Starting phenix.real_space_refine on Sat Aug 8 22:40:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jt2_61790/08_2026/9jt2_61790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jt2_61790/08_2026/9jt2_61790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2026/9jt2_61790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2026/9jt2_61790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2026/9jt2_61790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2026/9jt2_61790.map" } resolution = 3.19 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= 0.001 sd= 0.059 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 P 165 5.49 5 Mg 6 5.21 5 S 92 5.16 5 C 19204 2.51 5 N 5488 2.21 5 O 6223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s 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: 31178 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3715 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 441} Chain breaks: 1 Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3304 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 19, 'TRANS': 390} Chain breaks: 1 Chain: "C" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNA': 19} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "D" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "E" Number of atoms: 3715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3715 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 441} Chain breaks: 1 Chain: "F" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3297 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 18, 'TRANS': 390} Chain breaks: 1 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "H" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 18} Chain: "I" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3696 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "J" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3149 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 15, 'TRANS': 373} Chain breaks: 2 Chain: "K" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 385 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "M" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3696 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "N" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3149 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 15, 'TRANS': 373} Chain breaks: 2 Chain: "O" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNA': 19} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "P" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "Q" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 7} Chain: "R" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.15, per 1000 atoms: 0.23 Number of scatterers: 31178 At special positions: 0 Unit cell: (170, 158.1, 178.5, 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) S 92 16.00 P 165 15.00 Mg 6 11.99 O 6223 8.00 N 5488 7.00 C 19204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6406 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 36 sheets defined 29.3% alpha, 16.0% beta 61 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 49 through 66 removed outlier: 4.197A pdb=" N SER A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 119 through 138 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.577A pdb=" N LEU A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 225 through 243 removed outlier: 3.948A pdb=" N THR A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.843A pdb=" N ALA A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.600A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.735A pdb=" N LYS A 483 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.986A pdb=" N ILE B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 186 through 196 removed outlier: 4.097A pdb=" N GLY B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 236 through 241 removed outlier: 3.842A pdb=" N LEU B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.524A pdb=" N ARG B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 4.115A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.762A pdb=" N GLY B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 32 Processing helix chain 'E' and resid 51 through 66 removed outlier: 3.643A pdb=" N ASP E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 removed outlier: 4.083A pdb=" N LYS E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 107 through 112' Processing helix chain 'E' and resid 118 through 138 removed outlier: 3.939A pdb=" N VAL E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP E 138 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.806A pdb=" N ALA E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 removed outlier: 3.997A pdb=" N ILE E 205 " --> pdb=" O TRP E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 243 removed outlier: 3.799A pdb=" N THR E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN E 232 " --> pdb=" O GLY E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 328 removed outlier: 3.817A pdb=" N HIS E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 356 removed outlier: 4.091A pdb=" N GLY E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE E 350 " --> pdb=" O GLU E 346 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 439 Processing helix chain 'E' and resid 455 through 469 removed outlier: 3.857A pdb=" N GLY E 465 " --> pdb=" O ALA E 461 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU E 466 " --> pdb=" O ARG E 462 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 484 removed outlier: 3.634A pdb=" N LYS E 483 " --> pdb=" O ASP E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 25 removed outlier: 4.109A pdb=" N ILE F 10 " --> pdb=" O THR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.797A pdb=" N ALA F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 187 through 196 removed outlier: 3.794A pdb=" N ALA F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 262 removed outlier: 3.851A pdb=" N GLN F 248 " --> pdb=" O ASP F 244 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.447A pdb=" N LEU F 358 " --> pdb=" O PHE F 354 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 382 removed outlier: 3.582A pdb=" N LEU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU F 382 " --> pdb=" O TRP F 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 removed outlier: 3.540A pdb=" N GLU I 30 " --> pdb=" O LEU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 67 removed outlier: 3.566A pdb=" N GLY I 66 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL I 67 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 114 removed outlier: 3.765A pdb=" N LEU I 109 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP I 110 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS I 111 " --> pdb=" O SER I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 138 removed outlier: 4.100A pdb=" N ALA I 121 " --> pdb=" O ASP I 117 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL I 122 " --> pdb=" O HIS I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 160 removed outlier: 3.593A pdb=" N ARG I 157 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN I 160 " --> pdb=" O GLU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 190 removed outlier: 3.712A pdb=" N MET I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS I 189 " --> pdb=" O MET I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 225 through 243 removed outlier: 3.939A pdb=" N ARG I 229 " --> pdb=" O ASP I 225 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 230 " --> pdb=" O ILE I 226 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP I 231 " --> pdb=" O ALA I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 328 removed outlier: 3.914A pdb=" N LYS I 314 " --> pdb=" O GLU I 310 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE I 315 " --> pdb=" O ASP I 311 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE I 316 " --> pdb=" O ALA I 312 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 325 " --> pdb=" O ALA I 321 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS I 326 " --> pdb=" O ALA I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 358 removed outlier: 3.547A pdb=" N ASP I 348 " --> pdb=" O ASP I 344 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 358 " --> pdb=" O LEU I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 440 Processing helix chain 'I' and resid 455 through 468 removed outlier: 3.907A pdb=" N VAL I 467 " --> pdb=" O LYS I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 471 No H-bonds generated for 'chain 'I' and resid 469 through 471' Processing helix chain 'I' and resid 480 through 484 removed outlier: 3.637A pdb=" N LYS I 483 " --> pdb=" O ASP I 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 27 removed outlier: 4.032A pdb=" N LEU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 90 Processing helix chain 'J' and resid 186 through 193 removed outlier: 3.617A pdb=" N ILE J 190 " --> pdb=" O PRO J 186 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA J 191 " --> pdb=" O ARG J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 225 removed outlier: 3.802A pdb=" N GLU J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 241 Processing helix chain 'J' and resid 244 through 263 removed outlier: 3.563A pdb=" N THR J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 365 removed outlier: 4.378A pdb=" N ALA J 360 " --> pdb=" O ALA J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 383 removed outlier: 3.946A pdb=" N GLY J 373 " --> pdb=" O ALA J 369 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLN J 374 " --> pdb=" O ALA J 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 31 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.608A pdb=" N ILE M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU M 61 " --> pdb=" O ARG M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 112 Processing helix chain 'M' and resid 118 through 139 removed outlier: 3.564A pdb=" N GLY M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 159 removed outlier: 3.714A pdb=" N ARG M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 189 Processing helix chain 'M' and resid 227 through 243 removed outlier: 3.734A pdb=" N TRP M 231 " --> pdb=" O ALA M 227 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN M 232 " --> pdb=" O GLY M 228 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU M 233 " --> pdb=" O ARG M 229 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR M 235 " --> pdb=" O TRP M 231 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER M 236 " --> pdb=" O ASN M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 328 removed outlier: 3.577A pdb=" N LYS M 313 " --> pdb=" O ARG M 309 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS M 326 " --> pdb=" O ALA M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 358 removed outlier: 3.736A pdb=" N ALA M 347 " --> pdb=" O LYS M 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 440 Processing helix chain 'M' and resid 455 through 469 removed outlier: 3.952A pdb=" N VAL M 467 " --> pdb=" O LYS M 463 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS M 469 " --> pdb=" O GLY M 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 484 removed outlier: 3.766A pdb=" N LYS M 483 " --> pdb=" O ASP M 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 26 removed outlier: 3.695A pdb=" N GLU N 13 " --> pdb=" O GLN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 90 Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 143 removed outlier: 3.785A pdb=" N LEU N 141 " --> pdb=" O THR N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 194 Processing helix chain 'N' and resid 244 through 263 removed outlier: 4.154A pdb=" N GLN N 248 " --> pdb=" O ASP N 244 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN N 249 " --> pdb=" O ILE N 245 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR N 263 " --> pdb=" O LEU N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 363 removed outlier: 3.558A pdb=" N LEU N 359 " --> pdb=" O ALA N 355 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY N 361 " --> pdb=" O PRO N 357 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS N 363 " --> pdb=" O LEU N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.720A pdb=" N ILE A 336 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 367 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS A 338 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU A 337 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 261 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.797A pdb=" N ARG A 248 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 removed outlier: 5.589A pdb=" N ILE A 42 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL A 145 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 43 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE A 147 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY A 45 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA A 149 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 47 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.548A pdb=" N ALA B 44 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG B 55 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 46 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ILE B 97 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 58 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL B 99 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN B 60 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N TYR B 101 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 62 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 107 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA7, first strand: chain 'B' and resid 335 through 337 removed outlier: 3.944A pdb=" N MET B 402 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AA9, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.564A pdb=" N SER B 304 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 317 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.796A pdb=" N THR E 387 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL E 334 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL E 365 " --> pdb=" O VAL E 334 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 336 " --> pdb=" O VAL E 365 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL E 367 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS E 338 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA E 258 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP E 283 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'E' and resid 93 through 95 removed outlier: 5.939A pdb=" N ILE E 42 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ALA E 102 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 46 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU E 104 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLY E 48 " --> pdb=" O LEU E 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 95 removed outlier: 5.939A pdb=" N ILE E 42 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 145 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA E 146 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 375 through 376 removed outlier: 7.373A pdb=" N GLY F 160 " --> pdb=" O VAL F 413 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 413 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU F 162 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.941A pdb=" N ILE F 43 " --> pdb=" O ASP F 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AB8, first strand: chain 'F' and resid 78 through 80 Processing sheet with id=AB9, first strand: chain 'F' and resid 304 through 307 removed outlier: 4.460A pdb=" N MET F 402 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 5 through 7 removed outlier: 6.612A pdb=" N VAL I 334 " --> pdb=" O ASP I 363 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL I 365 " --> pdb=" O VAL I 334 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE I 336 " --> pdb=" O VAL I 365 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL I 367 " --> pdb=" O ILE I 336 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS I 338 " --> pdb=" O VAL I 367 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N CYS I 259 " --> pdb=" O PHE I 335 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU I 337 " --> pdb=" O CYS I 259 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL I 261 " --> pdb=" O LEU I 337 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 19 through 21 removed outlier: 3.838A pdb=" N HIS I 19 " --> pdb=" O PHE I 15 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 93 through 103 removed outlier: 5.761A pdb=" N ILE I 42 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU I 97 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE I 44 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY I 99 " --> pdb=" O ILE I 44 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL I 46 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR I 101 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY I 48 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA I 103 " --> pdb=" O GLY I 48 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N VAL I 145 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS I 43 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE I 147 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY I 45 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ALA I 149 " --> pdb=" O GLY I 45 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL I 47 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA I 146 " --> pdb=" O GLN I 198 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL I 200 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE I 148 " --> pdb=" O VAL I 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 375 through 376 Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 46 removed outlier: 5.364A pdb=" N ARG J 55 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 76 through 79 Processing sheet with id=AC7, first strand: chain 'J' and resid 267 through 270 removed outlier: 3.598A pdb=" N PHE J 323 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N HIS J 321 " --> pdb=" O PHE J 278 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TRP J 334 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR J 172 " --> pdb=" O MET J 402 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET J 402 " --> pdb=" O THR J 172 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 178 through 179 Processing sheet with id=AC9, first strand: chain 'J' and resid 305 through 308 removed outlier: 7.011A pdb=" N PHE J 306 " --> pdb=" O SER J 316 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN J 308 " --> pdb=" O ARG J 314 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG J 314 " --> pdb=" O ASN J 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 4 through 7 removed outlier: 4.698A pdb=" N GLU M 4 " --> pdb=" O ASP M 390 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL M 334 " --> pdb=" O ASP M 363 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL M 365 " --> pdb=" O VAL M 334 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE M 336 " --> pdb=" O VAL M 365 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL M 367 " --> pdb=" O ILE M 336 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS M 338 " --> pdb=" O VAL M 367 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS M 259 " --> pdb=" O PHE M 335 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU M 337 " --> pdb=" O CYS M 259 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL M 261 " --> pdb=" O LEU M 337 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 20 through 21 Processing sheet with id=AD3, first strand: chain 'M' and resid 93 through 103 removed outlier: 5.853A pdb=" N ILE M 42 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU M 97 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE M 44 " --> pdb=" O GLU M 97 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLY M 99 " --> pdb=" O ILE M 44 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL M 46 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR M 101 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY M 48 " --> pdb=" O THR M 101 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA M 103 " --> pdb=" O GLY M 48 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N VAL M 145 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS M 43 " --> pdb=" O VAL M 145 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE M 147 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY M 45 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ALA M 149 " --> pdb=" O GLY M 45 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL M 47 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA M 146 " --> pdb=" O GLN M 198 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL M 200 " --> pdb=" O ALA M 146 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE M 148 " --> pdb=" O VAL M 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 375 through 376 removed outlier: 3.603A pdb=" N LEU N 165 " --> pdb=" O LEU M 376 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 29 through 31 removed outlier: 3.641A pdb=" N ILE N 57 " --> pdb=" O ALA N 44 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG N 55 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N ILE N 97 " --> pdb=" O MET N 56 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA N 58 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL N 99 " --> pdb=" O ALA N 58 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN N 60 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR N 101 " --> pdb=" O GLN N 60 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 31 removed outlier: 3.641A pdb=" N ILE N 57 " --> pdb=" O ALA N 44 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG N 55 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N ILE N 97 " --> pdb=" O MET N 56 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA N 58 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL N 99 " --> pdb=" O ALA N 58 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN N 60 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR N 101 " --> pdb=" O GLN N 60 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL N 96 " --> pdb=" O VAL N 113 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG N 102 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER N 107 " --> pdb=" O ARG N 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 76 through 79 Processing sheet with id=AD8, first strand: chain 'N' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'N' and resid 177 through 179 removed outlier: 3.771A pdb=" N GLU N 232 " --> pdb=" O ILE N 179 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2439 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 158 hydrogen bonds 316 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 6.37 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8942 1.34 - 1.46: 6615 1.46 - 1.58: 16185 1.58 - 1.69: 320 1.69 - 1.81: 168 Bond restraints: 32230 Sorted by residual: bond pdb=" C1' DC Q 5 " pdb=" N1 DC Q 5 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.63e+01 bond pdb=" C ALA J 356 " pdb=" N PRO J 357 " ideal model delta sigma weight residual 1.336 1.371 -0.035 9.80e-03 1.04e+04 1.25e+01 bond pdb=" C3' DA L 2 " pdb=" C2' DA L 2 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG L 9 " pdb=" C2' DG L 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT D 18 " pdb=" O3' DT D 18 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.04e+01 ... (remaining 32225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 43070 2.06 - 4.13: 1143 4.13 - 6.19: 100 6.19 - 8.26: 14 8.26 - 10.32: 12 Bond angle restraints: 44339 Sorted by residual: angle pdb=" O4' C C 12 " pdb=" C1' C C 12 " pdb=" N1 C C 12 " ideal model delta sigma weight residual 108.20 112.09 -3.89 8.00e-01 1.56e+00 2.37e+01 angle pdb=" O4' DG P 9 " pdb=" C4' DG P 9 " pdb=" C3' DG P 9 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" C3' A O 18 " pdb=" O3' A O 18 " pdb=" P U O 19 " ideal model delta sigma weight residual 119.70 125.08 -5.38 1.20e+00 6.94e-01 2.01e+01 angle pdb=" C3' DT D 18 " pdb=" O3' DT D 18 " pdb=" P DA D 19 " ideal model delta sigma weight residual 119.70 125.08 -5.38 1.20e+00 6.94e-01 2.01e+01 angle pdb=" N3 DT P 3 " pdb=" C4 DT P 3 " pdb=" O4 DT P 3 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 44334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.59: 17485 30.59 - 61.17: 1488 61.17 - 91.76: 132 91.76 - 122.35: 0 122.35 - 152.94: 3 Dihedral angle restraints: 19108 sinusoidal: 9117 harmonic: 9991 Sorted by residual: dihedral pdb=" CA GLY I 358 " pdb=" C GLY I 358 " pdb=" N THR I 359 " pdb=" CA THR I 359 " ideal model delta harmonic sigma weight residual 180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA SER N 286 " pdb=" C SER N 286 " pdb=" N ARG N 287 " pdb=" CA ARG N 287 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLU F 282 " pdb=" C GLU F 282 " pdb=" N ARG F 283 " pdb=" CA ARG F 283 " ideal model delta harmonic sigma weight residual 180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 19105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3710 0.052 - 0.104: 848 0.104 - 0.156: 262 0.156 - 0.208: 13 0.208 - 0.260: 8 Chirality restraints: 4841 Sorted by residual: chirality pdb=" CB ILE M 351 " pdb=" CA ILE M 351 " pdb=" CG1 ILE M 351 " pdb=" CG2 ILE M 351 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE J 206 " pdb=" CA ILE J 206 " pdb=" CG1 ILE J 206 " pdb=" CG2 ILE J 206 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 456 " pdb=" CA ILE A 456 " pdb=" CG1 ILE A 456 " pdb=" CG2 ILE A 456 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 4838 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY N 118 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO N 119 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO N 119 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO N 119 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 12 " 0.033 2.00e-02 2.50e+03 1.73e-02 6.71e+00 pdb=" N1 C C 12 " -0.038 2.00e-02 2.50e+03 pdb=" C2 C C 12 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C C 12 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C C 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C C 12 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 12 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 12 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 334 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C VAL A 334 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 334 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 335 " 0.014 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 191 2.54 - 3.13: 21312 3.13 - 3.72: 47014 3.72 - 4.31: 63871 4.31 - 4.90: 106764 Nonbonded interactions: 239152 Sorted by model distance: nonbonded pdb=" OP1 A C 3 " pdb="MG MG C 101 " model vdw 1.948 2.170 nonbonded pdb=" OP1 A K 3 " pdb="MG MG I 501 " model vdw 2.088 2.170 nonbonded pdb=" OP1 DT Q 6 " pdb="MG MG B 501 " model vdw 2.136 2.170 nonbonded pdb=" OP3 A K 1 " pdb="MG MG I 501 " model vdw 2.142 2.170 nonbonded pdb=" OP1 DC R 5 " pdb="MG MG F 501 " model vdw 2.158 2.170 ... (remaining 239147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 160 or resid 180 through 485)) selection = (chain 'E' and (resid 2 through 160 or resid 180 through 485)) selection = (chain 'I' and resid 2 through 485) selection = (chain 'M' and resid 2 through 485) } ncs_group { reference = (chain 'B' and (resid 7 through 145 or resid 161 through 384 or resid 400 throug \ h 424)) selection = (chain 'F' and (resid 7 through 145 or resid 161 through 384 or resid 400 throug \ h 424)) selection = (chain 'J' and (resid 7 through 384 or resid 400 through 424)) selection = (chain 'N' and (resid 7 through 384 or resid 400 through 424)) } ncs_group { reference = (chain 'C' and resid 1 through 18) selection = (chain 'G' and resid 1 through 18) selection = chain 'K' selection = (chain 'O' and resid 1 through 18) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 2 through 19) selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } 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: 14.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.330 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32230 Z= 0.245 Angle : 0.731 10.323 44339 Z= 0.480 Chirality : 0.049 0.260 4841 Planarity : 0.005 0.088 5148 Dihedral : 19.838 152.937 12702 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 1.12 % Allowed : 31.71 % Favored : 67.18 % 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: -2.27 (0.13), residues: 3427 helix: -0.22 (0.17), residues: 904 sheet: -0.60 (0.20), residues: 733 loop : -2.69 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 218 TYR 0.030 0.001 TYR M 266 PHE 0.026 0.001 PHE J 403 TRP 0.018 0.001 TRP B 204 HIS 0.006 0.001 HIS N 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.25 (32230) covalent geometry : angle 0.73084 / 0.48 (44339) hydrogen bonds : bond 0.14608 / 10.16 ( 1017) hydrogen bonds : angle 6.31040 / 4.51 ( 2755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 66 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7018 (tp30) REVERT: F 212 TRP cc_start: 0.6172 (m100) cc_final: 0.5640 (m100) REVERT: M 14 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: N 187 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.3958 (mtt180) REVERT: N 344 TYR cc_start: 0.6907 (p90) cc_final: 0.6121 (p90) outliers start: 33 outliers final: 9 residues processed: 292 average time/residue: 0.2241 time to fit residues: 103.5846 Evaluate side-chains 258 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 237 LYS Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain M residue 14 GLU Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 456 ILE Chi-restraints excluded: chain N residue 187 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 ASN B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN M 392 HIS N 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.135860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.096215 restraints weight = 55123.588| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.49 r_work: 0.3061 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32230 Z= 0.199 Angle : 0.609 9.577 44339 Z= 0.335 Chirality : 0.044 0.248 4841 Planarity : 0.005 0.070 5148 Dihedral : 16.025 156.837 5955 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.53 % Allowed : 28.96 % Favored : 67.51 % 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: -1.99 (0.14), residues: 3427 helix: 0.46 (0.18), residues: 912 sheet: -0.80 (0.19), residues: 765 loop : -2.64 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 283 TYR 0.015 0.001 TYR N 343 PHE 0.018 0.001 PHE A 282 TRP 0.018 0.001 TRP J 212 HIS 0.005 0.001 HIS J 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (32230) covalent geometry : angle 0.60950 / 0.33 (44339) hydrogen bonds : bond 0.05496 / 3.74 ( 1017) hydrogen bonds : angle 5.08712 / 3.63 ( 2755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 254 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7974 (p0) REVERT: A 207 ASP cc_start: 0.7630 (t0) cc_final: 0.7406 (t0) REVERT: A 304 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7179 (m-70) REVERT: B 122 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8049 (mtp180) REVERT: F 37 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: F 66 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: F 212 TRP cc_start: 0.6487 (m100) cc_final: 0.5462 (m100) REVERT: F 328 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6358 (tm-30) REVERT: F 330 MET cc_start: 0.7880 (ptp) cc_final: 0.7458 (ptp) REVERT: J 346 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7563 (p) REVERT: M 120 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7578 (tpp80) REVERT: M 300 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8867 (m) REVERT: N 168 MET cc_start: 0.8120 (mmm) cc_final: 0.7883 (mmm) REVERT: N 169 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6523 (mt) REVERT: N 187 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.3847 (mtt90) REVERT: N 344 TYR cc_start: 0.7273 (p90) cc_final: 0.5674 (p90) REVERT: N 353 GLN cc_start: 0.5744 (OUTLIER) cc_final: 0.4670 (pm20) outliers start: 104 outliers final: 56 residues processed: 328 average time/residue: 0.2024 time to fit residues: 106.5018 Evaluate side-chains 307 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 240 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 330 MET Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 312 optimal weight: 9.9990 chunk 337 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.0270 chunk 265 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 300 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 chunk 197 optimal weight: 0.3980 chunk 63 optimal weight: 8.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 320 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099253 restraints weight = 54905.933| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.50 r_work: 0.3107 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32230 Z= 0.111 Angle : 0.528 8.277 44339 Z= 0.293 Chirality : 0.041 0.193 4841 Planarity : 0.004 0.061 5148 Dihedral : 15.911 157.890 5940 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.12 % Allowed : 29.09 % Favored : 67.79 % 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: -1.74 (0.14), residues: 3427 helix: 0.80 (0.18), residues: 923 sheet: -0.73 (0.19), residues: 765 loop : -2.55 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 218 TYR 0.012 0.001 TYR N 277 PHE 0.013 0.001 PHE M 282 TRP 0.016 0.001 TRP J 212 HIS 0.006 0.001 HIS M 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (32230) covalent geometry : angle 0.52775 / 0.29 (44339) hydrogen bonds : bond 0.04154 / 2.84 ( 1017) hydrogen bonds : angle 4.80603 / 3.42 ( 2755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 263 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7962 (p0) REVERT: B 51 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: E 234 MET cc_start: 0.8785 (mmt) cc_final: 0.8453 (mmt) REVERT: F 14 ILE cc_start: 0.8517 (mt) cc_final: 0.8152 (tp) REVERT: F 66 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7386 (tp30) REVERT: F 162 GLU cc_start: 0.8703 (pp20) cc_final: 0.8491 (pt0) REVERT: F 212 TRP cc_start: 0.6370 (m100) cc_final: 0.5402 (m100) REVERT: F 328 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6324 (tm-30) REVERT: I 420 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8698 (mt) REVERT: J 177 MET cc_start: 0.8224 (tmm) cc_final: 0.7995 (tmm) REVERT: J 346 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7557 (p) REVERT: N 23 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7124 (t80) REVERT: N 35 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7237 (mtm-85) REVERT: N 168 MET cc_start: 0.8157 (mmm) cc_final: 0.7745 (mmm) REVERT: N 187 ARG cc_start: 0.4983 (OUTLIER) cc_final: 0.3835 (mtt90) REVERT: N 344 TYR cc_start: 0.7288 (p90) cc_final: 0.5674 (p90) outliers start: 92 outliers final: 54 residues processed: 328 average time/residue: 0.2042 time to fit residues: 108.1020 Evaluate side-chains 308 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 215 HIS Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 76 optimal weight: 9.9990 chunk 92 optimal weight: 0.0060 chunk 287 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 305 optimal weight: 0.0870 chunk 306 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS B 320 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096831 restraints weight = 54772.029| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.51 r_work: 0.3065 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32230 Z= 0.170 Angle : 0.557 8.973 44339 Z= 0.307 Chirality : 0.043 0.221 4841 Planarity : 0.004 0.060 5148 Dihedral : 15.848 158.072 5935 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.04 % Allowed : 28.38 % Favored : 67.58 % 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: -1.70 (0.14), residues: 3427 helix: 0.95 (0.18), residues: 919 sheet: -0.77 (0.19), residues: 763 loop : -2.56 (0.13), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 187 TYR 0.015 0.001 TYR N 178 PHE 0.015 0.001 PHE A 282 TRP 0.015 0.001 TRP J 212 HIS 0.011 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (32230) covalent geometry : angle 0.55682 / 0.31 (44339) hydrogen bonds : bond 0.04804 / 3.25 ( 1017) hydrogen bonds : angle 4.77525 / 3.41 ( 2755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 251 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 206 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7973 (p0) REVERT: A 207 ASP cc_start: 0.7627 (t70) cc_final: 0.7401 (t0) REVERT: A 304 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7144 (m-70) REVERT: B 76 SER cc_start: 0.7018 (OUTLIER) cc_final: 0.6147 (t) REVERT: E 267 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8260 (ttt90) REVERT: F 14 ILE cc_start: 0.8555 (mt) cc_final: 0.8191 (tp) REVERT: F 37 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6410 (pm20) REVERT: F 126 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7366 (pt) REVERT: F 328 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6791 (tm-30) REVERT: F 330 MET cc_start: 0.8046 (ptp) cc_final: 0.7376 (ptp) REVERT: I 206 ASP cc_start: 0.7972 (t0) cc_final: 0.7752 (t0) REVERT: I 292 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8706 (mtpt) REVERT: I 420 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8766 (mt) REVERT: N 23 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6494 (t80) REVERT: N 187 ARG cc_start: 0.5003 (OUTLIER) cc_final: 0.3708 (mtt90) REVERT: N 323 PHE cc_start: 0.8190 (p90) cc_final: 0.7909 (p90) outliers start: 119 outliers final: 80 residues processed: 342 average time/residue: 0.2052 time to fit residues: 113.2288 Evaluate side-chains 338 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 247 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 14 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 320 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 150 optimal weight: 0.0670 chunk 300 optimal weight: 9.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 GLN E 118 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095288 restraints weight = 55221.020| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.51 r_work: 0.3040 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32230 Z= 0.191 Angle : 0.577 9.160 44339 Z= 0.317 Chirality : 0.044 0.238 4841 Planarity : 0.004 0.062 5148 Dihedral : 15.882 159.235 5935 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.78 % Allowed : 28.21 % Favored : 67.01 % 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: -1.77 (0.14), residues: 3427 helix: 0.94 (0.18), residues: 920 sheet: -0.89 (0.19), residues: 772 loop : -2.60 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 218 TYR 0.028 0.001 TYR N 335 PHE 0.018 0.001 PHE A 282 TRP 0.015 0.001 TRP J 212 HIS 0.009 0.001 HIS N 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (32230) covalent geometry : angle 0.57681 / 0.32 (44339) hydrogen bonds : bond 0.05217 / 3.52 ( 1017) hydrogen bonds : angle 4.78058 / 3.42 ( 2755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 250 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: A 206 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8089 (p0) REVERT: A 207 ASP cc_start: 0.7678 (t70) cc_final: 0.7453 (t0) REVERT: A 304 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7168 (m-70) REVERT: B 53 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: B 76 SER cc_start: 0.7016 (OUTLIER) cc_final: 0.6135 (t) REVERT: B 122 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8035 (mtp180) REVERT: E 61 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: E 267 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8242 (ttt90) REVERT: F 14 ILE cc_start: 0.8583 (mt) cc_final: 0.8320 (tp) REVERT: F 81 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7125 (tt) REVERT: F 126 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7336 (pt) REVERT: F 279 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5562 (tpm170) REVERT: F 328 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: F 330 MET cc_start: 0.8192 (ptp) cc_final: 0.7921 (ptp) REVERT: I 206 ASP cc_start: 0.8068 (t0) cc_final: 0.7778 (t0) REVERT: I 292 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8683 (mtpt) REVERT: I 420 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8790 (mt) REVERT: J 177 MET cc_start: 0.8288 (tmm) cc_final: 0.7988 (tmm) REVERT: J 247 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7376 (mt-10) REVERT: N 23 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.6580 (t80) REVERT: N 176 GLU cc_start: 0.6371 (tm-30) cc_final: 0.6134 (tm-30) REVERT: N 187 ARG cc_start: 0.5066 (OUTLIER) cc_final: 0.3662 (mtt90) REVERT: N 323 PHE cc_start: 0.8242 (p90) cc_final: 0.7993 (p90) REVERT: N 353 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5395 (mp10) outliers start: 141 outliers final: 88 residues processed: 359 average time/residue: 0.2052 time to fit residues: 119.3721 Evaluate side-chains 342 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 238 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 279 ARG Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 155 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 320 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 282 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095880 restraints weight = 55024.596| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.50 r_work: 0.3051 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32230 Z= 0.162 Angle : 0.555 9.126 44339 Z= 0.305 Chirality : 0.043 0.267 4841 Planarity : 0.004 0.061 5148 Dihedral : 15.866 159.645 5935 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.65 % Allowed : 28.21 % Favored : 67.14 % 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: -1.74 (0.14), residues: 3427 helix: 0.99 (0.18), residues: 920 sheet: -0.87 (0.19), residues: 779 loop : -2.61 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 283 TYR 0.020 0.001 TYR N 178 PHE 0.017 0.001 PHE J 211 TRP 0.015 0.001 TRP J 212 HIS 0.008 0.001 HIS N 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (32230) covalent geometry : angle 0.55476 / 0.30 (44339) hydrogen bonds : bond 0.04801 / 3.24 ( 1017) hydrogen bonds : angle 4.71826 / 3.37 ( 2755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 248 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: A 198 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7391 (tp40) REVERT: A 206 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8112 (p0) REVERT: A 207 ASP cc_start: 0.7657 (t70) cc_final: 0.7430 (t0) REVERT: A 304 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7143 (m-70) REVERT: B 53 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: B 76 SER cc_start: 0.6951 (OUTLIER) cc_final: 0.6090 (t) REVERT: E 15 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8115 (p90) REVERT: E 61 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: E 244 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6712 (mtt-85) REVERT: E 267 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8190 (ttt90) REVERT: F 14 ILE cc_start: 0.8570 (mt) cc_final: 0.8214 (tp) REVERT: F 37 GLU cc_start: 0.7097 (pt0) cc_final: 0.6753 (pm20) REVERT: F 116 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7140 (p0) REVERT: F 126 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7337 (pt) REVERT: F 151 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6944 (mp) REVERT: F 279 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5774 (tpm170) REVERT: F 283 ARG cc_start: 0.6057 (mpp-170) cc_final: 0.5652 (ptt-90) REVERT: F 328 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: F 330 MET cc_start: 0.8162 (ptp) cc_final: 0.7923 (ptp) REVERT: I 206 ASP cc_start: 0.8082 (t0) cc_final: 0.7769 (t0) REVERT: I 292 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8655 (mtpt) REVERT: I 420 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8766 (mt) REVERT: J 53 MET cc_start: 0.8401 (mpp) cc_final: 0.8170 (mpp) REVERT: J 247 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7358 (mt-10) REVERT: N 23 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.6504 (t80) REVERT: N 176 GLU cc_start: 0.6377 (tm-30) cc_final: 0.6138 (tm-30) REVERT: N 187 ARG cc_start: 0.5167 (OUTLIER) cc_final: 0.3703 (mtt90) REVERT: N 248 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.6321 (mp10) REVERT: N 323 PHE cc_start: 0.8267 (p90) cc_final: 0.8006 (p90) REVERT: N 353 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.5608 (mp10) outliers start: 137 outliers final: 91 residues processed: 355 average time/residue: 0.2052 time to fit residues: 118.8624 Evaluate side-chains 353 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 241 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 279 ARG Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 77 MET Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 211 ILE Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 248 GLN Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 344 TYR Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.0470 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 323 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS N 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093229 restraints weight = 55116.868| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.40 r_work: 0.3014 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 32230 Z= 0.245 Angle : 0.630 9.741 44339 Z= 0.341 Chirality : 0.046 0.260 4841 Planarity : 0.005 0.062 5148 Dihedral : 15.935 159.846 5935 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.50 % Favored : 88.44 % Rotamer: Outliers : 5.26 % Allowed : 27.91 % Favored : 66.84 % 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: -1.87 (0.14), residues: 3427 helix: 0.93 (0.18), residues: 908 sheet: -0.98 (0.19), residues: 757 loop : -2.66 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 218 TYR 0.015 0.002 TYR I 413 PHE 0.019 0.002 PHE A 282 TRP 0.013 0.002 TRP J 212 HIS 0.009 0.001 HIS N 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (32230) covalent geometry : angle 0.63012 / 0.34 (44339) hydrogen bonds : bond 0.05840 / 3.93 ( 1017) hydrogen bonds : angle 4.84697 / 3.47 ( 2755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 246 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: A 198 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7578 (tp40) REVERT: A 206 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8238 (p0) REVERT: A 207 ASP cc_start: 0.7904 (t70) cc_final: 0.7683 (t0) REVERT: A 304 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.7315 (m-70) REVERT: B 53 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8262 (mtp) REVERT: B 76 SER cc_start: 0.6998 (OUTLIER) cc_final: 0.6009 (t) REVERT: E 15 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8260 (p90) REVERT: E 61 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: E 244 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6925 (mtt-85) REVERT: E 267 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8345 (ttt90) REVERT: F 37 GLU cc_start: 0.7203 (pt0) cc_final: 0.6752 (pm20) REVERT: F 81 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7039 (tt) REVERT: F 121 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: F 126 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7322 (pt) REVERT: F 151 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6977 (mp) REVERT: F 212 TRP cc_start: 0.6554 (m100) cc_final: 0.5398 (m100) REVERT: F 328 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: F 330 MET cc_start: 0.8293 (ptp) cc_final: 0.8075 (ptp) REVERT: I 206 ASP cc_start: 0.8267 (t0) cc_final: 0.7878 (t70) REVERT: I 292 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8809 (mtpt) REVERT: I 420 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8921 (mt) REVERT: J 247 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7559 (mt-10) REVERT: J 382 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9045 (mp) REVERT: N 23 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.6761 (t80) REVERT: N 176 GLU cc_start: 0.6551 (tm-30) cc_final: 0.6327 (tm-30) REVERT: N 187 ARG cc_start: 0.5365 (OUTLIER) cc_final: 0.3692 (mtt90) REVERT: N 248 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6397 (mp10) REVERT: N 323 PHE cc_start: 0.8311 (p90) cc_final: 0.8048 (p90) REVERT: N 353 GLN cc_start: 0.5883 (OUTLIER) cc_final: 0.5650 (mp10) outliers start: 155 outliers final: 105 residues processed: 369 average time/residue: 0.2065 time to fit residues: 123.1582 Evaluate side-chains 363 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 236 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 201 TRP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 421 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 382 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 77 MET Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 248 GLN Chi-restraints excluded: chain N residue 252 SER Chi-restraints excluded: chain N residue 330 MET Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 344 TYR Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 330 optimal weight: 3.9990 chunk 345 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 340 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 302 optimal weight: 0.0010 chunk 341 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 GLN ** 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 = 0.3800 r_free = 0.3800 target = 0.134506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095748 restraints weight = 54736.482| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.49 r_work: 0.3050 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32230 Z= 0.141 Angle : 0.556 8.927 44339 Z= 0.305 Chirality : 0.042 0.228 4841 Planarity : 0.004 0.061 5148 Dihedral : 15.923 160.299 5935 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.98 % Favored : 89.99 % Rotamer: Outliers : 4.37 % Allowed : 28.86 % Favored : 66.77 % 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: -1.74 (0.14), residues: 3427 helix: 1.01 (0.18), residues: 918 sheet: -0.88 (0.19), residues: 753 loop : -2.58 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 279 TYR 0.020 0.001 TYR N 178 PHE 0.024 0.001 PHE N 403 TRP 0.018 0.001 TRP J 212 HIS 0.008 0.001 HIS N 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (32230) covalent geometry : angle 0.55565 / 0.30 (44339) hydrogen bonds : bond 0.04694 / 3.16 ( 1017) hydrogen bonds : angle 4.70933 / 3.37 ( 2755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 243 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: A 198 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7375 (tp40) REVERT: A 206 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8208 (p0) REVERT: A 207 ASP cc_start: 0.7752 (t70) cc_final: 0.7549 (t0) REVERT: A 304 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7078 (m-70) REVERT: B 53 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8031 (mtp) REVERT: B 76 SER cc_start: 0.7019 (OUTLIER) cc_final: 0.6091 (t) REVERT: E 15 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8153 (p90) REVERT: E 267 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8145 (ttt90) REVERT: F 37 GLU cc_start: 0.7107 (pt0) cc_final: 0.6673 (pm20) REVERT: F 121 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6911 (pt0) REVERT: F 126 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7324 (pt) REVERT: F 151 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6910 (mp) REVERT: F 212 TRP cc_start: 0.6443 (m100) cc_final: 0.5278 (m100) REVERT: F 238 GLU cc_start: 0.7305 (pm20) cc_final: 0.6110 (tm-30) REVERT: F 328 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: F 367 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.6909 (mmtt) REVERT: I 206 ASP cc_start: 0.8052 (t0) cc_final: 0.7731 (t0) REVERT: I 292 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8595 (mtpt) REVERT: I 420 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8756 (mt) REVERT: J 247 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7369 (mt-10) REVERT: N 23 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.6592 (t80) REVERT: N 176 GLU cc_start: 0.6484 (tm-30) cc_final: 0.6282 (tm-30) REVERT: N 187 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.3626 (mtt90) REVERT: N 248 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.6311 (mp10) outliers start: 129 outliers final: 94 residues processed: 344 average time/residue: 0.1984 time to fit residues: 111.4217 Evaluate side-chains 347 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 235 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 421 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 77 MET Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 248 GLN Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 344 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 65 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 156 optimal weight: 0.0030 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093869 restraints weight = 55158.037| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.43 r_work: 0.3002 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 32230 Z= 0.250 Angle : 0.643 9.971 44339 Z= 0.348 Chirality : 0.046 0.269 4841 Planarity : 0.005 0.063 5148 Dihedral : 15.996 160.262 5935 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.79 % Favored : 88.15 % Rotamer: Outliers : 4.58 % Allowed : 28.93 % Favored : 66.50 % 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: -1.90 (0.14), residues: 3427 helix: 0.87 (0.18), residues: 912 sheet: -1.02 (0.19), residues: 757 loop : -2.66 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 279 TYR 0.015 0.002 TYR N 277 PHE 0.019 0.002 PHE A 282 TRP 0.015 0.002 TRP J 212 HIS 0.012 0.001 HIS J 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (32230) covalent geometry : angle 0.64317 / 0.35 (44339) hydrogen bonds : bond 0.05967 / 4.01 ( 1017) hydrogen bonds : angle 4.86266 / 3.48 ( 2755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 238 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: A 198 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7379 (tp40) REVERT: A 206 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8320 (p0) REVERT: A 207 ASP cc_start: 0.7716 (t70) cc_final: 0.7491 (t0) REVERT: A 304 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.7215 (m-70) REVERT: B 53 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8132 (mtp) REVERT: B 76 SER cc_start: 0.7006 (OUTLIER) cc_final: 0.6040 (t) REVERT: B 79 TYR cc_start: 0.7376 (t80) cc_final: 0.7160 (t80) REVERT: B 200 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5401 (mptt) REVERT: E 15 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8202 (p90) REVERT: E 61 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: E 244 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.6740 (mtt-85) REVERT: E 267 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8232 (ttt90) REVERT: F 121 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6930 (pt0) REVERT: F 126 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7407 (pt) REVERT: F 151 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6945 (mp) REVERT: F 212 TRP cc_start: 0.6514 (m100) cc_final: 0.5325 (m100) REVERT: F 328 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: F 367 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.6988 (mmtt) REVERT: I 206 ASP cc_start: 0.8080 (t0) cc_final: 0.7598 (t0) REVERT: I 292 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8744 (mtpt) REVERT: I 420 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8843 (mt) REVERT: J 53 MET cc_start: 0.8557 (mpp) cc_final: 0.8269 (mpp) REVERT: J 247 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7394 (mt-10) REVERT: N 23 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.6887 (t80) REVERT: N 55 ARG cc_start: 0.7974 (mmt180) cc_final: 0.7614 (mmp-170) REVERT: N 248 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6347 (mp10) outliers start: 135 outliers final: 103 residues processed: 343 average time/residue: 0.2035 time to fit residues: 113.5027 Evaluate side-chains 351 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 228 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 201 TRP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 400 TYR Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 421 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 211 ILE Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 248 GLN Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 344 TYR Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 254 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 309 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 330 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.133796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094845 restraints weight = 54855.860| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.41 r_work: 0.3041 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32230 Z= 0.156 Angle : 0.576 8.989 44339 Z= 0.314 Chirality : 0.043 0.236 4841 Planarity : 0.004 0.062 5148 Dihedral : 15.986 160.704 5931 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.33 % Favored : 89.64 % Rotamer: Outliers : 4.07 % Allowed : 29.40 % Favored : 66.53 % 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: -1.78 (0.14), residues: 3427 helix: 0.97 (0.18), residues: 920 sheet: -0.95 (0.19), residues: 756 loop : -2.58 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 120 TYR 0.015 0.001 TYR M 266 PHE 0.029 0.001 PHE N 403 TRP 0.017 0.001 TRP J 212 HIS 0.011 0.001 HIS J 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (32230) covalent geometry : angle 0.57623 / 0.31 (44339) hydrogen bonds : bond 0.04847 / 3.26 ( 1017) hydrogen bonds : angle 4.74788 / 3.39 ( 2755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 239 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: A 198 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7603 (tp40) REVERT: A 206 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8344 (p0) REVERT: A 304 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7171 (m-70) REVERT: B 53 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: B 76 SER cc_start: 0.6870 (OUTLIER) cc_final: 0.5912 (t) REVERT: B 200 LYS cc_start: 0.5719 (OUTLIER) cc_final: 0.5366 (mptt) REVERT: E 15 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8287 (p90) REVERT: E 61 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: E 244 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.6936 (mtt-85) REVERT: E 267 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8201 (ttt90) REVERT: F 121 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: F 126 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7339 (pt) REVERT: F 151 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6970 (mp) REVERT: F 168 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8063 (ttm) REVERT: F 212 TRP cc_start: 0.6513 (m100) cc_final: 0.5289 (m100) REVERT: F 238 GLU cc_start: 0.7545 (pm20) cc_final: 0.6235 (tm-30) REVERT: F 328 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: F 367 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.6921 (mmtt) REVERT: I 206 ASP cc_start: 0.8257 (t0) cc_final: 0.7887 (t70) REVERT: I 292 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8686 (mtpt) REVERT: I 420 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8877 (mt) REVERT: J 53 MET cc_start: 0.8547 (mpp) cc_final: 0.8292 (mpp) REVERT: J 247 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7559 (mt-10) REVERT: J 402 MET cc_start: 0.8301 (mtt) cc_final: 0.8033 (mtp) REVERT: N 23 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.6815 (t80) REVERT: N 55 ARG cc_start: 0.8032 (mmt180) cc_final: 0.7705 (mmp-170) REVERT: N 187 ARG cc_start: 0.5821 (mmp80) cc_final: 0.3816 (mtm180) REVERT: N 248 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6395 (mp10) outliers start: 120 outliers final: 95 residues processed: 331 average time/residue: 0.2014 time to fit residues: 108.7859 Evaluate side-chains 348 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 232 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 400 TYR Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 421 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 194 SER Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 248 GLN Chi-restraints excluded: chain N residue 317 PHE Chi-restraints excluded: chain N residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 307 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 chunk 272 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 335 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 GLN ** 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 = 0.3805 r_free = 0.3805 target = 0.134852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096268 restraints weight = 54845.797| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.50 r_work: 0.3058 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32230 Z= 0.136 Angle : 0.561 9.035 44339 Z= 0.305 Chirality : 0.042 0.218 4841 Planarity : 0.004 0.059 5148 Dihedral : 15.956 160.456 5931 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.87 % Allowed : 29.50 % Favored : 66.63 % 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: -1.66 (0.14), residues: 3427 helix: 1.08 (0.18), residues: 921 sheet: -0.81 (0.19), residues: 771 loop : -2.57 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 218 TYR 0.014 0.001 TYR M 266 PHE 0.018 0.001 PHE F 354 TRP 0.017 0.001 TRP J 212 HIS 0.011 0.001 HIS J 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (32230) covalent geometry : angle 0.56078 / 0.31 (44339) hydrogen bonds : bond 0.04404 / 2.95 ( 1017) hydrogen bonds : angle 4.65185 / 3.32 ( 2755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8696.77 seconds wall clock time: 149 minutes 35.86 seconds (8975.86 seconds total)