Starting phenix.real_space_refine on Sat Aug 8 07:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22eu_68220/08_2026/22eu_68220.cif Found real_map, /net/cci-nas-00/data/ceres_data/22eu_68220/08_2026/22eu_68220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22eu_68220/08_2026/22eu_68220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22eu_68220/08_2026/22eu_68220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22eu_68220/08_2026/22eu_68220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22eu_68220/08_2026/22eu_68220.map" } resolution = 2.67 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= 0.004 sd= 0.047 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 Zn 2 6.06 5 P 119 5.49 5 S 83 5.16 5 C 16105 2.51 5 N 4636 2.21 5 O 5222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26167 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2550 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain: "B" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "C" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "D" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "E" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "F" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1730 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 204} Chain: "G" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1730 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 204} Chain: "M" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1511 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 799 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 21, 'rna3p': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20656 SG CYS F 43 62.639 46.606 145.437 1.00176.47 S ATOM 20941 SG CYS F 78 62.171 48.662 145.540 1.00202.31 S ATOM 21029 SG CYS F 90 58.030 48.164 144.294 1.00166.20 S ATOM 22386 SG CYS G 43 64.489 111.296 29.881 1.00128.98 S ATOM 22409 SG CYS G 46 64.373 112.018 33.510 1.00130.75 S ATOM 22424 SG CYS G 48 66.854 109.557 31.924 1.00166.34 S ATOM 22759 SG CYS G 90 63.033 108.649 32.470 1.00109.37 S Time building chain proxies: 6.42, per 1000 atoms: 0.25 Number of scatterers: 26167 At special positions: 0 Unit cell: (132.48, 156.48, 176.64, 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) Zn 2 29.99 S 83 16.00 P 119 15.00 O 5222 8.00 N 4636 7.00 C 16105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 48 " distance=2.78 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 46 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 48 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 90 " Number of angles added : 6 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5618 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 20 sheets defined 55.9% alpha, 12.4% beta 23 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 14 through 23 Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 85 removed outlier: 3.504A pdb=" N ASN A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.544A pdb=" N SER A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 125 No H-bonds generated for 'chain 'A' and resid 124 through 125' Processing helix chain 'A' and resid 126 through 136 removed outlier: 4.803A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.568A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.839A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 287 through 298 removed outlier: 4.181A pdb=" N ILE A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 31 removed outlier: 3.521A pdb=" N ALA B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.588A pdb=" N GLN B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 120 removed outlier: 3.654A pdb=" N ILE B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.606A pdb=" N ARG B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 239 through 257 removed outlier: 3.710A pdb=" N PHE B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 278 removed outlier: 3.750A pdb=" N LEU B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLN B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 304 removed outlier: 3.866A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 327 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 359 through 380 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.503A pdb=" N GLN B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 418 Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.559A pdb=" N LEU B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 436 No H-bonds generated for 'chain 'B' and resid 435 through 436' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 484 through 487 Processing helix chain 'B' and resid 488 through 498 Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 523 through 550 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 13 through 28 Processing helix chain 'C' and resid 33 through 49 Processing helix chain 'C' and resid 99 through 120 removed outlier: 3.652A pdb=" N ILE C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 194 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.578A pdb=" N ASP C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 239 through 256 Processing helix chain 'C' and resid 259 through 279 Processing helix chain 'C' and resid 282 through 308 removed outlier: 3.799A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 359 through 380 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.559A pdb=" N GLN C 408 " --> pdb=" O PRO C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 418 Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 435 through 436 No H-bonds generated for 'chain 'C' and resid 435 through 436' Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 485 through 487 No H-bonds generated for 'chain 'C' and resid 485 through 487' Processing helix chain 'C' and resid 488 through 498 Processing helix chain 'C' and resid 505 through 520 Processing helix chain 'C' and resid 523 through 551 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 13 through 31 Processing helix chain 'D' and resid 34 through 48 removed outlier: 3.844A pdb=" N GLN D 38 " --> pdb=" O ASN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 120 removed outlier: 3.662A pdb=" N ILE D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TRP D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.601A pdb=" N ARG D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.546A pdb=" N ALA D 229 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 258 removed outlier: 3.777A pdb=" N PHE D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 279 removed outlier: 3.759A pdb=" N GLU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.749A pdb=" N MET D 283 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.701A pdb=" N GLU D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 359 through 380 Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.951A pdb=" N GLN D 408 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 418 Processing helix chain 'D' and resid 429 through 434 removed outlier: 3.508A pdb=" N LEU D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 436 No H-bonds generated for 'chain 'D' and resid 435 through 436' Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 484 through 487 Processing helix chain 'D' and resid 488 through 499 removed outlier: 4.139A pdb=" N ASP D 499 " --> pdb=" O LYS D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 520 Processing helix chain 'D' and resid 526 through 550 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 13 through 29 Processing helix chain 'E' and resid 33 through 48 removed outlier: 3.604A pdb=" N ASP E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 120 removed outlier: 3.616A pdb=" N THR E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 Processing helix chain 'E' and resid 205 through 210 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 239 through 256 removed outlier: 3.718A pdb=" N PHE E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 263 through 278 Processing helix chain 'E' and resid 282 through 308 removed outlier: 3.571A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 327 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 359 through 380 Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.611A pdb=" N GLY E 389 " --> pdb=" O PRO E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 418 removed outlier: 3.953A pdb=" N GLU E 409 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE E 411 " --> pdb=" O GLN E 407 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 434 Processing helix chain 'E' and resid 435 through 436 No H-bonds generated for 'chain 'E' and resid 435 through 436' Processing helix chain 'E' and resid 437 through 439 No H-bonds generated for 'chain 'E' and resid 437 through 439' Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'E' and resid 484 through 487 Processing helix chain 'E' and resid 488 through 498 Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 523 through 551 Processing helix chain 'F' and resid 10 through 16 removed outlier: 3.809A pdb=" N HIS F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 40 removed outlier: 3.797A pdb=" N ILE F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.875A pdb=" N ASP F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.876A pdb=" N LEU F 106 " --> pdb=" O PRO F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 116 Processing helix chain 'F' and resid 133 through 148 removed outlier: 3.582A pdb=" N LEU F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 181 removed outlier: 4.373A pdb=" N GLU F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU F 169 " --> pdb=" O TYR F 165 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.597A pdb=" N GLY F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'G' and resid 10 through 16 Processing helix chain 'G' and resid 22 through 26 Processing helix chain 'G' and resid 27 through 40 removed outlier: 4.059A pdb=" N ILE G 31 " --> pdb=" O GLU G 27 " (cutoff:3.500A) Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 64 through 69 removed outlier: 4.343A pdb=" N PHE G 69 " --> pdb=" O PRO G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.802A pdb=" N ASP G 95 " --> pdb=" O GLY G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 116 removed outlier: 3.623A pdb=" N ASP G 116 " --> pdb=" O ASN G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 113 through 116' Processing helix chain 'G' and resid 134 through 148 Processing helix chain 'G' and resid 152 through 181 removed outlier: 4.291A pdb=" N GLU G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU G 169 " --> pdb=" O TYR G 165 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU G 178 " --> pdb=" O HIS G 174 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP G 179 " --> pdb=" O GLU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 201 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.702A pdb=" N ARG A 218 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.379A pdb=" N HIS B 60 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 165 removed outlier: 4.730A pdb=" N LYS B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE B 151 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE B 142 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP B 74 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASP B 144 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 72 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER B 146 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET B 70 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B 148 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU B 453 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 80 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU B 455 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP B 82 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 454 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 445 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 456 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG B 442 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE B 91 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE B 444 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ILE B 93 " --> pdb=" O PHE B 444 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N GLN B 446 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR B 90 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 330 through 336 removed outlier: 4.210A pdb=" N ARG B 332 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 84 removed outlier: 6.944A pdb=" N ASN C 148 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET C 70 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER C 146 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE C 72 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP C 144 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP C 74 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE C 142 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE C 151 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 200 through 204 removed outlier: 6.213A pdb=" N THR C 90 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ARG C 442 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE C 91 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE C 444 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE C 93 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N GLN C 446 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 330 through 336 removed outlier: 3.999A pdb=" N ARG C 332 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 78 through 84 removed outlier: 6.523A pdb=" N GLN D 80 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR D 73 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP D 82 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER D 71 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN D 84 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER D 69 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU D 67 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE D 150 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 69 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE D 75 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N PHE D 142 " --> pdb=" O PHE D 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 200 through 204 removed outlier: 3.523A pdb=" N ALA D 396 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR D 90 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG D 442 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE D 91 " --> pdb=" O ARG D 442 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE D 444 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE D 93 " --> pdb=" O PHE D 444 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N GLN D 446 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 330 through 336 removed outlier: 6.699A pdb=" N THR D 347 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 333 " --> pdb=" O LYS D 345 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 345 " --> pdb=" O ILE D 333 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL D 335 " --> pdb=" O ILE D 343 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 343 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 84 removed outlier: 6.872A pdb=" N ASN E 148 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET E 70 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER E 146 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHE E 72 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP E 144 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE E 151 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS E 156 " --> pdb=" O PHE E 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 200 through 204 removed outlier: 6.543A pdb=" N GLY E 391 " --> pdb=" O GLN E 422 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL E 424 " --> pdb=" O GLY E 391 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 393 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR E 426 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE E 395 " --> pdb=" O THR E 426 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR E 90 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 330 through 336 removed outlier: 6.650A pdb=" N THR E 347 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE E 333 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS E 345 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL E 335 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE E 343 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AB9, first strand: chain 'F' and resid 118 through 120 Processing sheet with id=AC1, first strand: chain 'G' and resid 53 through 57 removed outlier: 3.787A pdb=" N HIS G 54 " --> pdb=" O SER G 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 118 through 120 1239 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8467 1.34 - 1.48: 6951 1.48 - 1.61: 11362 1.61 - 1.75: 5 1.75 - 1.88: 139 Bond restraints: 26924 Sorted by residual: bond pdb=" N GLY F 79 " pdb=" CA GLY F 79 " ideal model delta sigma weight residual 1.443 1.486 -0.043 8.60e-03 1.35e+04 2.50e+01 bond pdb=" N PHE F 42 " pdb=" CA PHE F 42 " ideal model delta sigma weight residual 1.454 1.512 -0.058 1.32e-02 5.74e+03 1.91e+01 bond pdb=" CA PHE F 42 " pdb=" C PHE F 42 " ideal model delta sigma weight residual 1.527 1.585 -0.058 1.34e-02 5.57e+03 1.90e+01 bond pdb=" CG PRO G 103 " pdb=" CD PRO G 103 " ideal model delta sigma weight residual 1.503 1.367 0.136 3.40e-02 8.65e+02 1.60e+01 bond pdb=" N ASP F 80 " pdb=" CA ASP F 80 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.25e-02 6.40e+03 1.44e+01 ... (remaining 26919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 36838 6.68 - 13.36: 46 13.36 - 20.04: 1 20.04 - 26.72: 0 26.72 - 33.41: 6 Bond angle restraints: 36891 Sorted by residual: angle pdb=" O3' U N 40 " pdb=" P A N 41 " pdb=" OP1 A N 41 " ideal model delta sigma weight residual 108.00 74.59 33.41 3.00e+00 1.11e-01 1.24e+02 angle pdb=" O3' DG M 25 " pdb=" P DG M 26 " pdb=" OP1 DG M 26 " ideal model delta sigma weight residual 108.00 75.00 33.00 3.00e+00 1.11e-01 1.21e+02 angle pdb=" O3' DA M 66 " pdb=" P DT M 67 " pdb=" OP1 DT M 67 " ideal model delta sigma weight residual 108.00 75.80 32.20 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C CYS F 43 " pdb=" CA CYS F 43 " pdb=" CB CYS F 43 " ideal model delta sigma weight residual 112.03 96.69 15.34 1.56e+00 4.11e-01 9.67e+01 angle pdb=" O3' DA M 66 " pdb=" P DT M 67 " pdb=" OP2 DT M 67 " ideal model delta sigma weight residual 108.00 79.00 29.00 3.00e+00 1.11e-01 9.35e+01 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15061 35.89 - 71.79: 1095 71.79 - 107.68: 73 107.68 - 143.57: 9 143.57 - 179.47: 15 Dihedral angle restraints: 16253 sinusoidal: 7629 harmonic: 8624 Sorted by residual: dihedral pdb=" O4' C N 19 " pdb=" C1' C N 19 " pdb=" N1 C N 19 " pdb=" C2 C N 19 " ideal model delta sinusoidal sigma weight residual 200.00 20.53 179.47 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U N 6 " pdb=" C1' U N 6 " pdb=" N1 U N 6 " pdb=" C2 U N 6 " ideal model delta sinusoidal sigma weight residual -160.00 4.20 -164.20 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" CD ARG B 68 " pdb=" NE ARG B 68 " pdb=" CZ ARG B 68 " pdb=" NH1 ARG B 68 " ideal model delta sinusoidal sigma weight residual 0.00 -79.73 79.73 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 16250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 4096 0.256 - 0.512: 5 0.512 - 0.767: 5 0.767 - 1.023: 0 1.023 - 1.279: 3 Chirality restraints: 4109 Sorted by residual: chirality pdb=" P A N 41 " pdb=" OP1 A N 41 " pdb=" OP2 A N 41 " pdb=" O5' A N 41 " both_signs ideal model delta sigma weight residual True 2.41 1.13 1.28 2.00e-01 2.50e+01 4.09e+01 chirality pdb=" P DT M 67 " pdb=" OP1 DT M 67 " pdb=" OP2 DT M 67 " pdb=" O5' DT M 67 " both_signs ideal model delta sigma weight residual True 2.34 1.10 1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" P DG M 26 " pdb=" OP1 DG M 26 " pdb=" OP2 DG M 26 " pdb=" O5' DG M 26 " both_signs ideal model delta sigma weight residual True 2.34 1.10 1.23 2.00e-01 2.50e+01 3.81e+01 ... (remaining 4106 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 68 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 68 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 68 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 68 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 68 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 164 " 0.983 9.50e-02 1.11e+02 4.41e-01 1.17e+02 pdb=" NE ARG E 164 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG E 164 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 164 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 164 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.749 9.50e-02 1.11e+02 3.36e-01 6.87e+01 pdb=" NE ARG A 145 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.023 2.00e-02 2.50e+03 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 479 2.65 - 3.21: 24594 3.21 - 3.77: 42592 3.77 - 4.34: 57547 4.34 - 4.90: 92115 Nonbonded interactions: 217327 Sorted by model distance: nonbonded pdb=" O2' A N 37 " pdb=" O5' C N 38 " model vdw 2.084 3.040 nonbonded pdb=" O2' C N 18 " pdb=" O2 C N 19 " model vdw 2.124 3.040 nonbonded pdb=" N CYS F 43 " pdb=" O CYS F 48 " model vdw 2.147 3.120 nonbonded pdb=" N GLU E 356 " pdb=" OE1 GLU E 356 " model vdw 2.179 3.120 nonbonded pdb=" N GLU E 224 " pdb=" OE1 GLU E 224 " model vdw 2.206 3.120 ... (remaining 217322 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 'B' and resid 1 through 551) selection = (chain 'C' and resid 1 through 551) selection = (chain 'D' and resid 1 through 551) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.610 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 : 0.008 0.747 26932 Z= 0.451 Angle : 0.900 33.405 36899 Z= 0.525 Chirality : 0.063 1.279 4109 Planarity : 0.013 0.494 4367 Dihedral : 22.350 179.468 10632 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 4.32 % Allowed : 27.27 % Favored : 68.41 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 2930 helix: 1.58 (0.14), residues: 1384 sheet: 0.07 (0.26), residues: 407 loop : -0.53 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 7 TYR 0.022 0.002 TYR B 249 PHE 0.022 0.002 PHE D 18 TRP 0.022 0.001 TRP D 39 HIS 0.006 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.37 (26924) covalent geometry : angle 0.88564 / 0.52 (36891) SS BOND : bond 0.74742 / 39.34 ( 1) SS BOND : angle 19.00862 / 11.09 ( 2) hydrogen bonds : bond 0.15562 / 10.27 ( 1283) hydrogen bonds : angle 5.98149 / 4.39 ( 3624) metal coordination : bond 0.19441 / 10.21 ( 7) metal coordination : angle 5.79321 / 2.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 272 time to evaluate : 1.014 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: B 219 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8555 (p) REVERT: B 509 ARG cc_start: 0.9191 (mmm-85) cc_final: 0.8931 (tpp80) REVERT: C 309 MET cc_start: 0.8557 (mtt) cc_final: 0.8341 (mtm) REVERT: D 42 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8492 (pp) REVERT: D 242 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7217 (t70) REVERT: D 299 MET cc_start: 0.9209 (mpp) cc_final: 0.8985 (mmt) REVERT: D 528 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8404 (tppt) REVERT: E 283 MET cc_start: 0.6697 (mmm) cc_final: 0.5700 (mmm) REVERT: E 513 ASN cc_start: 0.8680 (m-40) cc_final: 0.8477 (m-40) REVERT: F 34 HIS cc_start: 0.7953 (m-70) cc_final: 0.7603 (p-80) REVERT: F 92 ILE cc_start: 0.8591 (mm) cc_final: 0.8327 (mp) REVERT: F 141 GLN cc_start: 0.8667 (mt0) cc_final: 0.8397 (pt0) REVERT: G 149 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5923 (mp) outliers start: 114 outliers final: 42 residues processed: 366 average time/residue: 0.5798 time to fit residues: 247.2309 Evaluate side-chains 225 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 213 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN C 23 GLN D 22 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN E 140 ASN E 446 GLN F 30 ASN F 57 HIS ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.102547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.064416 restraints weight = 68215.412| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.79 r_work: 0.2858 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26932 Z= 0.172 Angle : 0.763 25.399 36899 Z= 0.377 Chirality : 0.069 1.967 4109 Planarity : 0.005 0.108 4367 Dihedral : 21.034 177.630 4738 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.58 % Allowed : 27.01 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 2930 helix: 1.79 (0.14), residues: 1406 sheet: 0.24 (0.26), residues: 394 loop : -0.39 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 7 TYR 0.018 0.002 TYR D 46 PHE 0.019 0.001 PHE G 64 TRP 0.011 0.001 TRP E 246 HIS 0.019 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (26924) covalent geometry : angle 0.75429 / 0.38 (36891) SS BOND : bond 0.06001 / 3.16 ( 1) SS BOND : angle 8.26521 / 4.62 ( 2) hydrogen bonds : bond 0.05550 / 3.78 ( 1283) hydrogen bonds : angle 4.74622 / 3.49 ( 3624) metal coordination : bond 0.01003 / 0.52 ( 7) metal coordination : angle 7.69358 / 3.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 194 time to evaluate : 0.923 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: A 60 GLN cc_start: 0.9345 (tt0) cc_final: 0.8974 (tm-30) REVERT: B 68 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7788 (tpt170) REVERT: B 194 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6902 (ttp-170) REVERT: B 309 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8023 (mpt) REVERT: B 507 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8927 (mm-30) REVERT: B 526 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8482 (tm) REVERT: C 207 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8693 (mp0) REVERT: C 283 MET cc_start: 0.1334 (mpt) cc_final: 0.1084 (mpt) REVERT: C 309 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8351 (mtm) REVERT: D 242 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6402 (t70) REVERT: D 528 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8474 (tppt) REVERT: E 89 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8897 (tp) REVERT: E 130 GLU cc_start: 0.8690 (mp0) cc_final: 0.8480 (mp0) REVERT: E 249 TYR cc_start: 0.7747 (t80) cc_final: 0.7393 (t80) REVERT: E 309 MET cc_start: 0.7663 (pmm) cc_final: 0.7452 (pmm) REVERT: E 466 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: G 39 GLN cc_start: 0.7869 (mt0) cc_final: 0.7650 (mt0) REVERT: G 59 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8317 (mtp-110) REVERT: G 64 PHE cc_start: 0.8632 (m-80) cc_final: 0.8370 (m-80) REVERT: G 88 GLN cc_start: 0.7232 (tm-30) cc_final: 0.7019 (tm130) REVERT: G 117 TYR cc_start: 0.8802 (m-80) cc_final: 0.8508 (m-80) REVERT: G 188 MET cc_start: 0.9439 (mmm) cc_final: 0.9210 (mmm) outliers start: 121 outliers final: 35 residues processed: 286 average time/residue: 0.6124 time to fit residues: 204.3816 Evaluate side-chains 216 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 211 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 226 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 197 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN G 57 HIS G 186 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.101412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063162 restraints weight = 68203.225| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.65 r_work: 0.2843 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26932 Z= 0.173 Angle : 0.723 26.297 36899 Z= 0.355 Chirality : 0.068 1.928 4109 Planarity : 0.004 0.057 4367 Dihedral : 20.859 178.308 4690 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.70 % Allowed : 26.59 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 2930 helix: 1.75 (0.14), residues: 1413 sheet: 0.23 (0.26), residues: 401 loop : -0.39 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 52 TYR 0.016 0.002 TYR C 105 PHE 0.020 0.001 PHE G 16 TRP 0.034 0.002 TRP F 185 HIS 0.009 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (26924) covalent geometry : angle 0.71814 / 0.35 (36891) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 4.16546 / 2.35 ( 2) hydrogen bonds : bond 0.05310 / 3.62 ( 1283) hydrogen bonds : angle 4.52564 / 3.34 ( 3624) metal coordination : bond 0.00838 / 0.47 ( 7) metal coordination : angle 5.90880 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 193 time to evaluate : 1.038 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: A 60 GLN cc_start: 0.9359 (tt0) cc_final: 0.9032 (tm-30) REVERT: B 187 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.7918 (m-10) REVERT: B 309 MET cc_start: 0.8674 (tpt) cc_final: 0.8464 (tpp) REVERT: B 394 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9076 (mt) REVERT: B 526 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8480 (tm) REVERT: B 537 ARG cc_start: 0.9350 (ptm160) cc_final: 0.9034 (ttp80) REVERT: C 137 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8378 (t0) REVERT: C 207 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8669 (mp0) REVERT: C 309 MET cc_start: 0.8656 (mtt) cc_final: 0.8422 (mtm) REVERT: D 7 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8794 (ttp80) REVERT: D 195 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7912 (ttp) REVERT: D 242 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6307 (t70) REVERT: E 48 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.6320 (mp10) REVERT: E 89 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8991 (tp) REVERT: E 272 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5179 (tp) REVERT: E 283 MET cc_start: 0.4484 (mmt) cc_final: 0.4140 (mpm) REVERT: E 309 MET cc_start: 0.7616 (pmm) cc_final: 0.7314 (pmm) REVERT: E 466 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: F 137 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8172 (pp) REVERT: F 141 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7990 (pp30) REVERT: F 202 TYR cc_start: 0.8162 (t80) cc_final: 0.7928 (t80) REVERT: G 64 PHE cc_start: 0.8733 (m-80) cc_final: 0.8439 (m-80) REVERT: G 117 TYR cc_start: 0.8848 (m-80) cc_final: 0.8504 (m-80) REVERT: G 188 MET cc_start: 0.9447 (mmm) cc_final: 0.9237 (mmm) outliers start: 124 outliers final: 53 residues processed: 289 average time/residue: 0.5478 time to fit residues: 187.9182 Evaluate side-chains 232 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 185 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 125 optimal weight: 0.3980 chunk 227 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 447 ASN D 27 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.101584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063486 restraints weight = 68264.418| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.55 r_work: 0.2853 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26932 Z= 0.139 Angle : 0.704 25.963 36899 Z= 0.339 Chirality : 0.068 1.958 4109 Planarity : 0.004 0.051 4367 Dihedral : 20.683 177.170 4681 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.09 % Allowed : 27.20 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 2930 helix: 1.80 (0.14), residues: 1411 sheet: 0.28 (0.26), residues: 404 loop : -0.40 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 175 TYR 0.015 0.001 TYR D 105 PHE 0.012 0.001 PHE G 16 TRP 0.031 0.001 TRP F 185 HIS 0.012 0.001 HIS G 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (26924) covalent geometry : angle 0.69746 / 0.34 (36891) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 3.77450 / 2.13 ( 2) hydrogen bonds : bond 0.04780 / 3.25 ( 1283) hydrogen bonds : angle 4.37420 / 3.23 ( 3624) metal coordination : bond 0.00894 / 0.45 ( 7) metal coordination : angle 7.47993 / 3.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 173 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9370 (tt0) cc_final: 0.9065 (tm-30) REVERT: B 68 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7672 (tpt170) REVERT: B 187 TRP cc_start: 0.8668 (OUTLIER) cc_final: 0.7983 (m-10) REVERT: B 194 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6994 (ttp-170) REVERT: B 394 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9097 (mt) REVERT: B 526 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8469 (tm) REVERT: C 207 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8574 (mp0) REVERT: C 210 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.6057 (p-80) REVERT: D 24 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: D 39 TRP cc_start: 0.8756 (m100) cc_final: 0.7881 (m100) REVERT: D 195 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7876 (ttp) REVERT: D 242 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6239 (t70) REVERT: E 48 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6317 (mp10) REVERT: E 249 TYR cc_start: 0.7735 (t80) cc_final: 0.7497 (t80) REVERT: E 272 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5325 (tp) REVERT: E 283 MET cc_start: 0.4938 (mmt) cc_final: 0.4585 (mpm) REVERT: E 309 MET cc_start: 0.7721 (pmm) cc_final: 0.7444 (pmm) REVERT: E 466 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: F 34 HIS cc_start: 0.7756 (m-70) cc_final: 0.7205 (p-80) REVERT: F 38 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5350 (ptt) REVERT: G 16 PHE cc_start: 0.8553 (m-80) cc_final: 0.8318 (m-80) REVERT: G 59 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8234 (mtp-110) REVERT: G 64 PHE cc_start: 0.8873 (m-80) cc_final: 0.8408 (m-80) REVERT: G 117 TYR cc_start: 0.8870 (m-80) cc_final: 0.8516 (m-80) REVERT: G 147 PHE cc_start: 0.7317 (m-10) cc_final: 0.6982 (m-10) REVERT: G 188 MET cc_start: 0.9463 (mmm) cc_final: 0.9237 (mmm) outliers start: 108 outliers final: 49 residues processed: 258 average time/residue: 0.5460 time to fit residues: 166.2266 Evaluate side-chains 225 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 162 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 187 TRP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 88 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN C 140 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.098989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.060596 restraints weight = 68072.767| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.56 r_work: 0.2756 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26932 Z= 0.238 Angle : 0.756 26.242 36899 Z= 0.368 Chirality : 0.069 1.934 4109 Planarity : 0.004 0.048 4367 Dihedral : 20.736 177.835 4677 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.47 % Allowed : 27.20 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 2930 helix: 1.78 (0.14), residues: 1413 sheet: 0.11 (0.25), residues: 405 loop : -0.49 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 534 TYR 0.019 0.002 TYR B 249 PHE 0.021 0.002 PHE E 75 TRP 0.017 0.002 TRP F 185 HIS 0.011 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (26924) covalent geometry : angle 0.74825 / 0.37 (36891) SS BOND : bond 0.00264 / 0.14 ( 1) SS BOND : angle 3.34657 / 1.87 ( 2) hydrogen bonds : bond 0.05565 / 3.78 ( 1283) hydrogen bonds : angle 4.47877 / 3.30 ( 3624) metal coordination : bond 0.00856 / 0.52 ( 7) metal coordination : angle 8.27100 / 3.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 171 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9381 (tt0) cc_final: 0.9148 (tm-30) REVERT: B 68 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7735 (tpt170) REVERT: B 187 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: B 526 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8465 (tm) REVERT: D 7 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8780 (ttp80) REVERT: D 39 TRP cc_start: 0.8764 (m100) cc_final: 0.8077 (m100) REVERT: D 195 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.8016 (ttp) REVERT: D 242 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6387 (t70) REVERT: E 48 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.6480 (mp10) REVERT: E 272 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5274 (tp) REVERT: E 283 MET cc_start: 0.4784 (mmt) cc_final: 0.4506 (mpm) REVERT: E 466 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: F 34 HIS cc_start: 0.7806 (m-70) cc_final: 0.7257 (p-80) REVERT: F 38 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.5155 (ptt) REVERT: F 202 TYR cc_start: 0.8171 (t80) cc_final: 0.7931 (t80) REVERT: G 59 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8240 (mtp-110) REVERT: G 64 PHE cc_start: 0.8863 (m-80) cc_final: 0.8384 (m-80) REVERT: G 117 TYR cc_start: 0.8931 (m-80) cc_final: 0.8448 (m-80) REVERT: G 188 MET cc_start: 0.9454 (mmm) cc_final: 0.9238 (mmm) outliers start: 118 outliers final: 55 residues processed: 265 average time/residue: 0.6021 time to fit residues: 188.4021 Evaluate side-chains 227 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062316 restraints weight = 68083.402| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.53 r_work: 0.2825 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26932 Z= 0.129 Angle : 0.723 26.079 36899 Z= 0.345 Chirality : 0.068 1.970 4109 Planarity : 0.004 0.062 4367 Dihedral : 20.620 176.843 4677 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.67 % Allowed : 27.77 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 2930 helix: 1.80 (0.14), residues: 1412 sheet: 0.29 (0.25), residues: 402 loop : -0.40 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 534 TYR 0.015 0.001 TYR D 46 PHE 0.015 0.001 PHE E 75 TRP 0.022 0.001 TRP F 185 HIS 0.012 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (26924) covalent geometry : angle 0.71519 / 0.34 (36891) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 3.18735 / 1.78 ( 2) hydrogen bonds : bond 0.04724 / 3.21 ( 1283) hydrogen bonds : angle 4.29339 / 3.17 ( 3624) metal coordination : bond 0.00730 / 0.38 ( 7) metal coordination : angle 7.99576 / 3.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 172 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9390 (tt0) cc_final: 0.9185 (tm-30) REVERT: B 68 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7620 (tpt170) REVERT: B 187 TRP cc_start: 0.8828 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: B 394 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9045 (mt) REVERT: B 526 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8483 (tm) REVERT: C 210 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.6121 (p-80) REVERT: D 39 TRP cc_start: 0.8493 (m100) cc_final: 0.7921 (m100) REVERT: D 195 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (ttp) REVERT: D 242 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6409 (t70) REVERT: E 272 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5302 (tp) REVERT: E 283 MET cc_start: 0.4944 (mmt) cc_final: 0.4613 (mpm) REVERT: E 309 MET cc_start: 0.7594 (ptp) cc_final: 0.7388 (pmm) REVERT: E 466 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: F 34 HIS cc_start: 0.7870 (m-70) cc_final: 0.7316 (p-80) REVERT: F 38 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.5031 (ptt) REVERT: G 59 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8152 (mtp-110) REVERT: G 64 PHE cc_start: 0.8929 (m-80) cc_final: 0.8424 (m-80) REVERT: G 117 TYR cc_start: 0.8932 (m-80) cc_final: 0.8590 (m-80) REVERT: G 141 GLN cc_start: 0.8689 (mp10) cc_final: 0.8478 (mp10) REVERT: G 145 ARG cc_start: 0.9077 (tmm-80) cc_final: 0.8560 (ptm-80) REVERT: G 188 MET cc_start: 0.9436 (mmm) cc_final: 0.9200 (mpm) outliers start: 97 outliers final: 54 residues processed: 243 average time/residue: 0.6062 time to fit residues: 173.4297 Evaluate side-chains 231 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 134 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 294 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 274 GLN F 57 HIS ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.060675 restraints weight = 68051.756| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.51 r_work: 0.2771 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26932 Z= 0.187 Angle : 0.734 26.161 36899 Z= 0.354 Chirality : 0.069 1.953 4109 Planarity : 0.004 0.066 4367 Dihedral : 20.568 178.083 4675 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.67 % Allowed : 27.46 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 2930 helix: 1.84 (0.14), residues: 1413 sheet: 0.24 (0.25), residues: 403 loop : -0.44 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 510 TYR 0.016 0.002 TYR G 202 PHE 0.013 0.001 PHE G 16 TRP 0.025 0.001 TRP F 185 HIS 0.012 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (26924) covalent geometry : angle 0.72616 / 0.35 (36891) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 3.05309 / 1.73 ( 2) hydrogen bonds : bond 0.05096 / 3.47 ( 1283) hydrogen bonds : angle 4.32845 / 3.18 ( 3624) metal coordination : bond 0.00696 / 0.42 ( 7) metal coordination : angle 8.29625 / 3.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 166 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.9406 (tt0) cc_final: 0.9192 (tm-30) REVERT: B 68 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7659 (tpt170) REVERT: B 187 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8031 (m-10) REVERT: B 309 MET cc_start: 0.8317 (tpp) cc_final: 0.7371 (mpp) REVERT: B 394 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9039 (mt) REVERT: C 64 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: C 210 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.6193 (p-80) REVERT: C 299 MET cc_start: 0.8823 (tpt) cc_final: 0.8321 (ppp) REVERT: C 309 MET cc_start: 0.7953 (ptp) cc_final: 0.7255 (mpp) REVERT: D 39 TRP cc_start: 0.8544 (m100) cc_final: 0.7962 (m100) REVERT: D 187 TRP cc_start: 0.9241 (OUTLIER) cc_final: 0.8755 (m-10) REVERT: D 195 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8062 (ttp) REVERT: D 242 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6378 (t70) REVERT: E 272 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5448 (tp) REVERT: E 283 MET cc_start: 0.5038 (mmt) cc_final: 0.4726 (mpm) REVERT: E 309 MET cc_start: 0.7590 (ptp) cc_final: 0.7169 (pmm) REVERT: E 466 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: F 34 HIS cc_start: 0.7882 (m-70) cc_final: 0.7321 (p-80) REVERT: F 38 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.4623 (ptt) REVERT: F 43 CYS cc_start: -0.2274 (m) cc_final: -0.2492 (m) REVERT: F 202 TYR cc_start: 0.8161 (t80) cc_final: 0.7959 (t80) REVERT: G 59 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8289 (mtp-110) REVERT: G 64 PHE cc_start: 0.8942 (m-80) cc_final: 0.8452 (m-80) REVERT: G 117 TYR cc_start: 0.8920 (m-80) cc_final: 0.8432 (m-80) REVERT: G 188 MET cc_start: 0.9452 (mmm) cc_final: 0.9224 (mpm) outliers start: 97 outliers final: 52 residues processed: 235 average time/residue: 0.5022 time to fit residues: 139.1017 Evaluate side-chains 224 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 17 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN G 14 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.100196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061862 restraints weight = 68235.541| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.57 r_work: 0.2819 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26932 Z= 0.132 Angle : 0.729 26.127 36899 Z= 0.347 Chirality : 0.068 1.978 4109 Planarity : 0.004 0.049 4367 Dihedral : 20.470 178.036 4673 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.14 % Allowed : 28.07 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 2930 helix: 1.85 (0.14), residues: 1415 sheet: 0.33 (0.25), residues: 402 loop : -0.41 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 534 TYR 0.015 0.001 TYR E 105 PHE 0.032 0.001 PHE G 147 TRP 0.024 0.001 TRP F 185 HIS 0.013 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (26924) covalent geometry : angle 0.72075 / 0.35 (36891) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 3.37286 / 1.87 ( 2) hydrogen bonds : bond 0.04631 / 3.15 ( 1283) hydrogen bonds : angle 4.23123 / 3.11 ( 3624) metal coordination : bond 0.00689 / 0.35 ( 7) metal coordination : angle 8.27461 / 3.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 163 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7633 (tpt170) REVERT: B 187 TRP cc_start: 0.8906 (OUTLIER) cc_final: 0.8089 (m-10) REVERT: B 292 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8375 (pptt) REVERT: B 309 MET cc_start: 0.8286 (tpp) cc_final: 0.7381 (mpp) REVERT: B 394 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9054 (mt) REVERT: B 509 ARG cc_start: 0.9450 (tpp80) cc_final: 0.9245 (mmm160) REVERT: C 64 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: C 210 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.6190 (p-80) REVERT: C 343 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8564 (pp) REVERT: D 7 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8610 (ptp90) REVERT: D 39 TRP cc_start: 0.8522 (m100) cc_final: 0.7985 (m100) REVERT: D 195 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8056 (ttp) REVERT: D 242 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6270 (t70) REVERT: E 210 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8121 (m-70) REVERT: E 272 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5334 (tp) REVERT: E 283 MET cc_start: 0.5087 (mmt) cc_final: 0.4779 (mpm) REVERT: E 309 MET cc_start: 0.7579 (ptp) cc_final: 0.7269 (pmm) REVERT: E 466 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: F 34 HIS cc_start: 0.7854 (m-70) cc_final: 0.7289 (p-80) REVERT: F 38 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4606 (ptt) REVERT: F 50 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7001 (mp) REVERT: F 59 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7614 (mmp80) REVERT: G 59 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8289 (mtp-110) REVERT: G 64 PHE cc_start: 0.8948 (m-80) cc_final: 0.8461 (m-80) REVERT: G 117 TYR cc_start: 0.8920 (m-80) cc_final: 0.8423 (m-80) REVERT: G 145 ARG cc_start: 0.9142 (tmm-80) cc_final: 0.8644 (ptm-80) REVERT: G 188 MET cc_start: 0.9462 (mmm) cc_final: 0.9212 (mpm) outliers start: 83 outliers final: 50 residues processed: 221 average time/residue: 0.6079 time to fit residues: 158.0874 Evaluate side-chains 222 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 428 HIS Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 283 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 169 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN E 278 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.098517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059938 restraints weight = 68221.782| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.64 r_work: 0.2755 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26932 Z= 0.215 Angle : 0.768 26.204 36899 Z= 0.370 Chirality : 0.069 1.960 4109 Planarity : 0.004 0.075 4367 Dihedral : 20.515 179.393 4673 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.11 % Allowed : 28.30 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 2930 helix: 1.89 (0.14), residues: 1414 sheet: 0.25 (0.25), residues: 403 loop : -0.44 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 510 TYR 0.016 0.002 TYR B 105 PHE 0.022 0.002 PHE G 147 TRP 0.027 0.002 TRP F 185 HIS 0.014 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (26924) covalent geometry : angle 0.76033 / 0.37 (36891) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 3.06290 / 1.72 ( 2) hydrogen bonds : bond 0.05239 / 3.55 ( 1283) hydrogen bonds : angle 4.33420 / 3.18 ( 3624) metal coordination : bond 0.00591 / 0.37 ( 7) metal coordination : angle 8.33000 / 3.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 161 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7650 (tpt170) REVERT: B 187 TRP cc_start: 0.8963 (OUTLIER) cc_final: 0.8042 (m-10) REVERT: B 292 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8389 (pptt) REVERT: B 309 MET cc_start: 0.8365 (tpp) cc_final: 0.7422 (mpp) REVERT: B 394 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9066 (mt) REVERT: B 509 ARG cc_start: 0.9465 (tpp80) cc_final: 0.9243 (mmm160) REVERT: C 64 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: C 210 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.6297 (p-80) REVERT: C 299 MET cc_start: 0.8871 (tpt) cc_final: 0.8451 (mmt) REVERT: C 309 MET cc_start: 0.7959 (ptp) cc_final: 0.7276 (mpp) REVERT: C 343 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8639 (pp) REVERT: D 39 TRP cc_start: 0.8604 (m100) cc_final: 0.7966 (m100) REVERT: D 126 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9141 (mt0) REVERT: D 187 TRP cc_start: 0.9253 (OUTLIER) cc_final: 0.8796 (m-10) REVERT: D 195 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8095 (ttp) REVERT: D 242 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6321 (t70) REVERT: D 316 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8568 (mtm) REVERT: E 272 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.5041 (tp) REVERT: E 283 MET cc_start: 0.4825 (mmt) cc_final: 0.4625 (mpm) REVERT: E 309 MET cc_start: 0.7609 (ptp) cc_final: 0.7187 (pmm) REVERT: E 466 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: F 34 HIS cc_start: 0.7681 (m-70) cc_final: 0.7186 (p-80) REVERT: F 38 MET cc_start: 0.4161 (OUTLIER) cc_final: 0.3676 (ptt) REVERT: G 39 GLN cc_start: 0.7704 (mt0) cc_final: 0.7249 (tt0) REVERT: G 59 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8334 (mtp-110) REVERT: G 64 PHE cc_start: 0.8960 (m-80) cc_final: 0.8475 (m-80) REVERT: G 117 TYR cc_start: 0.8932 (m-80) cc_final: 0.8485 (m-80) REVERT: G 145 ARG cc_start: 0.9199 (tmm-80) cc_final: 0.8705 (ptm-80) outliers start: 82 outliers final: 48 residues processed: 217 average time/residue: 0.5960 time to fit residues: 152.9791 Evaluate side-chains 216 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 38 optimal weight: 0.1980 chunk 218 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 257 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062090 restraints weight = 68103.877| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.63 r_work: 0.2824 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26932 Z= 0.124 Angle : 0.737 26.253 36899 Z= 0.351 Chirality : 0.068 1.997 4109 Planarity : 0.004 0.058 4367 Dihedral : 20.422 178.922 4673 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.50 % Allowed : 28.94 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 2930 helix: 1.90 (0.14), residues: 1414 sheet: 0.40 (0.26), residues: 400 loop : -0.37 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 7 TYR 0.015 0.001 TYR C 105 PHE 0.026 0.001 PHE F 147 TRP 0.028 0.001 TRP F 185 HIS 0.013 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (26924) covalent geometry : angle 0.72934 / 0.35 (36891) SS BOND : bond 0.00270 / 0.14 ( 1) SS BOND : angle 3.47896 / 1.92 ( 2) hydrogen bonds : bond 0.04489 / 3.04 ( 1283) hydrogen bonds : angle 4.19278 / 3.08 ( 3624) metal coordination : bond 0.00679 / 0.31 ( 7) metal coordination : angle 8.29580 / 3.63 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 159 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7622 (tpt170) REVERT: B 187 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: B 292 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8391 (pptt) REVERT: B 309 MET cc_start: 0.8395 (tpp) cc_final: 0.7530 (mpp) REVERT: B 394 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9034 (mt) REVERT: B 509 ARG cc_start: 0.9472 (tpp80) cc_final: 0.9258 (mmm160) REVERT: C 64 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: C 210 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.6132 (p-80) REVERT: C 298 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8010 (mp10) REVERT: C 299 MET cc_start: 0.8837 (tpt) cc_final: 0.8448 (mmt) REVERT: C 309 MET cc_start: 0.7895 (ptp) cc_final: 0.7205 (mpp) REVERT: C 343 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8605 (pp) REVERT: D 39 TRP cc_start: 0.8525 (m100) cc_final: 0.8013 (m100) REVERT: D 126 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9064 (mt0) REVERT: D 187 TRP cc_start: 0.9217 (OUTLIER) cc_final: 0.8697 (m-10) REVERT: D 242 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6228 (t70) REVERT: D 272 LEU cc_start: 0.8684 (mt) cc_final: 0.8225 (pp) REVERT: D 316 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8531 (mtm) REVERT: E 210 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8122 (m-70) REVERT: E 272 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.4890 (tp) REVERT: E 283 MET cc_start: 0.4971 (mmt) cc_final: 0.4759 (mpm) REVERT: E 309 MET cc_start: 0.7673 (ptp) cc_final: 0.7395 (pmm) REVERT: E 466 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: G 39 GLN cc_start: 0.7675 (mt0) cc_final: 0.7153 (tt0) REVERT: G 45 TYR cc_start: 0.8415 (m-80) cc_final: 0.8120 (m-80) REVERT: G 59 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8303 (mtp-110) REVERT: G 64 PHE cc_start: 0.8973 (m-80) cc_final: 0.8478 (m-80) REVERT: G 117 TYR cc_start: 0.8919 (m-80) cc_final: 0.8477 (m-80) REVERT: G 145 ARG cc_start: 0.9214 (tmm-80) cc_final: 0.8730 (ptm-80) outliers start: 66 outliers final: 41 residues processed: 202 average time/residue: 0.5896 time to fit residues: 141.0610 Evaluate side-chains 208 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 428 HIS Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 271 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 263 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS ** D 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.099799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.061505 restraints weight = 67752.786| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.50 r_work: 0.2802 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26932 Z= 0.151 Angle : 0.748 26.141 36899 Z= 0.356 Chirality : 0.068 1.985 4109 Planarity : 0.004 0.057 4367 Dihedral : 20.400 179.740 4672 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.50 % Allowed : 29.02 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 2930 helix: 1.91 (0.14), residues: 1413 sheet: 0.37 (0.26), residues: 398 loop : -0.37 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 510 TYR 0.015 0.001 TYR B 105 PHE 0.022 0.001 PHE G 147 TRP 0.023 0.001 TRP F 185 HIS 0.013 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (26924) covalent geometry : angle 0.74073 / 0.35 (36891) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 3.32585 / 1.84 ( 2) hydrogen bonds : bond 0.04636 / 3.14 ( 1283) hydrogen bonds : angle 4.21071 / 3.09 ( 3624) metal coordination : bond 0.00649 / 0.35 ( 7) metal coordination : angle 8.17990 / 3.55 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10494.48 seconds wall clock time: 179 minutes 16.49 seconds (10756.49 seconds total)