CG2 ILEq2 34 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA4 CDLb2 404 " pdb=" CA3 CDLb2 404 " pdb=" CA6 CDLb2 404 " pdb=" OA6 CDLb2 404 " both_signs ideal model delta sigma weight residual False -2.57 -2.15 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 4834 not shown) Planarity restraints: 5675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PROq1 50 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PROq1 51 " -0.187 5.00e-02 4.00e+02 pdb=" CA PROq1 51 " 0.055 5.00e-02 4.00e+02 pdb=" CD PROq1 51 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHEb1 183 " -0.030 2.00e-02 2.50e+03 3.18e-02 1.77e+01 pdb=" CG PHEb1 183 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHEb1 183 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHEb1 183 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEb1 183 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEb1 183 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHEb1 183 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PROq2 50 " -0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PROq2 51 " 0.169 5.00e-02 4.00e+02 pdb=" CA PROq2 51 " -0.049 5.00e-02 4.00e+02 pdb=" CD PROq2 51 " -0.055 5.00e-02 4.00e+02 ... (remaining 5672 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 214 2.56 - 3.15: 24531 3.15 - 3.73: 49170 3.73 - 4.32: 66558 4.32 - 4.90: 111366 Nonbonded interactions: 251839 Sorted by model distance: nonbonded pdb=" NE2 HISb1 182 " pdb="FE HEMb1 401 " model vdw 1.981 3.080 nonbonded pdb=" NE2 HISc1 41 " pdb="FE HECc1 501 " model vdw 1.990 3.080 nonbonded pdb=" NE2 HISb2 182 " pdb="FE HEMb2 401 " model vdw 2.000 3.080 nonbonded pdb=" NE2 HISb2 97 " pdb="FE HEMb2 402 " model vdw 2.052 3.080 nonbonded pdb=" NE2 HISb1 97 " pdb="FE HEMb1 402 " model vdw 2.098 3.080 ... (remaining 251834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a1' and resid 2 through 445) selection = (chain 'a3' and (resid 2 through 222 or resid 229 through 445)) } ncs_group { reference = (chain 'a2' and (resid 20 through 227 or resid 235 through 439)) selection = chain 'a4' } ncs_group { reference = (chain 'b1' and (resid 2 through 402 or (resid 403 and (name N or name C1 or nam \ e C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C2A or name C2B \ or name C2C or name C2D or name C2E or name C2F or name C2G or name C2H or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )) or (resid 404 and (name CB2 or name OB2 or name CB3 or name OB3 or \ name C1 or name C11 or name C12 or name C31 or name C32 or name C33 or name C51 \ or name C52 or name C71 or name C72 or name CA2 or name CA3 or name CA4 or name \ CA5 or name CA6 or name CA7 or name CB4 or name CB5 or name CB6 or name CB7 or n \ ame O1 or name OA2 or name OA3 or name OA4 or name OA5 or name OA6 or name OA7 o \ r name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or name OB7 or name O \ B8 or name OB9 or name PA1 or name PB2)))) selection = (chain 'b2' and resid 2 through 404) } ncs_group { reference = (chain 'c1' and resid 2 through 501) selection = (chain 'c2' and resid 2 through 501) } ncs_group { reference = (chain 'd1' and resid 11 through 109) selection = (chain 'd2' and resid 11 through 109) } ncs_group { reference = (chain 'f1' and resid 2 through 196) selection = (chain 'f2' and resid 2 through 196) } ncs_group { reference = chain 'h1' selection = chain 'h2' } ncs_group { reference = chain 'i1' selection = (chain 'i2' and resid 5 through 59) } ncs_group { reference = (chain 'q1' and resid 2 through 73) selection = (chain 'q2' and resid 2 through 73) } ncs_group { reference = (chain 'x1' and resid 8 through 38) selection = (chain 'x2' and (resid 1 or (resid 2 and (name N or name CA or name C or name O \ )) or resid 3 through 48)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.760 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.389 32809 Z= 0.487 Angle : 1.077 15.525 44556 Z= 0.581 Chirality : 0.059 0.553 4837 Planarity : 0.009 0.108 5675 Dihedral : 12.975 179.409 12037 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.50 % Rotamer: Outliers : 0.42 % Allowed : 3.60 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.51 (0.11), residues: 3883 helix: -1.87 (0.09), residues: 2017 sheet: -1.42 (0.25), residues: 377 loop : -3.10 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGa2 245 TYR 0.033 0.003 TYRc1 164 PHE 0.071 0.003 PHEb1 183 TRP 0.037 0.004 TRPa3 443 HIS 0.020 0.002 HISi2 57 Details of bonding type rmsd covalent geometry : bond 0.00945 (32785) covalent geometry : angle 1.07496 (44538) SS BOND : bond 0.00801 ( 6) SS BOND : angle 2.77700 ( 12) hydrogen bonds : bond 0.11762 ( 1778) hydrogen bonds : angle 6.20490 ( 5118) metal coordination : bond 0.14072 ( 8) metal coordination : angle 4.25427 ( 6) Misc. bond : bond 0.21744 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1118 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 57 TYR cc_start: 0.7779 (t80) cc_final: 0.6449 (t80) REVERT: a1 130 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7595 (tp30) REVERT: a1 327 ASP cc_start: 0.8442 (t70) cc_final: 0.7821 (p0) REVERT: a1 329 MET cc_start: 0.8543 (mmm) cc_final: 0.8031 (tpt) REVERT: a1 346 CYS cc_start: 0.7797 (m) cc_final: 0.7123 (t) REVERT: a2 206 LEU cc_start: 0.8869 (tp) cc_final: 0.8448 (tt) REVERT: a2 351 ASN cc_start: 0.7356 (m110) cc_final: 0.6780 (t0) REVERT: a2 356 ASP cc_start: 0.7594 (m-30) cc_final: 0.7237 (t0) REVERT: b1 35 SER cc_start: 0.8897 (p) cc_final: 0.7999 (m) REVERT: b1 73 VAL cc_start: 0.9690 (t) cc_final: 0.9473 (m) REVERT: b1 240 MET cc_start: 0.8412 (mmp) cc_final: 0.7991 (mmm) REVERT: b1 243 VAL cc_start: 0.9078 (m) cc_final: 0.8799 (m) REVERT: b1 269 LYS cc_start: 0.8250 (pttt) cc_final: 0.7902 (ptpt) REVERT: b1 275 LEU cc_start: 0.8392 (mt) cc_final: 0.7651 (mt) REVERT: b1 292 LEU cc_start: 0.8409 (tp) cc_final: 0.8206 (tt) REVERT: b1 304 MET cc_start: 0.8564 (mmm) cc_final: 0.8288 (mmm) REVERT: b1 312 GLN cc_start: 0.8676 (mp10) cc_final: 0.8290 (mm-40) REVERT: c1 75 ASN cc_start: 0.8447 (t0) cc_final: 0.8201 (t0) REVERT: c1 106 ASN cc_start: 0.6599 (t0) cc_final: 0.6009 (t0) REVERT: c1 163 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6613 (mm) REVERT: c1 187 THR cc_start: 0.9264 (m) cc_final: 0.9017 (p) REVERT: c1 207 MET cc_start: 0.7946 (ttm) cc_final: 0.7396 (tmm) REVERT: c1 211 MET cc_start: 0.7514 (mmt) cc_final: 0.6801 (tmm) REVERT: f1 2 HIS cc_start: 0.8325 (p-80) cc_final: 0.7648 (p90) REVERT: f1 3 THR cc_start: 0.8978 (p) cc_final: 0.8628 (t) REVERT: f1 43 THR cc_start: 0.8399 (m) cc_final: 0.8174 (p) REVERT: f1 104 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7620 (pttt) REVERT: f1 135 LEU cc_start: 0.5916 (mt) cc_final: 0.5607 (mt) REVERT: f1 136 ILE cc_start: 0.8210 (mm) cc_final: 0.7767 (mt) REVERT: d1 18 LYS cc_start: 0.8387 (tttt) cc_final: 0.8091 (ptpt) REVERT: d1 22 ASN cc_start: 0.8610 (t0) cc_final: 0.8379 (m110) REVERT: d1 42 ASP cc_start: 0.8233 (m-30) cc_final: 0.7897 (m-30) REVERT: d1 47 ILE cc_start: 0.9358 (mm) cc_final: 0.9085 (tp) REVERT: d1 66 LEU cc_start: 0.9002 (mt) cc_final: 0.8741 (mm) REVERT: d1 74 ILE cc_start: 0.8763 (mt) cc_final: 0.8353 (pt) REVERT: q1 3 GLN cc_start: 0.8634 (pm20) cc_final: 0.8432 (pm20) REVERT: q1 47 ARG cc_start: 0.8583 (mtt180) cc_final: 0.7105 (mmt180) REVERT: h1 20 VAL cc_start: 0.8593 (t) cc_final: 0.7623 (p) REVERT: h1 37 LEU cc_start: 0.8924 (tm) cc_final: 0.8606 (tt) REVERT: h1 43 ARG cc_start: 0.6892 (ttm170) cc_final: 0.6445 (mmm-85) REVERT: a3 53 ASN cc_start: 0.7864 (t160) cc_final: 0.7553 (t0) REVERT: a3 82 MET cc_start: 0.7447 (mtt) cc_final: 0.6966 (mtt) REVERT: a3 223 TYR cc_start: 0.5352 (t80) cc_final: 0.5146 (p90) REVERT: a3 234 CYS cc_start: 0.7575 (m) cc_final: 0.7246 (m) REVERT: a3 307 PHE cc_start: 0.8239 (p90) cc_final: 0.7414 (p90) REVERT: a3 329 MET cc_start: 0.8812 (mmm) cc_final: 0.8559 (mmm) REVERT: a3 369 LEU cc_start: 0.8669 (mt) cc_final: 0.8312 (tt) REVERT: a3 411 CYS cc_start: 0.8548 (m) cc_final: 0.8294 (m) REVERT: a3 439 SER cc_start: 0.8103 (t) cc_final: 0.7623 (p) REVERT: a4 68 LEU cc_start: 0.9455 (tp) cc_final: 0.9213 (tp) REVERT: a4 207 ILE cc_start: 0.9342 (mm) cc_final: 0.8968 (mm) REVERT: a4 308 ASP cc_start: 0.8577 (t0) cc_final: 0.7605 (m-30) REVERT: a4 402 ILE cc_start: 0.8645 (mt) cc_final: 0.8278 (mt) REVERT: b2 27 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7465 (mt) REVERT: b2 35 SER cc_start: 0.8811 (p) cc_final: 0.8055 (p) REVERT: b2 43 LEU cc_start: 0.8846 (tt) cc_final: 0.8234 (mt) REVERT: b2 44 GLN cc_start: 0.9019 (mm110) cc_final: 0.8147 (mm-40) REVERT: b2 96 MET cc_start: 0.6918 (mmt) cc_final: 0.6711 (mmt) REVERT: b2 200 LEU cc_start: 0.9414 (tp) cc_final: 0.9140 (tt) REVERT: b2 207 ASN cc_start: 0.8164 (p0) cc_final: 0.7930 (p0) REVERT: b2 252 ASP cc_start: 0.8183 (m-30) cc_final: 0.7892 (m-30) REVERT: b2 263 ASN cc_start: 0.8224 (t0) cc_final: 0.7984 (t0) REVERT: b2 278 TYR cc_start: 0.8454 (t80) cc_final: 0.7835 (t80) REVERT: b2 280 ILE cc_start: 0.8939 (mt) cc_final: 0.8732 (mm) REVERT: b2 320 ILE cc_start: 0.8368 (mt) cc_final: 0.8113 (tp) REVERT: b2 322 GLN cc_start: 0.7934 (tt0) cc_final: 0.7710 (tt0) REVERT: c2 6 HIS cc_start: 0.8022 (t-90) cc_final: 0.7505 (m-70) REVERT: c2 76 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7800 (tp30) REVERT: c2 229 LEU cc_start: 0.9314 (mt) cc_final: 0.9099 (mt) REVERT: f2 69 LEU cc_start: 0.8728 (mm) cc_final: 0.8490 (tp) REVERT: f2 71 MET cc_start: 0.6135 (mmt) cc_final: 0.5765 (mmt) REVERT: f2 181 GLU cc_start: 0.8346 (tt0) cc_final: 0.7913 (tp30) REVERT: d2 88 PHE cc_start: 0.8125 (m-80) cc_final: 0.7813 (m-80) REVERT: d2 90 LEU cc_start: 0.9289 (tp) cc_final: 0.8865 (tt) REVERT: q2 2 ARG cc_start: 0.7912 (mtp85) cc_final: 0.6832 (ptt180) REVERT: q2 24 ARG cc_start: 0.7771 (ptp-110) cc_final: 0.7093 (tpt170) REVERT: q2 41 THR cc_start: 0.9379 (m) cc_final: 0.9004 (p) REVERT: q2 42 ARG cc_start: 0.8087 (tmt170) cc_final: 0.5879 (mtp85) REVERT: h2 26 GLN cc_start: 0.7441 (tp40) cc_final: 0.6974 (pm20) REVERT: h2 51 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7091 (pm20) REVERT: i2 17 THR cc_start: 0.8798 (m) cc_final: 0.8507 (t) REVERT: i2 35 PHE cc_start: 0.8947 (t80) cc_final: 0.8713 (t80) outliers start: 14 outliers final: 3 residues processed: 1127 average time/residue: 0.2409 time to fit residues: 416.9807 Evaluate side-chains 641 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 636 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain c1 residue 163 ILE Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain b2 residue 27 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 29 GLN a1 53 ASN ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 189 HIS a1 264 ASN a1 328 HIS a1 341 GLN a2 22 GLN a2 248 ASN a2 290 ASN a2 297 GLN a2 313 ASN ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 85 ASN c1 50 HIS c1 197 HIS c1 224 HIS ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 53 ASN f1 100 HIS ** d1 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q1 73 ASN ** h1 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i1 45 HIS a3 18 GLN a3 21 ASN a3 53 ASN a3 61 HIS a3 69 ASN a3 141 ASN a3 173 ASN a3 189 HIS a3 341 GLN a4 156 GLN a4 222 GLN a4 248 ASN a4 290 ASN a4 385 GLN b2 8 HIS b2 137 GLN b2 148 ASN b2 267 HIS b2 312 GLN c2 23 HIS c2 50 HIS ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 197 HIS f2 86 ASN f2 108 GLN q2 6 HIS q2 23 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104939 restraints weight = 69118.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107712 restraints weight = 38042.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.109668 restraints weight = 25238.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110917 restraints weight = 18797.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111851 restraints weight = 15358.892| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.818 32809 Z= 0.164 Angle : 0.777 28.607 44556 Z= 0.376 Chirality : 0.045 0.228 4837 Planarity : 0.006 0.090 5675 Dihedral : 12.248 145.322 4742 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.27 % Allowed : 12.94 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.70 (0.13), residues: 3883 helix: -0.08 (0.11), residues: 2030 sheet: -1.09 (0.26), residues: 379 loop : -2.63 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGa1 381 TYR 0.022 0.002 TYRb1 131 PHE 0.023 0.002 PHEb2 183 TRP 0.021 0.002 TRPa3 443 HIS 0.014 0.001 HISa1 252 Details of bonding type rmsd covalent geometry : bond 0.00363 (32785) covalent geometry : angle 0.75664 (44538) SS BOND : bond 0.00584 ( 6) SS BOND : angle 3.70778 ( 12) hydrogen bonds : bond 0.05279 ( 1778) hydrogen bonds : angle 5.01248 ( 5118) metal coordination : bond 0.03755 ( 8) metal coordination : angle 14.34760 ( 6) Misc. bond : bond 0.34610 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 736 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8440 (tt0) cc_final: 0.8078 (tt0) REVERT: a1 130 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7494 (tp30) REVERT: a1 271 GLN cc_start: 0.8240 (mm-40) cc_final: 0.8025 (tp-100) REVERT: a1 320 LEU cc_start: 0.9314 (tp) cc_final: 0.9090 (tp) REVERT: a2 206 LEU cc_start: 0.8969 (tp) cc_final: 0.8531 (tt) REVERT: b1 35 SER cc_start: 0.8553 (p) cc_final: 0.7798 (m) REVERT: b1 175 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8643 (tp) REVERT: b1 228 ASP cc_start: 0.7134 (m-30) cc_final: 0.6520 (m-30) REVERT: b1 243 VAL cc_start: 0.9057 (m) cc_final: 0.8768 (m) REVERT: b1 269 LYS cc_start: 0.7703 (pttt) cc_final: 0.7445 (ptpt) REVERT: b1 275 LEU cc_start: 0.8159 (mt) cc_final: 0.7532 (mt) REVERT: b1 278 TYR cc_start: 0.8386 (t80) cc_final: 0.8174 (t80) REVERT: b1 292 LEU cc_start: 0.8269 (tp) cc_final: 0.8047 (tt) REVERT: b1 311 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8429 (mmtp) REVERT: c1 106 ASN cc_start: 0.6186 (t0) cc_final: 0.5913 (t0) REVERT: c1 124 GLU cc_start: 0.7577 (pm20) cc_final: 0.7228 (pm20) REVERT: c1 163 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6805 (mm) REVERT: c1 187 THR cc_start: 0.9277 (m) cc_final: 0.9026 (p) REVERT: c1 210 MET cc_start: 0.7667 (mmp) cc_final: 0.7426 (mmm) REVERT: c1 211 MET cc_start: 0.7426 (mmt) cc_final: 0.6730 (tmm) REVERT: f1 74 ILE cc_start: 0.5179 (tt) cc_final: 0.4908 (tt) REVERT: f1 104 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7341 (pttt) REVERT: f1 135 LEU cc_start: 0.5954 (mt) cc_final: 0.5726 (mt) REVERT: d1 47 ILE cc_start: 0.9364 (mm) cc_final: 0.9159 (tp) REVERT: q1 3 GLN cc_start: 0.8580 (pm20) cc_final: 0.7973 (pm20) REVERT: q1 47 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7170 (mmt180) REVERT: q1 65 GLU cc_start: 0.7643 (tp30) cc_final: 0.7427 (tp30) REVERT: h1 39 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7740 (mm) REVERT: h1 42 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: a3 82 MET cc_start: 0.7310 (mtt) cc_final: 0.6658 (mtt) REVERT: a3 369 LEU cc_start: 0.8580 (mt) cc_final: 0.8212 (tt) REVERT: a3 411 CYS cc_start: 0.7821 (m) cc_final: 0.7200 (m) REVERT: a3 438 ARG cc_start: 0.8480 (tpt-90) cc_final: 0.8073 (tpp-160) REVERT: a4 68 LEU cc_start: 0.9404 (tp) cc_final: 0.9065 (tp) REVERT: a4 158 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7480 (t-90) REVERT: a4 308 ASP cc_start: 0.8244 (t0) cc_final: 0.7580 (m-30) REVERT: a4 402 ILE cc_start: 0.8624 (mt) cc_final: 0.8240 (mt) REVERT: b2 43 LEU cc_start: 0.8856 (tt) cc_final: 0.8328 (mt) REVERT: b2 51 LEU cc_start: 0.8970 (mm) cc_final: 0.8683 (mm) REVERT: b2 162 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8146 (mm-30) REVERT: b2 200 LEU cc_start: 0.9375 (tp) cc_final: 0.9057 (tt) REVERT: b2 252 ASP cc_start: 0.7860 (m-30) cc_final: 0.7641 (p0) REVERT: b2 263 ASN cc_start: 0.8121 (t0) cc_final: 0.7919 (t0) REVERT: b2 278 TYR cc_start: 0.8139 (t80) cc_final: 0.7689 (t80) REVERT: b2 313 ARG cc_start: 0.8231 (ptm160) cc_final: 0.8024 (ttp80) REVERT: b2 316 MET cc_start: 0.7637 (ttm) cc_final: 0.7389 (mtm) REVERT: b2 341 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8050 (mp10) REVERT: c2 6 HIS cc_start: 0.7972 (t-90) cc_final: 0.7629 (m-70) REVERT: c2 71 GLN cc_start: 0.8129 (tp40) cc_final: 0.7628 (tp40) REVERT: c2 80 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7058 (mmt) REVERT: c2 117 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (p) REVERT: c2 152 PHE cc_start: 0.8378 (t80) cc_final: 0.8171 (t80) REVERT: f2 69 LEU cc_start: 0.8819 (mm) cc_final: 0.8477 (tp) REVERT: f2 87 MET cc_start: 0.5288 (ttp) cc_final: 0.5048 (tpt) REVERT: f2 153 PHE cc_start: 0.3801 (m-80) cc_final: 0.3210 (m-80) REVERT: f2 184 SER cc_start: 0.5169 (m) cc_final: 0.4826 (t) REVERT: q2 2 ARG cc_start: 0.7880 (mtp85) cc_final: 0.6875 (ptt180) REVERT: q2 9 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.8027 (ttm-80) REVERT: q2 24 ARG cc_start: 0.7912 (ptp-110) cc_final: 0.7099 (tpt170) REVERT: q2 42 ARG cc_start: 0.7717 (tmt170) cc_final: 0.5487 (mtp85) REVERT: h2 59 PHE cc_start: 0.8834 (m-10) cc_final: 0.8539 (m-10) REVERT: h2 73 LEU cc_start: 0.8517 (tt) cc_final: 0.8254 (tp) REVERT: i2 16 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7700 (mmm-85) REVERT: i2 35 PHE cc_start: 0.8822 (t80) cc_final: 0.8470 (t80) outliers start: 109 outliers final: 57 residues processed: 801 average time/residue: 0.2139 time to fit residues: 274.1333 Evaluate side-chains 657 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 593 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 134 ILE Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 407 VAL Chi-restraints excluded: chain a2 residue 76 THR Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 98 VAL Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 175 LEU Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 163 ILE Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain d1 residue 16 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 246 ASP Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 110 LEU Chi-restraints excluded: chain b2 residue 183 PHE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 80 MET Chi-restraints excluded: chain c2 residue 117 VAL Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain d2 residue 16 ILE Chi-restraints excluded: chain q2 residue 17 SER Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 65 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 374 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.0570 chunk 226 optimal weight: 8.9990 chunk 304 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 75 ASN ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 274 ASN a4 351 ASN b2 8 HIS ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS c2 180 GLN d2 73 GLN q2 6 HIS q2 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101052 restraints weight = 69522.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103855 restraints weight = 37787.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105771 restraints weight = 24926.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107048 restraints weight = 18673.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107926 restraints weight = 15220.899| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.939 32809 Z= 0.197 Angle : 0.762 23.436 44556 Z= 0.370 Chirality : 0.045 0.176 4837 Planarity : 0.005 0.067 5675 Dihedral : 11.738 142.402 4740 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.41 % Allowed : 14.80 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.08 (0.13), residues: 3883 helix: 0.54 (0.11), residues: 2028 sheet: -0.76 (0.27), residues: 364 loop : -2.51 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGh1 43 TYR 0.019 0.002 TYRc1 164 PHE 0.033 0.002 PHEb1 276 TRP 0.023 0.002 TRPi1 52 HIS 0.011 0.001 HISi2 57 Details of bonding type rmsd covalent geometry : bond 0.00453 (32785) covalent geometry : angle 0.74831 (44538) SS BOND : bond 0.00547 ( 6) SS BOND : angle 3.30036 ( 12) hydrogen bonds : bond 0.05220 ( 1778) hydrogen bonds : angle 4.85255 ( 5118) metal coordination : bond 0.01114 ( 8) metal coordination : angle 11.59895 ( 6) Misc. bond : bond 0.36183 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 620 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8654 (tt0) cc_final: 0.8270 (tt0) REVERT: a1 130 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7345 (tp30) REVERT: a2 90 GLU cc_start: 0.8083 (mp0) cc_final: 0.7753 (mp0) REVERT: a2 99 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8696 (p) REVERT: a2 163 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8862 (tt) REVERT: b1 35 SER cc_start: 0.8769 (p) cc_final: 0.8073 (m) REVERT: b1 36 LEU cc_start: 0.9100 (mt) cc_final: 0.8787 (mt) REVERT: b1 121 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.7074 (m-10) REVERT: b1 138 MET cc_start: 0.7682 (tpp) cc_final: 0.7472 (tpp) REVERT: b1 175 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8673 (tp) REVERT: b1 228 ASP cc_start: 0.7035 (m-30) cc_final: 0.6819 (m-30) REVERT: b1 243 VAL cc_start: 0.8891 (m) cc_final: 0.8549 (m) REVERT: b1 252 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.5606 (t0) REVERT: b1 275 LEU cc_start: 0.7928 (mt) cc_final: 0.7231 (mt) REVERT: b1 282 ARG cc_start: 0.9164 (ttp-110) cc_final: 0.8509 (ttp-110) REVERT: c1 55 CYS cc_start: 0.8498 (p) cc_final: 0.8128 (p) REVERT: c1 106 ASN cc_start: 0.6470 (t0) cc_final: 0.6096 (t0) REVERT: c1 124 GLU cc_start: 0.7627 (pm20) cc_final: 0.7289 (pm20) REVERT: c1 187 THR cc_start: 0.9280 (m) cc_final: 0.9046 (p) REVERT: c1 210 MET cc_start: 0.7734 (mmp) cc_final: 0.7478 (mmm) REVERT: c1 211 MET cc_start: 0.7339 (mmt) cc_final: 0.6802 (tmm) REVERT: c1 224 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7867 (t-90) REVERT: f1 74 ILE cc_start: 0.5239 (tt) cc_final: 0.5002 (tt) REVERT: f1 104 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7333 (pttt) REVERT: d1 16 ILE cc_start: 0.8769 (mm) cc_final: 0.8553 (tt) REVERT: d1 34 ASP cc_start: 0.8249 (p0) cc_final: 0.7932 (p0) REVERT: d1 47 ILE cc_start: 0.9460 (mm) cc_final: 0.9230 (tp) REVERT: q1 2 ARG cc_start: 0.7005 (ptt90) cc_final: 0.6748 (ptt90) REVERT: q1 3 GLN cc_start: 0.8696 (pm20) cc_final: 0.8357 (pm20) REVERT: q1 17 SER cc_start: 0.8833 (t) cc_final: 0.8432 (p) REVERT: q1 47 ARG cc_start: 0.8472 (mtt180) cc_final: 0.7270 (mmt180) REVERT: i1 37 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8453 (mm-40) REVERT: a3 82 MET cc_start: 0.7377 (mtt) cc_final: 0.6741 (mtt) REVERT: a3 93 GLU cc_start: 0.7312 (tt0) cc_final: 0.6812 (tt0) REVERT: a3 369 LEU cc_start: 0.8656 (mt) cc_final: 0.8232 (tt) REVERT: a3 375 VAL cc_start: 0.8871 (m) cc_final: 0.8617 (p) REVERT: a3 438 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8299 (tpp80) REVERT: a4 68 LEU cc_start: 0.9369 (tp) cc_final: 0.9047 (tp) REVERT: a4 158 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7498 (t-90) REVERT: a4 308 ASP cc_start: 0.8121 (t0) cc_final: 0.7587 (m-30) REVERT: b2 20 ASP cc_start: 0.7714 (m-30) cc_final: 0.7241 (p0) REVERT: b2 43 LEU cc_start: 0.8832 (tt) cc_final: 0.8289 (mt) REVERT: b2 51 LEU cc_start: 0.9000 (mm) cc_final: 0.8725 (mm) REVERT: b2 162 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8076 (mm-30) REVERT: b2 200 LEU cc_start: 0.9426 (tp) cc_final: 0.9175 (tt) REVERT: b2 252 ASP cc_start: 0.7997 (m-30) cc_final: 0.7647 (p0) REVERT: b2 263 ASN cc_start: 0.8170 (t0) cc_final: 0.7832 (t0) REVERT: b2 278 TYR cc_start: 0.8199 (t80) cc_final: 0.7700 (t80) REVERT: b2 313 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7994 (ttp80) REVERT: b2 315 MET cc_start: 0.8256 (mtp) cc_final: 0.7769 (mtp) REVERT: c2 6 HIS cc_start: 0.8016 (t-90) cc_final: 0.7645 (m-70) REVERT: c2 71 GLN cc_start: 0.8048 (tp40) cc_final: 0.7605 (tp40) REVERT: c2 80 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7279 (mmt) REVERT: c2 152 PHE cc_start: 0.8428 (t80) cc_final: 0.8136 (t80) REVERT: f2 69 LEU cc_start: 0.8852 (mm) cc_final: 0.8484 (tp) REVERT: f2 71 MET cc_start: 0.5069 (OUTLIER) cc_final: 0.4639 (mmp) REVERT: f2 87 MET cc_start: 0.5392 (ttp) cc_final: 0.5171 (tpt) REVERT: f2 153 PHE cc_start: 0.4114 (m-80) cc_final: 0.3242 (m-80) REVERT: f2 184 SER cc_start: 0.5142 (m) cc_final: 0.4838 (t) REVERT: q2 2 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7088 (ptt180) REVERT: q2 42 ARG cc_start: 0.7768 (tmt170) cc_final: 0.5427 (mtp85) REVERT: i2 16 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7697 (mmm-85) REVERT: i2 35 PHE cc_start: 0.8665 (t80) cc_final: 0.8411 (t80) REVERT: i2 44 GLU cc_start: 0.7013 (tp30) cc_final: 0.6482 (tm-30) outliers start: 147 outliers final: 98 residues processed: 711 average time/residue: 0.2097 time to fit residues: 241.7643 Evaluate side-chains 677 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 570 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 35 CYS Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 134 ILE Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 211 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 234 CYS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 348 SER Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 407 VAL Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 163 LEU Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 45 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 175 LEU Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 225 THR Chi-restraints excluded: chain b1 residue 252 ASP Chi-restraints excluded: chain b1 residue 283 SER Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 24 CYS Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 246 ASP Chi-restraints excluded: chain a3 residue 270 LEU Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a3 residue 407 VAL Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 207 ILE Chi-restraints excluded: chain a4 residue 351 ASN Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 126 THR Chi-restraints excluded: chain b2 residue 133 LEU Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 349 ILE Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 52 VAL Chi-restraints excluded: chain c2 residue 80 MET Chi-restraints excluded: chain c2 residue 127 VAL Chi-restraints excluded: chain c2 residue 157 ILE Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 187 THR Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain f2 residue 71 MET Chi-restraints excluded: chain f2 residue 147 ILE Chi-restraints excluded: chain q2 residue 8 THR Chi-restraints excluded: chain q2 residue 17 SER Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain h2 residue 50 THR Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 363 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 323 HIS a2 277 HIS ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 26 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 328 HIS a3 363 ASN a4 297 GLN a4 313 ASN a4 351 ASN b2 8 HIS b2 201 HIS ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS q2 36 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099345 restraints weight = 69219.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102038 restraints weight = 38416.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103911 restraints weight = 25705.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105036 restraints weight = 19365.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105877 restraints weight = 16076.151| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.055 32809 Z= 0.221 Angle : 0.769 20.216 44556 Z= 0.374 Chirality : 0.046 0.265 4837 Planarity : 0.005 0.058 5675 Dihedral : 11.480 147.077 4738 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 93.00 % Rotamer: Outliers : 5.08 % Allowed : 15.29 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.82 (0.13), residues: 3883 helix: 0.73 (0.11), residues: 2041 sheet: -0.61 (0.27), residues: 361 loop : -2.40 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGd2 101 TYR 0.021 0.002 TYRb2 358 PHE 0.025 0.002 PHEa4 435 TRP 0.017 0.002 TRPa3 443 HIS 0.011 0.001 HISc2 121 Details of bonding type rmsd covalent geometry : bond 0.00509 (32785) covalent geometry : angle 0.75846 (44538) SS BOND : bond 0.00619 ( 6) SS BOND : angle 2.97984 ( 12) hydrogen bonds : bond 0.05318 ( 1778) hydrogen bonds : angle 4.85176 ( 5118) metal coordination : bond 0.00871 ( 8) metal coordination : angle 10.17649 ( 6) Misc. bond : bond 0.38851 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 590 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8740 (tt0) cc_final: 0.8159 (tt0) REVERT: a1 130 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7523 (tp30) REVERT: a1 271 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7937 (tp-100) REVERT: a1 327 ASP cc_start: 0.8212 (t70) cc_final: 0.7878 (p0) REVERT: a2 90 GLU cc_start: 0.8280 (mp0) cc_final: 0.7809 (mp0) REVERT: a2 163 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8846 (tt) REVERT: a2 240 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7935 (tmt90) REVERT: b1 35 SER cc_start: 0.8877 (p) cc_final: 0.8057 (m) REVERT: b1 36 LEU cc_start: 0.9104 (mt) cc_final: 0.8817 (mt) REVERT: b1 73 VAL cc_start: 0.9686 (t) cc_final: 0.9391 (m) REVERT: b1 96 MET cc_start: 0.7316 (mmm) cc_final: 0.7088 (mtt) REVERT: b1 121 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.7135 (m-10) REVERT: b1 228 ASP cc_start: 0.7282 (m-30) cc_final: 0.7021 (m-30) REVERT: b1 243 VAL cc_start: 0.8973 (m) cc_final: 0.8702 (m) REVERT: b1 275 LEU cc_start: 0.8079 (mt) cc_final: 0.7612 (mt) REVERT: b1 282 ARG cc_start: 0.9114 (ttp-110) cc_final: 0.8493 (ttp-110) REVERT: b1 328 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8512 (tt) REVERT: c1 55 CYS cc_start: 0.8408 (p) cc_final: 0.8072 (p) REVERT: c1 106 ASN cc_start: 0.6505 (t0) cc_final: 0.6080 (t0) REVERT: c1 109 LEU cc_start: 0.8877 (tp) cc_final: 0.8425 (pt) REVERT: c1 187 THR cc_start: 0.9300 (m) cc_final: 0.9021 (p) REVERT: c1 206 LYS cc_start: 0.8841 (mttt) cc_final: 0.8581 (mtpt) REVERT: c1 210 MET cc_start: 0.7705 (mmp) cc_final: 0.7462 (mmm) REVERT: c1 211 MET cc_start: 0.7390 (mmt) cc_final: 0.6815 (tmm) REVERT: c1 224 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7963 (t-90) REVERT: f1 74 ILE cc_start: 0.5253 (tt) cc_final: 0.5030 (tt) REVERT: f1 104 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7378 (pttt) REVERT: d1 34 ASP cc_start: 0.8313 (p0) cc_final: 0.7963 (p0) REVERT: d1 47 ILE cc_start: 0.9481 (mm) cc_final: 0.9259 (tp) REVERT: d1 105 GLU cc_start: 0.7053 (pt0) cc_final: 0.6701 (pt0) REVERT: q1 3 GLN cc_start: 0.8676 (pm20) cc_final: 0.8281 (pm20) REVERT: q1 17 SER cc_start: 0.8891 (t) cc_final: 0.8444 (p) REVERT: q1 47 ARG cc_start: 0.8518 (mtt180) cc_final: 0.7280 (mmt180) REVERT: h1 42 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: i1 37 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8395 (mp10) REVERT: a3 19 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7880 (mm) REVERT: a3 82 MET cc_start: 0.7639 (mtt) cc_final: 0.7165 (mtt) REVERT: a3 93 GLU cc_start: 0.7405 (tt0) cc_final: 0.6973 (tt0) REVERT: a3 245 GLU cc_start: 0.7626 (tp30) cc_final: 0.7244 (tm-30) REVERT: a3 369 LEU cc_start: 0.8651 (mt) cc_final: 0.8247 (tt) REVERT: a3 375 VAL cc_start: 0.8992 (m) cc_final: 0.8706 (p) REVERT: a3 438 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8361 (tpp80) REVERT: a4 68 LEU cc_start: 0.9408 (tp) cc_final: 0.9059 (tp) REVERT: a4 153 GLN cc_start: 0.7813 (pm20) cc_final: 0.7520 (pm20) REVERT: a4 158 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.7714 (t-90) REVERT: a4 308 ASP cc_start: 0.8097 (t0) cc_final: 0.7493 (m-30) REVERT: b2 20 ASP cc_start: 0.7797 (m-30) cc_final: 0.7567 (p0) REVERT: b2 43 LEU cc_start: 0.8798 (tt) cc_final: 0.8197 (mt) REVERT: b2 44 GLN cc_start: 0.8824 (mm110) cc_final: 0.8529 (mm110) REVERT: b2 85 ASN cc_start: 0.8610 (m-40) cc_final: 0.8303 (m-40) REVERT: b2 129 MET cc_start: 0.8666 (mtm) cc_final: 0.8387 (mtp) REVERT: b2 162 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7975 (mm-30) REVERT: b2 200 LEU cc_start: 0.9435 (tp) cc_final: 0.9160 (tt) REVERT: b2 230 LEU cc_start: 0.9170 (tp) cc_final: 0.8890 (tp) REVERT: b2 263 ASN cc_start: 0.8155 (t0) cc_final: 0.7851 (t0) REVERT: b2 313 ARG cc_start: 0.8321 (ptm160) cc_final: 0.8084 (ttp80) REVERT: b2 341 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8126 (mp10) REVERT: b2 365 MET cc_start: 0.7393 (mmp) cc_final: 0.7070 (mtt) REVERT: c2 6 HIS cc_start: 0.8206 (t-90) cc_final: 0.7673 (m-70) REVERT: c2 71 GLN cc_start: 0.8273 (tp40) cc_final: 0.7953 (tp40) REVERT: c2 80 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: c2 152 PHE cc_start: 0.8566 (t80) cc_final: 0.8236 (t80) REVERT: f2 69 LEU cc_start: 0.8877 (mm) cc_final: 0.8427 (tp) REVERT: f2 87 MET cc_start: 0.5461 (ttp) cc_final: 0.5182 (tpt) REVERT: f2 96 LEU cc_start: 0.6150 (tt) cc_final: 0.5649 (mp) REVERT: f2 139 CYS cc_start: 0.4605 (t) cc_final: 0.4392 (m) REVERT: f2 184 SER cc_start: 0.5084 (m) cc_final: 0.4833 (t) REVERT: q2 2 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7047 (ptt180) REVERT: q2 42 ARG cc_start: 0.7828 (tmt170) cc_final: 0.5525 (mtp85) REVERT: h2 59 PHE cc_start: 0.8856 (m-10) cc_final: 0.8529 (m-10) REVERT: i2 16 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7514 (mmm-85) REVERT: i2 17 THR cc_start: 0.9051 (p) cc_final: 0.8517 (t) REVERT: i2 35 PHE cc_start: 0.8762 (t80) cc_final: 0.8469 (t80) REVERT: i2 44 GLU cc_start: 0.7194 (tp30) cc_final: 0.6612 (tm-30) outliers start: 169 outliers final: 108 residues processed: 696 average time/residue: 0.2085 time to fit residues: 235.9305 Evaluate side-chains 664 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 547 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 35 CYS Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 134 ILE Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 211 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 234 CYS Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 307 PHE Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 348 SER Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 366 VAL Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 407 VAL Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 163 LEU Chi-restraints excluded: chain a2 residue 240 ARG Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 92 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 160 LEU Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 225 THR Chi-restraints excluded: chain b1 residue 240 MET Chi-restraints excluded: chain b1 residue 250 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 42 SER Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 24 CYS Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 246 ASP Chi-restraints excluded: chain a3 residue 255 ILE Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 207 ILE Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 133 LEU Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 234 LEU Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 349 ILE Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 80 MET Chi-restraints excluded: chain c2 residue 127 VAL Chi-restraints excluded: chain c2 residue 157 ILE Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 187 THR Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain f2 residue 193 VAL Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain q2 residue 17 SER Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 48 VAL Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain h2 residue 42 GLU Chi-restraints excluded: chain h2 residue 50 THR Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 373 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 204 optimal weight: 0.2980 chunk 168 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 323 HIS ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 26 ASN c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 164 HIS d1 73 GLN a3 173 ASN a4 351 ASN b2 8 HIS ** b2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS q2 23 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.100792 restraints weight = 69219.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103456 restraints weight = 38643.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105282 restraints weight = 25938.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106567 restraints weight = 19634.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107296 restraints weight = 16008.083| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.944 32809 Z= 0.173 Angle : 0.726 18.569 44556 Z= 0.351 Chirality : 0.045 0.264 4837 Planarity : 0.005 0.056 5675 Dihedral : 11.209 149.598 4738 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 4.74 % Allowed : 16.46 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.52 (0.13), residues: 3883 helix: 0.97 (0.11), residues: 2047 sheet: -0.43 (0.27), residues: 362 loop : -2.27 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGf2 32 TYR 0.020 0.001 TYRb2 358 PHE 0.025 0.001 PHEa4 435 TRP 0.015 0.001 TRPa3 443 HIS 0.010 0.001 HISi2 57 Details of bonding type rmsd covalent geometry : bond 0.00397 (32785) covalent geometry : angle 0.71703 (44538) SS BOND : bond 0.00340 ( 6) SS BOND : angle 2.27334 ( 12) hydrogen bonds : bond 0.04934 ( 1778) hydrogen bonds : angle 4.69036 ( 5118) metal coordination : bond 0.00823 ( 8) metal coordination : angle 9.21766 ( 6) Misc. bond : bond 0.34592 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 602 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8704 (tt0) cc_final: 0.8072 (tt0) REVERT: a1 130 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7501 (tp30) REVERT: a1 327 ASP cc_start: 0.8157 (t70) cc_final: 0.7870 (p0) REVERT: a2 90 GLU cc_start: 0.8393 (mp0) cc_final: 0.7882 (mp0) REVERT: a2 163 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8859 (tt) REVERT: a2 240 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7774 (ttt180) REVERT: b1 8 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7299 (t70) REVERT: b1 35 SER cc_start: 0.8875 (p) cc_final: 0.7965 (m) REVERT: b1 96 MET cc_start: 0.7395 (mmm) cc_final: 0.7162 (mtt) REVERT: b1 121 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7200 (m-10) REVERT: b1 228 ASP cc_start: 0.7274 (m-30) cc_final: 0.7040 (m-30) REVERT: b1 243 VAL cc_start: 0.8919 (m) cc_final: 0.8683 (m) REVERT: b1 282 ARG cc_start: 0.9039 (ttp-110) cc_final: 0.8801 (ttp-110) REVERT: b1 328 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8397 (tt) REVERT: c1 55 CYS cc_start: 0.8535 (p) cc_final: 0.8201 (p) REVERT: c1 106 ASN cc_start: 0.6633 (t0) cc_final: 0.6229 (t0) REVERT: c1 109 LEU cc_start: 0.8926 (tp) cc_final: 0.8422 (pt) REVERT: c1 187 THR cc_start: 0.9330 (m) cc_final: 0.9044 (p) REVERT: c1 206 LYS cc_start: 0.8826 (mttt) cc_final: 0.8571 (mtpt) REVERT: c1 207 MET cc_start: 0.8166 (ttm) cc_final: 0.7680 (ttp) REVERT: c1 210 MET cc_start: 0.7681 (mmp) cc_final: 0.7409 (mmm) REVERT: c1 211 MET cc_start: 0.7358 (mmt) cc_final: 0.6784 (tmm) REVERT: c1 224 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.8020 (t-90) REVERT: f1 104 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7442 (pttt) REVERT: d1 34 ASP cc_start: 0.8406 (p0) cc_final: 0.8015 (p0) REVERT: d1 47 ILE cc_start: 0.9476 (mm) cc_final: 0.9272 (tp) REVERT: d1 105 GLU cc_start: 0.7032 (pt0) cc_final: 0.6633 (pt0) REVERT: q1 3 GLN cc_start: 0.8655 (pm20) cc_final: 0.8244 (pm20) REVERT: q1 17 SER cc_start: 0.8918 (t) cc_final: 0.8434 (p) REVERT: q1 47 ARG cc_start: 0.8540 (mtt180) cc_final: 0.7227 (mmt180) REVERT: q1 67 GLU cc_start: 0.6776 (mm-30) cc_final: 0.5877 (mm-30) REVERT: h1 42 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: a3 82 MET cc_start: 0.7824 (mtt) cc_final: 0.7409 (mtt) REVERT: a3 245 GLU cc_start: 0.7611 (tp30) cc_final: 0.7329 (tm-30) REVERT: a3 369 LEU cc_start: 0.8594 (mt) cc_final: 0.8203 (tt) REVERT: a3 375 VAL cc_start: 0.8990 (m) cc_final: 0.8690 (p) REVERT: a3 438 ARG cc_start: 0.8639 (tpt-90) cc_final: 0.8368 (tpp80) REVERT: a3 441 MET cc_start: 0.8156 (tpp) cc_final: 0.7873 (tpp) REVERT: a4 68 LEU cc_start: 0.9375 (tp) cc_final: 0.8997 (tp) REVERT: a4 158 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7508 (t-90) REVERT: a4 308 ASP cc_start: 0.8127 (t0) cc_final: 0.7525 (m-30) REVERT: a4 351 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7268 (p0) REVERT: b2 20 ASP cc_start: 0.7787 (m-30) cc_final: 0.7556 (p0) REVERT: b2 43 LEU cc_start: 0.8795 (tt) cc_final: 0.8198 (mt) REVERT: b2 44 GLN cc_start: 0.8859 (mm110) cc_final: 0.8534 (mm110) REVERT: b2 91 PHE cc_start: 0.8349 (m-80) cc_final: 0.8031 (m-80) REVERT: b2 129 MET cc_start: 0.8671 (mtm) cc_final: 0.8378 (mtp) REVERT: b2 200 LEU cc_start: 0.9338 (tp) cc_final: 0.9126 (tt) REVERT: b2 263 ASN cc_start: 0.8137 (t0) cc_final: 0.7788 (t0) REVERT: b2 282 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7898 (ptt180) REVERT: b2 313 ARG cc_start: 0.8195 (ptm160) cc_final: 0.7869 (ttp80) REVERT: b2 316 MET cc_start: 0.8835 (tpp) cc_final: 0.8404 (mmt) REVERT: c2 6 HIS cc_start: 0.8223 (t-90) cc_final: 0.7689 (m-70) REVERT: c2 114 SER cc_start: 0.9270 (m) cc_final: 0.8935 (t) REVERT: c2 180 GLN cc_start: 0.7812 (tm130) cc_final: 0.7562 (tm-30) REVERT: c2 215 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8712 (tp) REVERT: f2 69 LEU cc_start: 0.8869 (mm) cc_final: 0.8389 (tp) REVERT: f2 87 MET cc_start: 0.5339 (ttp) cc_final: 0.5137 (tpt) REVERT: f2 96 LEU cc_start: 0.6057 (tt) cc_final: 0.5493 (mp) REVERT: f2 153 PHE cc_start: 0.3949 (m-80) cc_final: 0.3366 (m-80) REVERT: f2 184 SER cc_start: 0.5058 (m) cc_final: 0.4830 (t) REVERT: d2 45 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6953 (tt0) REVERT: q2 2 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7085 (ptt180) REVERT: q2 42 ARG cc_start: 0.7856 (tmt170) cc_final: 0.5636 (mtp85) REVERT: h2 59 PHE cc_start: 0.8806 (m-10) cc_final: 0.8429 (m-10) REVERT: h2 66 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7741 (t0) REVERT: h2 73 LEU cc_start: 0.8642 (tt) cc_final: 0.8409 (tp) REVERT: i2 8 ARG cc_start: 0.8680 (ptt-90) cc_final: 0.8172 (ptp-170) REVERT: i2 16 ARG cc_start: 0.7896 (mmm160) cc_final: 0.7509 (mmm-85) REVERT: i2 17 THR cc_start: 0.9051 (p) cc_final: 0.8489 (t) REVERT: i2 35 PHE cc_start: 0.8718 (t80) cc_final: 0.8416 (t80) outliers start: 158 outliers final: 106 residues processed: 697 average time/residue: 0.2035 time to fit residues: 231.7179 Evaluate side-chains 675 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 557 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 35 CYS Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 134 ILE Chi-restraints excluded: chain a1 residue 167 VAL Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 407 VAL Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 163 LEU Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 240 ARG Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 41 LEU Chi-restraints excluded: chain b1 residue 45 ILE Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 160 LEU Chi-restraints excluded: chain b1 residue 184 ILE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 240 MET Chi-restraints excluded: chain b1 residue 292 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 353 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 42 SER Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 24 CYS Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 255 ILE Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 207 ILE Chi-restraints excluded: chain a4 residue 351 ASN Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 126 THR Chi-restraints excluded: chain b2 residue 133 LEU Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 234 LEU Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 349 ILE Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 121 HIS Chi-restraints excluded: chain c2 residue 157 ILE Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 187 THR Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain c2 residue 215 LEU Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain f2 residue 58 PHE Chi-restraints excluded: chain f2 residue 147 ILE Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 70 MET Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 48 VAL Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 42 GLU Chi-restraints excluded: chain h2 residue 50 THR Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 66 ASP Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 105 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 366 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 313 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 0.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.1766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 323 HIS a2 305 GLN b1 26 ASN c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 57 GLN a3 61 HIS a4 351 ASN b2 8 HIS ** b2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 201 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.119964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101293 restraints weight = 69060.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104053 restraints weight = 37993.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105938 restraints weight = 25270.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107209 restraints weight = 19016.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108096 restraints weight = 15529.946| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.897 32809 Z= 0.158 Angle : 0.721 25.642 44556 Z= 0.345 Chirality : 0.044 0.276 4837 Planarity : 0.005 0.064 5675 Dihedral : 10.996 152.082 4738 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.72 % Rotamer: Outliers : 4.77 % Allowed : 17.39 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.30 (0.14), residues: 3883 helix: 1.13 (0.11), residues: 2043 sheet: -0.23 (0.27), residues: 366 loop : -2.16 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGd2 101 TYR 0.019 0.001 TYRb2 358 PHE 0.025 0.001 PHEa4 435 TRP 0.014 0.001 TRPb2 141 HIS 0.024 0.001 HISc2 121 Details of bonding type rmsd covalent geometry : bond 0.00362 (32785) covalent geometry : angle 0.70318 (44538) SS BOND : bond 0.00404 ( 6) SS BOND : angle 2.31845 ( 12) hydrogen bonds : bond 0.04766 ( 1778) hydrogen bonds : angle 4.60487 ( 5118) metal coordination : bond 0.01513 ( 8) metal coordination : angle 13.21667 ( 6) Misc. bond : bond 0.33139 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 600 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8748 (tt0) cc_final: 0.8097 (tt0) REVERT: a1 130 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7459 (tp30) REVERT: a1 327 ASP cc_start: 0.8135 (t70) cc_final: 0.7868 (p0) REVERT: a1 415 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8735 (m-10) REVERT: a2 38 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8286 (tt) REVERT: a2 90 GLU cc_start: 0.8595 (mp0) cc_final: 0.8140 (mp0) REVERT: b1 8 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7263 (t70) REVERT: b1 35 SER cc_start: 0.8883 (p) cc_final: 0.7832 (m) REVERT: b1 121 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: b1 228 ASP cc_start: 0.7308 (m-30) cc_final: 0.6945 (m-30) REVERT: b1 243 VAL cc_start: 0.8966 (m) cc_final: 0.8652 (m) REVERT: b1 254 ASP cc_start: 0.8115 (p0) cc_final: 0.7888 (p0) REVERT: c1 55 CYS cc_start: 0.8549 (p) cc_final: 0.8223 (p) REVERT: c1 106 ASN cc_start: 0.6604 (t0) cc_final: 0.6218 (t0) REVERT: c1 109 LEU cc_start: 0.8969 (tp) cc_final: 0.8470 (pt) REVERT: c1 187 THR cc_start: 0.9326 (m) cc_final: 0.9027 (p) REVERT: c1 206 LYS cc_start: 0.8882 (mttt) cc_final: 0.8605 (mtpt) REVERT: c1 210 MET cc_start: 0.7849 (mmp) cc_final: 0.7629 (mmm) REVERT: c1 211 MET cc_start: 0.7336 (mmt) cc_final: 0.6812 (tmm) REVERT: c1 224 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8125 (t-90) REVERT: f1 17 GLU cc_start: 0.7955 (mp0) cc_final: 0.7264 (tm-30) REVERT: f1 87 MET cc_start: 0.4500 (tpp) cc_final: 0.4289 (tpt) REVERT: f1 104 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7439 (pttt) REVERT: f1 135 LEU cc_start: 0.5772 (mt) cc_final: 0.5516 (tp) REVERT: f1 171 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6864 (tt) REVERT: d1 34 ASP cc_start: 0.8392 (p0) cc_final: 0.8008 (p0) REVERT: d1 47 ILE cc_start: 0.9468 (mm) cc_final: 0.9263 (tp) REVERT: d1 105 GLU cc_start: 0.7103 (pt0) cc_final: 0.6717 (pt0) REVERT: q1 3 GLN cc_start: 0.8633 (pm20) cc_final: 0.8208 (pm20) REVERT: q1 47 ARG cc_start: 0.8567 (mtt180) cc_final: 0.7254 (mmt180) REVERT: h1 38 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: h1 42 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: a3 19 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7995 (mm) REVERT: a3 82 MET cc_start: 0.7805 (mtt) cc_final: 0.7407 (mtt) REVERT: a3 93 GLU cc_start: 0.7234 (tt0) cc_final: 0.6799 (tt0) REVERT: a3 245 GLU cc_start: 0.7574 (tp30) cc_final: 0.7325 (tm-30) REVERT: a3 369 LEU cc_start: 0.8554 (mt) cc_final: 0.8148 (tt) REVERT: a3 375 VAL cc_start: 0.8952 (m) cc_final: 0.8676 (p) REVERT: a3 438 ARG cc_start: 0.8723 (tpt-90) cc_final: 0.8477 (tpp80) REVERT: a3 441 MET cc_start: 0.8449 (tpp) cc_final: 0.8134 (tpp) REVERT: a4 68 LEU cc_start: 0.9364 (tp) cc_final: 0.8970 (tp) REVERT: a4 153 GLN cc_start: 0.7849 (pm20) cc_final: 0.7608 (mt0) REVERT: a4 158 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7710 (t-90) REVERT: a4 308 ASP cc_start: 0.8100 (t0) cc_final: 0.7609 (m-30) REVERT: b2 20 ASP cc_start: 0.7797 (m-30) cc_final: 0.7581 (p0) REVERT: b2 43 LEU cc_start: 0.8799 (tt) cc_final: 0.8184 (mt) REVERT: b2 44 GLN cc_start: 0.8870 (mm110) cc_final: 0.8527 (mm110) REVERT: b2 91 PHE cc_start: 0.8363 (m-80) cc_final: 0.7980 (m-80) REVERT: b2 129 MET cc_start: 0.8659 (mtm) cc_final: 0.8353 (mtp) REVERT: b2 200 LEU cc_start: 0.9305 (tp) cc_final: 0.9064 (tt) REVERT: b2 230 LEU cc_start: 0.9064 (tp) cc_final: 0.8733 (tp) REVERT: b2 263 ASN cc_start: 0.8142 (t0) cc_final: 0.7767 (t0) REVERT: b2 287 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7977 (pttm) REVERT: b2 313 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7743 (ttp80) REVERT: b2 316 MET cc_start: 0.8870 (tpp) cc_final: 0.8542 (tpt) REVERT: b2 341 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8182 (mp10) REVERT: c2 114 SER cc_start: 0.9273 (m) cc_final: 0.8931 (t) REVERT: c2 215 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8667 (tp) REVERT: f2 69 LEU cc_start: 0.8858 (mm) cc_final: 0.8371 (tp) REVERT: f2 96 LEU cc_start: 0.6187 (tt) cc_final: 0.5629 (mp) REVERT: f2 153 PHE cc_start: 0.3920 (m-80) cc_final: 0.3315 (m-80) REVERT: f2 184 SER cc_start: 0.5089 (m) cc_final: 0.4884 (t) REVERT: d2 45 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6949 (tt0) REVERT: q2 2 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7033 (ptt180) REVERT: q2 42 ARG cc_start: 0.7834 (tmt170) cc_final: 0.5649 (mtp85) REVERT: h2 59 PHE cc_start: 0.8801 (m-10) cc_final: 0.8400 (m-10) REVERT: h2 73 LEU cc_start: 0.8652 (tt) cc_final: 0.8384 (tp) REVERT: i2 8 ARG cc_start: 0.8619 (ptt-90) cc_final: 0.8295 (ptp-170) REVERT: i2 16 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7636 (mmm-85) outliers start: 159 outliers final: 111 residues processed: 699 average time/residue: 0.2020 time to fit residues: 231.8392 Evaluate side-chains 682 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 560 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 35 CYS Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 415 PHE Chi-restraints excluded: chain a2 residue 33 LEU Chi-restraints excluded: chain a2 residue 38 LEU Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 137 VAL Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 41 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 146 ILE Chi-restraints excluded: chain b1 residue 160 LEU Chi-restraints excluded: chain b1 residue 184 ILE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 353 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 42 SER Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain f1 residue 171 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain q1 residue 57 LEU Chi-restraints excluded: chain h1 residue 24 CYS Chi-restraints excluded: chain h1 residue 38 GLU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 255 ILE Chi-restraints excluded: chain a3 residue 270 LEU Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 309 THR Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 71 LEU Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 207 ILE Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 133 LEU Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 234 LEU Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 349 ILE Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 157 ILE Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain c2 residue 208 LEU Chi-restraints excluded: chain c2 residue 215 LEU Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain f2 residue 58 PHE Chi-restraints excluded: chain f2 residue 78 LEU Chi-restraints excluded: chain f2 residue 147 ILE Chi-restraints excluded: chain d2 residue 44 LYS Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 48 VAL Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 42 GLU Chi-restraints excluded: chain h2 residue 50 THR Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 162 optimal weight: 9.9990 chunk 361 optimal weight: 0.6980 chunk 351 optimal weight: 6.9990 chunk 171 optimal weight: 0.0020 chunk 176 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 chunk 248 optimal weight: 0.9990 chunk 25 optimal weight: 0.0060 chunk 380 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1 26 ASN ** b1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 141 ASN a3 173 ASN a3 274 ASN b2 8 HIS b2 44 GLN ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.122837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104095 restraints weight = 69119.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106944 restraints weight = 38073.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108887 restraints weight = 25218.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110134 restraints weight = 18898.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111056 restraints weight = 15523.904| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.690 32809 Z= 0.129 Angle : 0.698 23.609 44556 Z= 0.332 Chirality : 0.043 0.227 4837 Planarity : 0.005 0.067 5675 Dihedral : 10.664 152.859 4738 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.84 % Allowed : 18.80 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.07 (0.14), residues: 3883 helix: 1.35 (0.12), residues: 2046 sheet: -0.34 (0.27), residues: 367 loop : -2.05 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGb1 282 TYR 0.032 0.001 TYRb1 278 PHE 0.026 0.001 PHEa4 435 TRP 0.021 0.001 TRPb1 163 HIS 0.011 0.001 HISc2 121 Details of bonding type rmsd covalent geometry : bond 0.00287 (32785) covalent geometry : angle 0.68206 (44538) SS BOND : bond 0.00530 ( 6) SS BOND : angle 2.55052 ( 12) hydrogen bonds : bond 0.04299 ( 1778) hydrogen bonds : angle 4.41964 ( 5118) metal coordination : bond 0.01450 ( 8) metal coordination : angle 12.16432 ( 6) Misc. bond : bond 0.26176 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 623 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: a1 82 MET cc_start: 0.7828 (tpp) cc_final: 0.7535 (tpt) REVERT: a1 130 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7322 (tp30) REVERT: a1 153 LEU cc_start: 0.9247 (tp) cc_final: 0.8907 (tt) REVERT: a1 327 ASP cc_start: 0.8046 (t70) cc_final: 0.7796 (p0) REVERT: a1 415 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8627 (m-10) REVERT: a2 38 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8316 (tt) REVERT: a2 90 GLU cc_start: 0.8621 (mp0) cc_final: 0.8192 (mp0) REVERT: a2 110 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: b1 8 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7185 (t70) REVERT: b1 35 SER cc_start: 0.8649 (p) cc_final: 0.7230 (m) REVERT: b1 36 LEU cc_start: 0.9237 (mm) cc_final: 0.8957 (mt) REVERT: b1 121 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: b1 243 VAL cc_start: 0.8928 (m) cc_final: 0.8616 (m) REVERT: b1 316 MET cc_start: 0.7761 (ttt) cc_final: 0.7487 (ttm) REVERT: b1 344 GLU cc_start: 0.8074 (tp30) cc_final: 0.7873 (tp30) REVERT: b1 365 MET cc_start: 0.6767 (mmm) cc_final: 0.6312 (mmp) REVERT: c1 106 ASN cc_start: 0.6336 (t0) cc_final: 0.6104 (t0) REVERT: c1 109 LEU cc_start: 0.8910 (tp) cc_final: 0.8429 (pt) REVERT: c1 124 GLU cc_start: 0.7709 (pm20) cc_final: 0.7307 (pm20) REVERT: c1 187 THR cc_start: 0.9343 (m) cc_final: 0.9017 (p) REVERT: c1 210 MET cc_start: 0.7819 (mmp) cc_final: 0.7542 (tpt) REVERT: c1 211 MET cc_start: 0.7241 (mmt) cc_final: 0.6795 (tmm) REVERT: c1 224 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8200 (t-90) REVERT: f1 87 MET cc_start: 0.3640 (tpp) cc_final: 0.3337 (tpt) REVERT: f1 104 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7384 (pttt) REVERT: f1 135 LEU cc_start: 0.5702 (mt) cc_final: 0.5461 (mm) REVERT: f1 171 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6982 (tt) REVERT: d1 34 ASP cc_start: 0.8436 (p0) cc_final: 0.8049 (p0) REVERT: d1 79 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7280 (tp40) REVERT: d1 105 GLU cc_start: 0.7074 (pt0) cc_final: 0.6644 (pt0) REVERT: q1 3 GLN cc_start: 0.8587 (pm20) cc_final: 0.8213 (pm20) REVERT: q1 17 SER cc_start: 0.8878 (t) cc_final: 0.8670 (p) REVERT: q1 47 ARG cc_start: 0.8519 (mtt180) cc_final: 0.7285 (mmt180) REVERT: h1 18 THR cc_start: 0.7811 (m) cc_final: 0.7549 (m) REVERT: h1 38 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: h1 42 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: a3 19 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7986 (mm) REVERT: a3 82 MET cc_start: 0.7811 (mtt) cc_final: 0.7450 (mtt) REVERT: a3 93 GLU cc_start: 0.7085 (tt0) cc_final: 0.6669 (tt0) REVERT: a3 113 LEU cc_start: 0.8843 (tp) cc_final: 0.8415 (tt) REVERT: a3 185 TYR cc_start: 0.8547 (t80) cc_final: 0.7951 (t80) REVERT: a3 245 GLU cc_start: 0.7382 (tp30) cc_final: 0.7146 (tm-30) REVERT: a3 255 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8697 (mt) REVERT: a3 369 LEU cc_start: 0.8370 (mt) cc_final: 0.8054 (tt) REVERT: a3 375 VAL cc_start: 0.8907 (m) cc_final: 0.8675 (p) REVERT: a3 441 MET cc_start: 0.8391 (tpp) cc_final: 0.7898 (tpp) REVERT: a4 68 LEU cc_start: 0.9292 (tp) cc_final: 0.8904 (tp) REVERT: a4 158 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7709 (t-90) REVERT: a4 308 ASP cc_start: 0.8029 (t0) cc_final: 0.7607 (m-30) REVERT: a4 324 PHE cc_start: 0.8330 (p90) cc_final: 0.7848 (p90) REVERT: b2 36 LEU cc_start: 0.8470 (mt) cc_final: 0.8163 (mt) REVERT: b2 43 LEU cc_start: 0.8764 (tt) cc_final: 0.8146 (mt) REVERT: b2 44 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8450 (mm110) REVERT: b2 91 PHE cc_start: 0.8332 (m-80) cc_final: 0.7972 (m-80) REVERT: b2 129 MET cc_start: 0.8607 (mtm) cc_final: 0.8289 (mtp) REVERT: b2 263 ASN cc_start: 0.8110 (t0) cc_final: 0.7696 (t0) REVERT: b2 287 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7880 (tttt) REVERT: b2 313 ARG cc_start: 0.8122 (ptm160) cc_final: 0.7824 (ttp80) REVERT: b2 316 MET cc_start: 0.8795 (tpp) cc_final: 0.8480 (tpt) REVERT: b2 341 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7899 (mp10) REVERT: c2 114 SER cc_start: 0.9237 (m) cc_final: 0.8965 (t) REVERT: f2 69 LEU cc_start: 0.8421 (mm) cc_final: 0.7999 (tp) REVERT: f2 96 LEU cc_start: 0.5903 (tt) cc_final: 0.5436 (mp) REVERT: f2 153 PHE cc_start: 0.3799 (m-80) cc_final: 0.3269 (m-80) REVERT: d2 45 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6654 (tt0) REVERT: q2 2 ARG cc_start: 0.7768 (mtp85) cc_final: 0.6927 (ptt180) REVERT: q2 23 GLN cc_start: 0.7689 (pt0) cc_final: 0.7353 (pt0) REVERT: q2 42 ARG cc_start: 0.7619 (tmt170) cc_final: 0.5458 (mtp85) REVERT: h2 59 PHE cc_start: 0.8695 (m-10) cc_final: 0.8288 (m-10) REVERT: h2 73 LEU cc_start: 0.8579 (tt) cc_final: 0.8158 (tp) REVERT: i2 8 ARG cc_start: 0.8595 (ptt-90) cc_final: 0.8276 (ptp-170) REVERT: i2 16 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7604 (mmm-85) outliers start: 128 outliers final: 85 residues processed: 707 average time/residue: 0.1971 time to fit residues: 227.4447 Evaluate side-chains 648 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 550 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 60 GLU Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 415 PHE Chi-restraints excluded: chain a2 residue 33 LEU Chi-restraints excluded: chain a2 residue 38 LEU Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 41 LEU Chi-restraints excluded: chain b1 residue 45 ILE Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 146 ILE Chi-restraints excluded: chain b1 residue 184 ILE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 56 SER Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain f1 residue 171 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 57 LEU Chi-restraints excluded: chain h1 residue 38 GLU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 13 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 120 CYS Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 255 ILE Chi-restraints excluded: chain a3 residue 270 LEU Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 309 THR Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 160 ILE Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 207 ILE Chi-restraints excluded: chain b2 residue 2 ILE Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 58 PHE Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 34 ILE Chi-restraints excluded: chain q2 residue 48 VAL Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 41 ASP Chi-restraints excluded: chain h2 residue 42 GLU Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 370 optimal weight: 0.9990 chunk 352 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 323 HIS b1 26 ASN c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 173 ASN a4 153 GLN b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 137 GLN b2 201 HIS c2 121 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.103122 restraints weight = 69075.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105918 restraints weight = 38120.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107832 restraints weight = 25327.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109056 restraints weight = 19055.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109832 restraints weight = 15649.676| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.764 32809 Z= 0.146 Angle : 0.715 23.695 44556 Z= 0.342 Chirality : 0.044 0.287 4837 Planarity : 0.005 0.085 5675 Dihedral : 10.526 152.866 4738 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.63 % Allowed : 20.12 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.01 (0.14), residues: 3883 helix: 1.40 (0.12), residues: 2042 sheet: -0.19 (0.27), residues: 369 loop : -2.00 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGd2 101 TYR 0.019 0.001 TYRb1 278 PHE 0.043 0.001 PHEb1 276 TRP 0.022 0.001 TRPb2 272 HIS 0.010 0.001 HISc2 121 Details of bonding type rmsd covalent geometry : bond 0.00338 (32785) covalent geometry : angle 0.70011 (44538) SS BOND : bond 0.00491 ( 6) SS BOND : angle 3.23504 ( 12) hydrogen bonds : bond 0.04425 ( 1778) hydrogen bonds : angle 4.42960 ( 5118) metal coordination : bond 0.01240 ( 8) metal coordination : angle 11.89519 ( 6) Misc. bond : bond 0.28305 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 573 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: a1 82 MET cc_start: 0.7777 (tpp) cc_final: 0.7518 (tpt) REVERT: a1 130 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7355 (tp30) REVERT: a1 320 LEU cc_start: 0.9147 (tp) cc_final: 0.8928 (tp) REVERT: a1 415 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8741 (m-10) REVERT: a2 38 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8272 (tt) REVERT: a2 90 GLU cc_start: 0.8638 (mp0) cc_final: 0.8266 (mp0) REVERT: b1 8 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7245 (t70) REVERT: b1 36 LEU cc_start: 0.9285 (mm) cc_final: 0.9023 (mt) REVERT: b1 121 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: b1 243 VAL cc_start: 0.8932 (m) cc_final: 0.8623 (m) REVERT: b1 316 MET cc_start: 0.7818 (ttt) cc_final: 0.7560 (ttm) REVERT: b1 363 LEU cc_start: 0.8002 (mm) cc_final: 0.7759 (mp) REVERT: b1 365 MET cc_start: 0.7085 (mmm) cc_final: 0.6879 (mmm) REVERT: c1 109 LEU cc_start: 0.8935 (tp) cc_final: 0.8444 (pt) REVERT: c1 117 VAL cc_start: 0.9072 (t) cc_final: 0.8865 (t) REVERT: c1 124 GLU cc_start: 0.7778 (pm20) cc_final: 0.7383 (pm20) REVERT: c1 187 THR cc_start: 0.9337 (m) cc_final: 0.9056 (p) REVERT: c1 211 MET cc_start: 0.7256 (mmt) cc_final: 0.6767 (tmm) REVERT: c1 224 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8317 (t-90) REVERT: f1 104 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7426 (pttt) REVERT: f1 135 LEU cc_start: 0.5382 (mt) cc_final: 0.5165 (mm) REVERT: f1 171 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6967 (tt) REVERT: d1 34 ASP cc_start: 0.8477 (p0) cc_final: 0.8077 (p0) REVERT: d1 105 GLU cc_start: 0.7121 (pt0) cc_final: 0.6853 (pt0) REVERT: q1 3 GLN cc_start: 0.8644 (pm20) cc_final: 0.8221 (pm20) REVERT: q1 17 SER cc_start: 0.8897 (t) cc_final: 0.8642 (p) REVERT: q1 47 ARG cc_start: 0.8551 (mtt180) cc_final: 0.7308 (mmt180) REVERT: h1 38 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: h1 42 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7709 (tp30) REVERT: a3 82 MET cc_start: 0.7840 (mtt) cc_final: 0.7469 (mtt) REVERT: a3 93 GLU cc_start: 0.7198 (tt0) cc_final: 0.6725 (tt0) REVERT: a3 185 TYR cc_start: 0.8572 (t80) cc_final: 0.7913 (t80) REVERT: a3 245 GLU cc_start: 0.7340 (tp30) cc_final: 0.7083 (tm-30) REVERT: a3 274 ASN cc_start: 0.7650 (m110) cc_final: 0.7384 (m-40) REVERT: a3 369 LEU cc_start: 0.8382 (mt) cc_final: 0.8018 (tt) REVERT: a3 375 VAL cc_start: 0.8961 (m) cc_final: 0.8714 (p) REVERT: a3 441 MET cc_start: 0.8603 (tpp) cc_final: 0.8137 (tpp) REVERT: a4 68 LEU cc_start: 0.9317 (tp) cc_final: 0.8922 (tp) REVERT: a4 368 TYR cc_start: 0.7675 (t80) cc_final: 0.7321 (t80) REVERT: b2 20 ASP cc_start: 0.7793 (m-30) cc_final: 0.7543 (p0) REVERT: b2 43 LEU cc_start: 0.8817 (tt) cc_final: 0.8167 (mt) REVERT: b2 44 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8632 (mm110) REVERT: b2 91 PHE cc_start: 0.8429 (m-80) cc_final: 0.8071 (m-80) REVERT: b2 111 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7223 (mm-30) REVERT: b2 129 MET cc_start: 0.8614 (mtm) cc_final: 0.8318 (mtp) REVERT: b2 263 ASN cc_start: 0.8110 (t0) cc_final: 0.7736 (t0) REVERT: b2 287 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7838 (tttt) REVERT: b2 313 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7750 (ttp80) REVERT: b2 316 MET cc_start: 0.8779 (tpp) cc_final: 0.8484 (mmt) REVERT: b2 344 GLU cc_start: 0.5695 (pm20) cc_final: 0.4799 (mp0) REVERT: c2 114 SER cc_start: 0.9240 (m) cc_final: 0.8870 (t) REVERT: f2 69 LEU cc_start: 0.8784 (mm) cc_final: 0.8279 (tp) REVERT: f2 96 LEU cc_start: 0.5927 (tt) cc_final: 0.5474 (mp) REVERT: f2 153 PHE cc_start: 0.3904 (m-80) cc_final: 0.3375 (m-80) REVERT: d2 45 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6680 (tt0) REVERT: q2 2 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7036 (ptt180) REVERT: q2 9 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7384 (mtp85) REVERT: q2 23 GLN cc_start: 0.7720 (pt0) cc_final: 0.7344 (pt0) REVERT: q2 42 ARG cc_start: 0.7664 (tmt170) cc_final: 0.5580 (mtp85) REVERT: q2 65 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6690 (tm-30) REVERT: h2 52 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: h2 55 THR cc_start: 0.6890 (m) cc_final: 0.6357 (p) REVERT: h2 59 PHE cc_start: 0.8599 (m-10) cc_final: 0.8327 (m-10) REVERT: h2 73 LEU cc_start: 0.8515 (tt) cc_final: 0.8210 (tp) REVERT: i2 8 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.8312 (ptp-170) outliers start: 121 outliers final: 96 residues processed: 646 average time/residue: 0.1954 time to fit residues: 207.8164 Evaluate side-chains 655 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 548 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 35 CYS Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 60 GLU Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 378 ASP Chi-restraints excluded: chain a1 residue 415 PHE Chi-restraints excluded: chain a2 residue 33 LEU Chi-restraints excluded: chain a2 residue 38 LEU Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 137 VAL Chi-restraints excluded: chain a2 residue 152 PHE Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 276 GLN Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 41 LEU Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 146 ILE Chi-restraints excluded: chain b1 residue 184 ILE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 235 LEU Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 240 MET Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 207 MET Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain c1 residue 226 TRP Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain f1 residue 171 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 38 GLU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 13 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 173 ASN Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 255 ILE Chi-restraints excluded: chain a3 residue 270 LEU Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 309 THR Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain b2 residue 2 ILE Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 111 GLU Chi-restraints excluded: chain b2 residue 133 LEU Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 121 HIS Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 58 PHE Chi-restraints excluded: chain f2 residue 78 LEU Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 34 ILE Chi-restraints excluded: chain q2 residue 38 LEU Chi-restraints excluded: chain q2 residue 48 VAL Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 42 GLU Chi-restraints excluded: chain h2 residue 52 GLU Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 64 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 351 optimal weight: 0.1980 chunk 272 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 377 optimal weight: 1.9990 chunk 354 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 323 HIS ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 312 GLN c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 173 ASN b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS ** q2 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100965 restraints weight = 69365.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103748 restraints weight = 38471.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105608 restraints weight = 25663.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106893 restraints weight = 19296.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107636 restraints weight = 15819.587| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.903 32809 Z= 0.192 Angle : 0.757 25.086 44556 Z= 0.362 Chirality : 0.045 0.284 4837 Planarity : 0.005 0.100 5675 Dihedral : 10.575 152.999 4738 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.90 % Allowed : 20.18 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.01 (0.14), residues: 3883 helix: 1.36 (0.11), residues: 2042 sheet: -0.17 (0.27), residues: 367 loop : -1.98 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGh2 43 TYR 0.033 0.002 TYRb2 273 PHE 0.039 0.002 PHEb1 276 TRP 0.020 0.001 TRPb2 272 HIS 0.025 0.001 HISc2 121 Details of bonding type rmsd covalent geometry : bond 0.00453 (32785) covalent geometry : angle 0.74196 (44538) SS BOND : bond 0.00596 ( 6) SS BOND : angle 3.32444 ( 12) hydrogen bonds : bond 0.04705 ( 1778) hydrogen bonds : angle 4.50562 ( 5118) metal coordination : bond 0.00947 ( 8) metal coordination : angle 11.97376 ( 6) Misc. bond : bond 0.32592 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 553 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: a1 82 MET cc_start: 0.7836 (tpp) cc_final: 0.7590 (tpt) REVERT: a1 130 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7380 (tp30) REVERT: a1 320 LEU cc_start: 0.9213 (tp) cc_final: 0.8942 (tp) REVERT: a1 329 MET cc_start: 0.8693 (mmm) cc_final: 0.8172 (tpp) REVERT: a1 415 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8784 (m-10) REVERT: b1 8 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7201 (t70) REVERT: b1 121 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: b1 243 VAL cc_start: 0.8977 (m) cc_final: 0.8693 (m) REVERT: b1 282 ARG cc_start: 0.8945 (ttp-110) cc_final: 0.8726 (ttp-110) REVERT: b1 316 MET cc_start: 0.7977 (ttt) cc_final: 0.7699 (ttm) REVERT: b1 363 LEU cc_start: 0.7964 (mm) cc_final: 0.7629 (mm) REVERT: b1 365 MET cc_start: 0.7146 (mmm) cc_final: 0.6894 (mmm) REVERT: c1 109 LEU cc_start: 0.8994 (tp) cc_final: 0.8473 (pt) REVERT: c1 124 GLU cc_start: 0.7830 (pm20) cc_final: 0.7424 (pm20) REVERT: c1 187 THR cc_start: 0.9364 (m) cc_final: 0.9073 (p) REVERT: c1 211 MET cc_start: 0.7393 (mmt) cc_final: 0.6928 (tmm) REVERT: c1 224 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8317 (t-90) REVERT: f1 104 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7401 (pttt) REVERT: f1 135 LEU cc_start: 0.5484 (mt) cc_final: 0.5225 (mm) REVERT: f1 171 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6987 (tt) REVERT: d1 34 ASP cc_start: 0.8430 (p0) cc_final: 0.8191 (p0) REVERT: d1 105 GLU cc_start: 0.7196 (pt0) cc_final: 0.6759 (pt0) REVERT: q1 3 GLN cc_start: 0.8549 (pm20) cc_final: 0.8189 (pm20) REVERT: q1 47 ARG cc_start: 0.8530 (mtt180) cc_final: 0.7315 (mmt180) REVERT: h1 38 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: h1 42 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: i1 37 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: a3 50 GLU cc_start: 0.7655 (tp30) cc_final: 0.7427 (tp30) REVERT: a3 82 MET cc_start: 0.7883 (mtt) cc_final: 0.7499 (mtt) REVERT: a3 185 TYR cc_start: 0.8648 (t80) cc_final: 0.7951 (t80) REVERT: a3 245 GLU cc_start: 0.7657 (tp30) cc_final: 0.7273 (tm-30) REVERT: a3 274 ASN cc_start: 0.7724 (m110) cc_final: 0.7459 (m-40) REVERT: a3 369 LEU cc_start: 0.8469 (mt) cc_final: 0.7975 (tt) REVERT: a3 375 VAL cc_start: 0.8969 (m) cc_final: 0.8663 (p) REVERT: a3 441 MET cc_start: 0.8714 (tpp) cc_final: 0.8260 (tpp) REVERT: a4 68 LEU cc_start: 0.9389 (tp) cc_final: 0.8971 (tp) REVERT: b2 20 ASP cc_start: 0.7844 (m-30) cc_final: 0.7608 (p0) REVERT: b2 43 LEU cc_start: 0.8846 (tt) cc_final: 0.8220 (mt) REVERT: b2 44 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8759 (mm110) REVERT: b2 111 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: b2 129 MET cc_start: 0.8665 (mtm) cc_final: 0.8365 (mtp) REVERT: b2 230 LEU cc_start: 0.9137 (tp) cc_final: 0.8864 (tp) REVERT: b2 240 MET cc_start: 0.8219 (mmp) cc_final: 0.7938 (mmt) REVERT: b2 252 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7702 (p0) REVERT: b2 263 ASN cc_start: 0.8111 (t0) cc_final: 0.7747 (t0) REVERT: b2 287 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7864 (tttt) REVERT: b2 313 ARG cc_start: 0.8189 (ptm160) cc_final: 0.7699 (ttp80) REVERT: b2 316 MET cc_start: 0.8827 (tpp) cc_final: 0.8345 (mmt) REVERT: b2 341 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8103 (mp10) REVERT: b2 344 GLU cc_start: 0.5728 (pm20) cc_final: 0.4918 (mp0) REVERT: c2 114 SER cc_start: 0.9273 (m) cc_final: 0.8955 (t) REVERT: f2 69 LEU cc_start: 0.8798 (mm) cc_final: 0.8299 (tp) REVERT: f2 96 LEU cc_start: 0.6066 (tt) cc_final: 0.5608 (mp) REVERT: f2 153 PHE cc_start: 0.4236 (m-80) cc_final: 0.3443 (m-80) REVERT: d2 45 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6720 (tt0) REVERT: q2 2 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7015 (ptt180) REVERT: q2 9 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7226 (mtp85) REVERT: q2 23 GLN cc_start: 0.7793 (pt0) cc_final: 0.7389 (pt0) REVERT: q2 42 ARG cc_start: 0.7732 (tmt170) cc_final: 0.5598 (mtp85) REVERT: q2 65 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6882 (tm-30) REVERT: h2 55 THR cc_start: 0.7130 (m) cc_final: 0.6470 (p) REVERT: h2 59 PHE cc_start: 0.8701 (m-10) cc_final: 0.8472 (m-10) REVERT: i2 8 ARG cc_start: 0.8715 (ptt-90) cc_final: 0.8142 (ptp-170) outliers start: 130 outliers final: 99 residues processed: 634 average time/residue: 0.2018 time to fit residues: 210.1810 Evaluate side-chains 642 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 532 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 35 CYS Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 60 GLU Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 378 ASP Chi-restraints excluded: chain a1 residue 415 PHE Chi-restraints excluded: chain a2 residue 33 LEU Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 137 VAL Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 276 GLN Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 41 LEU Chi-restraints excluded: chain b1 residue 45 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 146 ILE Chi-restraints excluded: chain b1 residue 184 ILE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 235 LEU Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 240 MET Chi-restraints excluded: chain b1 residue 269 LYS Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 207 MET Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain c1 residue 226 TRP Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain f1 residue 171 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 38 GLU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 37 GLN Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 173 ASN Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 255 ILE Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 309 THR Chi-restraints excluded: chain a3 residue 320 LEU Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 71 LEU Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain b2 residue 2 ILE Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 111 GLU Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 252 ASP Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 187 THR Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 58 PHE Chi-restraints excluded: chain f2 residue 78 LEU Chi-restraints excluded: chain f2 residue 147 ILE Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 34 ILE Chi-restraints excluded: chain q2 residue 48 VAL Chi-restraints excluded: chain q2 residue 73 ASN Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 138 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 0.0470 chunk 29 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 323 HIS b1 312 GLN c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 173 ASN b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 201 HIS c2 121 HIS q2 6 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103729 restraints weight = 69207.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106453 restraints weight = 38891.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108308 restraints weight = 26126.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109425 restraints weight = 19700.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110409 restraints weight = 16334.744| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.751 32809 Z= 0.142 Angle : 0.732 23.882 44556 Z= 0.348 Chirality : 0.043 0.294 4837 Planarity : 0.005 0.076 5675 Dihedral : 10.382 152.858 4738 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.30 % Allowed : 20.93 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.14 (0.14), residues: 3883 helix: 1.46 (0.11), residues: 2044 sheet: -0.14 (0.27), residues: 369 loop : -1.90 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGh2 43 TYR 0.019 0.001 TYRc1 164 PHE 0.024 0.001 PHEa4 435 TRP 0.017 0.001 TRPb1 163 HIS 0.011 0.001 HISc2 121 Details of bonding type rmsd covalent geometry : bond 0.00326 (32785) covalent geometry : angle 0.71865 (44538) SS BOND : bond 0.00435 ( 6) SS BOND : angle 2.61065 ( 12) hydrogen bonds : bond 0.04381 ( 1778) hydrogen bonds : angle 4.39504 ( 5118) metal coordination : bond 0.01009 ( 8) metal coordination : angle 11.48974 ( 6) Misc. bond : bond 0.27884 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 568 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a1 60 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: a1 82 MET cc_start: 0.7739 (tpp) cc_final: 0.7513 (tpt) REVERT: a1 130 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7336 (tp30) REVERT: a1 153 LEU cc_start: 0.9336 (tp) cc_final: 0.9026 (tt) REVERT: a1 320 LEU cc_start: 0.9207 (tp) cc_final: 0.8893 (tp) REVERT: a1 329 MET cc_start: 0.8712 (mmm) cc_final: 0.8201 (tpp) REVERT: a1 415 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8728 (m-10) REVERT: b1 8 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7241 (t70) REVERT: b1 121 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7304 (m-10) REVERT: b1 243 VAL cc_start: 0.8926 (m) cc_final: 0.8629 (m) REVERT: b1 316 MET cc_start: 0.7820 (ttt) cc_final: 0.7570 (ttm) REVERT: b1 363 LEU cc_start: 0.7850 (mm) cc_final: 0.7578 (mp) REVERT: b1 365 MET cc_start: 0.6777 (mmm) cc_final: 0.6372 (mmp) REVERT: c1 109 LEU cc_start: 0.8979 (tp) cc_final: 0.8480 (pt) REVERT: c1 124 GLU cc_start: 0.7797 (pm20) cc_final: 0.7395 (pm20) REVERT: c1 178 MET cc_start: 0.7243 (mmp) cc_final: 0.6716 (tpp) REVERT: c1 187 THR cc_start: 0.9341 (m) cc_final: 0.9059 (p) REVERT: c1 210 MET cc_start: 0.8010 (tpt) cc_final: 0.7796 (tpt) REVERT: c1 211 MET cc_start: 0.7271 (mmt) cc_final: 0.6858 (tmm) REVERT: c1 224 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.8303 (t-90) REVERT: f1 87 MET cc_start: 0.4607 (tpt) cc_final: 0.3743 (ttt) REVERT: f1 104 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7402 (pttt) REVERT: f1 171 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6946 (tt) REVERT: d1 34 ASP cc_start: 0.8470 (p0) cc_final: 0.8066 (p0) REVERT: q1 3 GLN cc_start: 0.8570 (pm20) cc_final: 0.8250 (pm20) REVERT: q1 22 GLU cc_start: 0.7638 (tp30) cc_final: 0.7362 (tp30) REVERT: q1 47 ARG cc_start: 0.8515 (mtt180) cc_final: 0.7357 (mmt180) REVERT: h1 38 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: h1 42 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: i1 37 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: a3 82 MET cc_start: 0.7841 (mtt) cc_final: 0.7495 (mtt) REVERT: a3 93 GLU cc_start: 0.7087 (tt0) cc_final: 0.6617 (tt0) REVERT: a3 185 TYR cc_start: 0.8611 (t80) cc_final: 0.7897 (t80) REVERT: a3 245 GLU cc_start: 0.7402 (tp30) cc_final: 0.7111 (tm-30) REVERT: a3 255 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8703 (mt) REVERT: a3 274 ASN cc_start: 0.7659 (m110) cc_final: 0.7427 (m-40) REVERT: a3 369 LEU cc_start: 0.8338 (mt) cc_final: 0.7971 (tt) REVERT: a3 375 VAL cc_start: 0.8868 (m) cc_final: 0.8596 (p) REVERT: a3 441 MET cc_start: 0.8696 (tpp) cc_final: 0.8395 (tpt) REVERT: a4 68 LEU cc_start: 0.9348 (tp) cc_final: 0.8928 (tp) REVERT: a4 120 MET cc_start: 0.7129 (mtt) cc_final: 0.6877 (mtm) REVERT: a4 308 ASP cc_start: 0.8083 (t0) cc_final: 0.7791 (m-30) REVERT: a4 368 TYR cc_start: 0.7661 (t80) cc_final: 0.7284 (t80) REVERT: b2 12 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8386 (ttmm) REVERT: b2 43 LEU cc_start: 0.8787 (tt) cc_final: 0.8179 (mt) REVERT: b2 44 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8704 (mm110) REVERT: b2 111 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: b2 129 MET cc_start: 0.8634 (mtm) cc_final: 0.8355 (mtp) REVERT: b2 230 LEU cc_start: 0.9169 (tp) cc_final: 0.8871 (tp) REVERT: b2 240 MET cc_start: 0.8283 (mmp) cc_final: 0.7992 (mmt) REVERT: b2 263 ASN cc_start: 0.8029 (t0) cc_final: 0.7682 (t0) REVERT: b2 287 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7736 (tttt) REVERT: b2 316 MET cc_start: 0.8763 (tpp) cc_final: 0.8457 (mmt) REVERT: b2 341 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8020 (mp10) REVERT: b2 344 GLU cc_start: 0.5598 (pm20) cc_final: 0.4841 (mp0) REVERT: b2 365 MET cc_start: 0.7478 (mmp) cc_final: 0.6607 (mmm) REVERT: c2 114 SER cc_start: 0.9214 (m) cc_final: 0.8895 (t) REVERT: f2 69 LEU cc_start: 0.8385 (mm) cc_final: 0.7884 (tp) REVERT: f2 96 LEU cc_start: 0.6048 (tt) cc_final: 0.5735 (mt) REVERT: f2 153 PHE cc_start: 0.4132 (m-80) cc_final: 0.3310 (m-80) REVERT: d2 45 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6647 (tt0) REVERT: q2 2 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7085 (ptt180) REVERT: q2 23 GLN cc_start: 0.7783 (pt0) cc_final: 0.7422 (pt0) REVERT: q2 42 ARG cc_start: 0.7660 (tmt170) cc_final: 0.5496 (mtp85) REVERT: q2 65 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6702 (tm-30) REVERT: h2 52 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8102 (tm-30) REVERT: h2 55 THR cc_start: 0.7023 (m) cc_final: 0.6138 (p) REVERT: i2 8 ARG cc_start: 0.8686 (ptt-90) cc_final: 0.8088 (ptp-170) outliers start: 110 outliers final: 84 residues processed: 640 average time/residue: 0.2048 time to fit residues: 214.8639 Evaluate side-chains 633 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 538 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 60 GLU Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 112 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 378 ASP Chi-restraints excluded: chain a1 residue 415 PHE Chi-restraints excluded: chain a1 residue 443 TRP Chi-restraints excluded: chain a2 residue 33 LEU Chi-restraints excluded: chain a2 residue 137 VAL Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 276 GLN Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 41 LEU Chi-restraints excluded: chain b1 residue 45 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 146 ILE Chi-restraints excluded: chain b1 residue 184 ILE Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 240 MET Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain c1 residue 226 TRP Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 56 SER Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain f1 residue 171 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 38 GLU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 37 GLN Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 173 ASN Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 255 ILE Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 309 THR Chi-restraints excluded: chain a3 residue 320 LEU Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 71 LEU Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain b2 residue 2 ILE Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 111 GLU Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 121 HIS Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 58 PHE Chi-restraints excluded: chain f2 residue 78 LEU Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain q2 residue 34 ILE Chi-restraints excluded: chain q2 residue 48 VAL Chi-restraints excluded: chain q2 residue 67 GLU Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 373 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 378 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 193 optimal weight: 0.0570 chunk 219 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 377 optimal weight: 0.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 323 HIS c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 173 ASN b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS ** q2 6 HIS ** 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 = 0.3692 r_free = 0.3692 target = 0.122466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104155 restraints weight = 69117.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106916 restraints weight = 38484.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108786 restraints weight = 25729.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109910 restraints weight = 19264.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110907 restraints weight = 15908.645| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.722 32809 Z= 0.140 Angle : 0.729 23.524 44556 Z= 0.348 Chirality : 0.044 0.282 4837 Planarity : 0.005 0.075 5675 Dihedral : 10.293 152.785 4738 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.36 % Allowed : 20.84 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.18 (0.14), residues: 3883 helix: 1.48 (0.11), residues: 2045 sheet: -0.09 (0.28), residues: 369 loop : -1.85 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGh2 36 TYR 0.024 0.001 TYRd2 20 PHE 0.055 0.001 PHEh2 59 TRP 0.028 0.001 TRPb2 272 HIS 0.009 0.001 HISi2 57 Details of bonding type rmsd covalent geometry : bond 0.00320 (32785) covalent geometry : angle 0.71595 (44538) SS BOND : bond 0.00270 ( 6) SS BOND : angle 2.92252 ( 12) hydrogen bonds : bond 0.04349 ( 1778) hydrogen bonds : angle 4.37466 ( 5118) metal coordination : bond 0.01039 ( 8) metal coordination : angle 11.35026 ( 6) Misc. bond : bond 0.27084 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6624.22 seconds wall clock time: 114 minutes 54.20 seconds (6894.20 seconds total)