Starting phenix.real_space_refine on Mon Aug 25 21:27:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jt2_61790/08_2025/9jt2_61790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jt2_61790/08_2025/9jt2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2025/9jt2_61790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2025/9jt2_61790.map" model { file = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2025/9jt2_61790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jt2_61790/08_2025/9jt2_61790.cif" } 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-2.0-5787/lib/python3.9/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: 6.83, per 1000 atoms: 0.22 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 3.98 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: 5.18 Time building geometry restraints manager: 2.80 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=" 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=" CA ILE M 456 " pdb=" C ILE M 456 " ideal model delta sigma weight residual 1.520 1.538 -0.019 8.80e-03 1.29e+04 4.49e+00 bond pdb=" CA ILE M 456 " pdb=" CB ILE M 456 " ideal model delta sigma weight residual 1.534 1.548 -0.014 6.80e-03 2.16e+04 4.17e+00 bond pdb=" C ASP N 216 " pdb=" N PRO N 217 " ideal model delta sigma weight residual 1.332 1.349 -0.017 8.20e-03 1.49e+04 4.12e+00 bond pdb=" C3' DT D 18 " pdb=" O3' DT D 18 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.36e+00 ... (remaining 32225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 43350 2.06 - 4.13: 864 4.13 - 6.19: 99 6.19 - 8.26: 14 8.26 - 10.32: 12 Bond angle restraints: 44339 Sorted by residual: angle pdb=" N ILE A 112 " pdb=" CA ILE A 112 " pdb=" C ILE A 112 " ideal model delta sigma weight residual 111.91 108.52 3.39 8.90e-01 1.26e+00 1.45e+01 angle pdb=" C ARG B 283 " pdb=" N GLU B 284 " pdb=" CA GLU B 284 " ideal model delta sigma weight residual 122.36 127.63 -5.27 1.42e+00 4.96e-01 1.38e+01 angle pdb=" N GLY I 66 " pdb=" CA GLY I 66 " pdb=" C GLY I 66 " ideal model delta sigma weight residual 113.18 121.77 -8.59 2.37e+00 1.78e-01 1.31e+01 angle pdb=" N LYS N 188 " pdb=" CA LYS N 188 " pdb=" C LYS N 188 " ideal model delta sigma weight residual 113.02 108.73 4.29 1.20e+00 6.94e-01 1.28e+01 angle pdb=" CB GLU A 473 " pdb=" CG GLU A 473 " pdb=" CD GLU A 473 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.70e+00 3.46e-01 1.24e+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: 3865 0.052 - 0.104: 774 0.104 - 0.156: 183 0.156 - 0.208: 11 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: 11.820 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 27.650 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 0.055 32230 Z= 0.162 Angle : 0.693 10.323 44339 Z= 0.383 Chirality : 0.045 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 aren 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 covalent geometry : bond 0.00311 (32230) covalent geometry : angle 0.69264 (44339) hydrogen bonds : bond 0.14608 ( 1017) hydrogen bonds : angle 6.31040 ( 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 : 1.008 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: 0.4733 (OUTLIER) cc_final: 0.3986 (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: 0.2010 time to fit residues: 92.3368 Evaluate side-chains 257 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 245 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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: 0.9990 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: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN 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 392 HIS M 424 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095463 restraints weight = 55139.095| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.50 r_work: 0.3048 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32230 Z= 0.216 Angle : 0.608 9.901 44339 Z= 0.329 Chirality : 0.044 0.256 4841 Planarity : 0.005 0.073 5148 Dihedral : 16.015 159.127 5955 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.76 % Allowed : 29.06 % 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 aren not related in a simple way. whole: -2.02 (0.14), residues: 3427 helix: 0.43 (0.18), residues: 928 sheet: -0.85 (0.19), residues: 758 loop : -2.66 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 283 TYR 0.017 0.001 TYR N 343 PHE 0.020 0.002 PHE A 282 TRP 0.019 0.001 TRP J 212 HIS 0.006 0.001 HIS N 379 Details of bonding type rmsd covalent geometry : bond 0.00509 (32230) covalent geometry : angle 0.60835 (44339) hydrogen bonds : bond 0.05428 ( 1017) hydrogen bonds : angle 5.04330 ( 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 360 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 249 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 206 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8033 (p0) REVERT: A 304 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7233 (m-70) REVERT: B 289 PHE cc_start: 0.8231 (m-80) cc_final: 0.8018 (m-80) REVERT: F 14 ILE cc_start: 0.8548 (mt) cc_final: 0.8287 (tp) REVERT: F 37 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6415 (pm20) REVERT: F 66 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: F 328 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: I 25 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8464 (mtt180) REVERT: J 187 ARG cc_start: 0.7168 (ppt170) cc_final: 0.6806 (ptt-90) REVERT: J 346 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7568 (p) REVERT: M 120 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7583 (tpp80) REVERT: M 300 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8850 (m) REVERT: N 23 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7496 (t80) REVERT: N 168 MET cc_start: 0.8115 (mmm) cc_final: 0.7883 (mmm) REVERT: N 187 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.3889 (mtt90) REVERT: N 344 TYR cc_start: 0.7243 (p90) cc_final: 0.5646 (p90) REVERT: N 353 GLN cc_start: 0.5652 (OUTLIER) cc_final: 0.4595 (pm20) outliers start: 111 outliers final: 61 residues processed: 333 average time/residue: 0.2052 time to fit residues: 108.0270 Evaluate side-chains 307 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 235 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 155 LEU Chi-restraints excluded: chain A residue 158 VAL 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 424 HIS Chi-restraints excluded: chain A residue 447 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 349 TYR 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 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 113 VAL 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 25 ARG 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 343 LYS Chi-restraints excluded: chain I residue 369 GLU 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 237 LYS 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 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 74 HIS 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 280 GLN 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 23 PHE Chi-restraints excluded: chain N residue 187 ARG 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: 8.9990 chunk 337 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 301 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 197 optimal weight: 0.0270 chunk 63 optimal weight: 7.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 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 = 0.3833 r_free = 0.3833 target = 0.137012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098176 restraints weight = 54977.114| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.49 r_work: 0.3091 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32230 Z= 0.116 Angle : 0.525 8.239 44339 Z= 0.284 Chirality : 0.041 0.208 4841 Planarity : 0.004 0.065 5148 Dihedral : 15.844 160.350 5944 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.53 % Allowed : 29.03 % Favored : 67.45 % 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 aren not related in a simple way. whole: -1.75 (0.14), residues: 3427 helix: 0.84 (0.18), residues: 920 sheet: -0.79 (0.19), residues: 768 loop : -2.57 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 218 TYR 0.016 0.001 TYR N 178 PHE 0.011 0.001 PHE M 282 TRP 0.016 0.001 TRP J 212 HIS 0.006 0.001 HIS N 379 Details of bonding type rmsd covalent geometry : bond 0.00259 (32230) covalent geometry : angle 0.52531 (44339) hydrogen bonds : bond 0.03990 ( 1017) hydrogen bonds : angle 4.74428 ( 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 367 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 263 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 206 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7989 (p0) REVERT: B 122 ARG cc_start: 0.8480 (mtm180) cc_final: 0.7964 (mtp180) REVERT: B 289 PHE cc_start: 0.8215 (m-80) cc_final: 0.7945 (m-80) REVERT: E 267 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8231 (ttt90) REVERT: F 14 ILE cc_start: 0.8525 (mt) cc_final: 0.8164 (tp) REVERT: F 126 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7400 (pt) REVERT: F 212 TRP cc_start: 0.6418 (m100) cc_final: 0.5401 (m100) REVERT: F 238 GLU cc_start: 0.7425 (pm20) cc_final: 0.6193 (tm-30) REVERT: F 283 ARG cc_start: 0.6130 (mpp-170) cc_final: 0.5824 (ptt-90) REVERT: F 328 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: I 420 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8729 (mt) REVERT: J 177 MET cc_start: 0.8106 (tmm) cc_final: 0.7880 (tmm) REVERT: M 300 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8869 (m) REVERT: N 168 MET cc_start: 0.8203 (mmm) cc_final: 0.7808 (mmm) REVERT: N 187 ARG cc_start: 0.5093 (OUTLIER) cc_final: 0.3894 (mtt90) REVERT: N 323 PHE cc_start: 0.8172 (p90) cc_final: 0.7906 (p90) REVERT: N 344 TYR cc_start: 0.7244 (p90) cc_final: 0.5683 (p90) outliers start: 104 outliers final: 59 residues processed: 339 average time/residue: 0.1855 time to fit residues: 100.5176 Evaluate side-chains 313 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL 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 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 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 267 ARG Chi-restraints excluded: chain E residue 280 GLN 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 81 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 126 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 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 413 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 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 235 ASN Chi-restraints excluded: chain J residue 237 LYS Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain M residue 29 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 298 THR Chi-restraints excluded: chain M residue 300 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 76 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 305 optimal weight: 0.3980 chunk 306 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 240 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 118 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097796 restraints weight = 54712.345| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.52 r_work: 0.3082 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32230 Z= 0.127 Angle : 0.523 8.720 44339 Z= 0.283 Chirality : 0.041 0.202 4841 Planarity : 0.004 0.061 5148 Dihedral : 15.785 160.641 5939 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.00 % Allowed : 28.62 % Favored : 67.38 % 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 aren not related in a simple way. whole: -1.63 (0.14), residues: 3427 helix: 1.03 (0.18), residues: 919 sheet: -0.72 (0.19), residues: 766 loop : -2.53 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 218 TYR 0.017 0.001 TYR N 342 PHE 0.012 0.001 PHE A 282 TRP 0.015 0.001 TRP J 212 HIS 0.008 0.001 HIS N 379 Details of bonding type rmsd covalent geometry : bond 0.00291 (32230) covalent geometry : angle 0.52257 (44339) hydrogen bonds : bond 0.04013 ( 1017) hydrogen bonds : angle 4.62598 ( 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 377 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 259 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: A 206 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8048 (p0) REVERT: A 304 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7851 (m90) REVERT: B 289 PHE cc_start: 0.8292 (m-80) cc_final: 0.8002 (m-80) REVERT: E 267 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8229 (ttt90) REVERT: F 14 ILE cc_start: 0.8539 (mt) cc_final: 0.8169 (tp) REVERT: F 37 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6376 (pm20) REVERT: F 126 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7436 (pt) REVERT: F 283 ARG cc_start: 0.6121 (mpp-170) cc_final: 0.5891 (ptt-90) REVERT: F 328 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: I 25 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8435 (mtt180) REVERT: I 206 ASP cc_start: 0.8028 (t70) cc_final: 0.7804 (t0) REVERT: I 292 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8662 (mtpt) REVERT: I 420 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8752 (mt) REVERT: J 247 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7310 (mt-10) REVERT: M 74 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.5970 (p90) REVERT: M 300 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8848 (m) REVERT: N 23 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.6764 (t80) REVERT: N 140 LYS cc_start: 0.8095 (ptmt) cc_final: 0.7788 (ttmm) REVERT: N 187 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.3862 (mtt90) REVERT: N 323 PHE cc_start: 0.8226 (p90) cc_final: 0.7956 (p90) REVERT: N 344 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.5493 (p90) outliers start: 118 outliers final: 75 residues processed: 349 average time/residue: 0.1868 time to fit residues: 104.2155 Evaluate side-chains 332 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 242 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 95 GLU Chi-restraints excluded: chain A residue 145 VAL 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 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 430 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 25 THR 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 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 26 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 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 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 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 F residue 413 VAL Chi-restraints excluded: chain I residue 25 ARG 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 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 237 LYS 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 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 300 SER 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 344 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 14 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 320 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 182 optimal weight: 0.0970 chunk 87 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 150 optimal weight: 0.0170 chunk 300 optimal weight: 10.0000 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097705 restraints weight = 55076.087| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.50 r_work: 0.3080 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32230 Z= 0.129 Angle : 0.519 8.289 44339 Z= 0.281 Chirality : 0.041 0.195 4841 Planarity : 0.004 0.060 5148 Dihedral : 15.764 161.490 5939 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.44 % Allowed : 28.55 % 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 aren not related in a simple way. whole: -1.55 (0.14), residues: 3427 helix: 1.13 (0.18), residues: 918 sheet: -0.66 (0.19), residues: 763 loop : -2.50 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 218 TYR 0.018 0.001 TYR N 178 PHE 0.018 0.001 PHE J 211 TRP 0.016 0.001 TRP J 212 HIS 0.008 0.001 HIS N 379 Details of bonding type rmsd covalent geometry : bond 0.00296 (32230) covalent geometry : angle 0.51941 (44339) hydrogen bonds : bond 0.03983 ( 1017) hydrogen bonds : angle 4.56745 ( 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 387 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 256 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: A 206 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8022 (p0) REVERT: A 207 ASP cc_start: 0.7612 (t70) cc_final: 0.7403 (t0) REVERT: A 304 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7869 (m90) REVERT: B 53 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: B 289 PHE cc_start: 0.8394 (m-80) cc_final: 0.8079 (m-80) REVERT: E 267 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8225 (ttt90) REVERT: F 14 ILE cc_start: 0.8559 (mt) cc_final: 0.8199 (tp) REVERT: F 37 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6321 (pm20) REVERT: F 126 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7413 (pt) REVERT: F 238 GLU cc_start: 0.7455 (pm20) cc_final: 0.6347 (tm-30) REVERT: F 283 ARG cc_start: 0.6122 (mpp-170) cc_final: 0.5920 (ptt-90) REVERT: F 328 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: I 206 ASP cc_start: 0.8070 (t70) cc_final: 0.7856 (t0) REVERT: I 292 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8664 (mtpt) REVERT: I 420 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8769 (mt) REVERT: J 177 MET cc_start: 0.8189 (tmm) cc_final: 0.7898 (tmm) REVERT: J 247 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7281 (mt-10) REVERT: M 300 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8855 (m) REVERT: N 23 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.6575 (t80) REVERT: N 140 LYS cc_start: 0.8094 (ptmt) cc_final: 0.7813 (ttmm) REVERT: N 169 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6537 (mm) REVERT: N 187 ARG cc_start: 0.5095 (OUTLIER) cc_final: 0.3778 (mtt90) REVERT: N 323 PHE cc_start: 0.8206 (p90) cc_final: 0.7949 (p90) outliers start: 131 outliers final: 86 residues processed: 357 average time/residue: 0.2023 time to fit residues: 115.6671 Evaluate side-chains 344 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 244 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 145 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 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 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 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 214 PHE 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 26 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 476 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 9 GLN 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 349 TYR Chi-restraints excluded: chain F residue 375 VAL 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 237 LYS 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 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 300 SER 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 420 LEU Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 442 LYS 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 131 ASP Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 169 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 344 TYR 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: 4.9990 chunk 80 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 224 optimal weight: 0.0870 chunk 10 optimal weight: 10.0000 chunk 320 optimal weight: 0.0270 chunk 94 optimal weight: 0.9980 chunk 342 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 282 optimal weight: 0.4980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 51 GLN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 353 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 = 0.3852 r_free = 0.3852 target = 0.138400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099920 restraints weight = 54910.097| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.48 r_work: 0.3119 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32230 Z= 0.100 Angle : 0.500 9.546 44339 Z= 0.269 Chirality : 0.040 0.182 4841 Planarity : 0.003 0.057 5148 Dihedral : 15.727 161.757 5939 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.73 % Allowed : 29.16 % Favored : 67.11 % 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 aren not related in a simple way. whole: -1.43 (0.14), residues: 3427 helix: 1.22 (0.18), residues: 924 sheet: -0.51 (0.19), residues: 763 loop : -2.48 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 218 TYR 0.012 0.001 TYR M 266 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 covalent geometry : bond 0.00220 (32230) covalent geometry : angle 0.49979 (44339) hydrogen bonds : bond 0.03338 ( 1017) hydrogen bonds : angle 4.43961 ( 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 373 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 263 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: A 304 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7577 (m90) REVERT: B 53 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7775 (mtp) REVERT: B 289 PHE cc_start: 0.8320 (m-80) cc_final: 0.8044 (m-80) REVERT: E 15 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.8005 (p90) REVERT: E 234 MET cc_start: 0.8832 (mmt) cc_final: 0.8510 (mmt) REVERT: F 14 ILE cc_start: 0.8533 (mt) cc_final: 0.8065 (tp) REVERT: F 116 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7215 (p0) REVERT: F 126 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7515 (pt) REVERT: F 212 TRP cc_start: 0.6297 (m100) cc_final: 0.5377 (m100) REVERT: F 283 ARG cc_start: 0.6094 (mpp-170) cc_final: 0.5746 (ptt-90) REVERT: F 328 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: F 367 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.6793 (mmtt) REVERT: I 25 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8357 (mtt180) REVERT: I 206 ASP cc_start: 0.8051 (t70) cc_final: 0.7847 (t0) REVERT: I 292 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8631 (mtpt) REVERT: I 420 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8698 (mt) REVERT: J 53 MET cc_start: 0.8497 (mpp) cc_final: 0.8163 (mpp) REVERT: J 177 MET cc_start: 0.8261 (tmm) cc_final: 0.7927 (tmm) REVERT: J 402 MET cc_start: 0.8170 (mtt) cc_final: 0.7967 (mtp) REVERT: M 300 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8841 (m) REVERT: N 23 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.6480 (t80) REVERT: N 140 LYS cc_start: 0.8100 (ptmt) cc_final: 0.7817 (ttmm) REVERT: N 187 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.3685 (mtt90) REVERT: N 202 PHE cc_start: 0.6677 (t80) cc_final: 0.6321 (t80) REVERT: N 323 PHE cc_start: 0.8179 (p90) cc_final: 0.7910 (p90) outliers start: 110 outliers final: 67 residues processed: 343 average time/residue: 0.1960 time to fit residues: 107.7785 Evaluate side-chains 331 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 250 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 145 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 215 VAL 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 383 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 321 HIS 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 77 MET Chi-restraints excluded: chain E residue 215 VAL 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 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 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 328 GLU Chi-restraints excluded: chain F residue 329 LEU 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 I residue 25 ARG 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 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 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 237 LYS Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU 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 300 SER 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 420 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 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 339 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 223 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 203 optimal weight: 0.0370 chunk 323 optimal weight: 0.0070 chunk 144 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 353 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 = 0.3869 r_free = 0.3869 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101338 restraints weight = 54933.837| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.40 r_work: 0.3148 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32230 Z= 0.097 Angle : 0.493 7.867 44339 Z= 0.264 Chirality : 0.039 0.183 4841 Planarity : 0.003 0.054 5148 Dihedral : 15.672 161.800 5939 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.26 % Allowed : 29.60 % 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 aren not related in a simple way. whole: -1.28 (0.14), residues: 3427 helix: 1.25 (0.18), residues: 943 sheet: -0.38 (0.19), residues: 756 loop : -2.38 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 93 TYR 0.011 0.001 TYR M 266 PHE 0.015 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 covalent geometry : bond 0.00213 (32230) covalent geometry : angle 0.49342 (44339) hydrogen bonds : bond 0.03110 ( 1017) hydrogen bonds : angle 4.31648 ( 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 372 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 276 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: A 206 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8003 (p0) REVERT: B 53 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7619 (mtp) REVERT: B 289 PHE cc_start: 0.8235 (m-80) cc_final: 0.7965 (m-80) REVERT: E 15 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.8013 (p90) REVERT: E 372 THR cc_start: 0.8266 (m) cc_final: 0.7978 (m) REVERT: F 13 GLU cc_start: 0.8197 (tp30) cc_final: 0.7971 (tp30) REVERT: F 14 ILE cc_start: 0.8490 (mt) cc_final: 0.8101 (tp) REVERT: F 238 GLU cc_start: 0.7389 (pm20) cc_final: 0.6192 (tm-30) REVERT: F 283 ARG cc_start: 0.6035 (mpp-170) cc_final: 0.5717 (ptt-90) REVERT: F 328 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: F 367 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6685 (mmtt) REVERT: I 25 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8415 (mtt180) REVERT: I 127 ASP cc_start: 0.8025 (m-30) cc_final: 0.7812 (m-30) REVERT: I 158 VAL cc_start: 0.8002 (t) cc_final: 0.7753 (p) REVERT: I 292 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8644 (mtpt) REVERT: I 420 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8651 (mt) REVERT: J 53 MET cc_start: 0.8497 (mpp) cc_final: 0.8214 (mpp) REVERT: J 177 MET cc_start: 0.8443 (tmm) cc_final: 0.8096 (tmm) REVERT: N 23 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.6325 (t80) REVERT: N 140 LYS cc_start: 0.8094 (ptmt) cc_final: 0.7830 (ttmm) REVERT: N 187 ARG cc_start: 0.5048 (OUTLIER) cc_final: 0.3672 (mtt90) REVERT: N 202 PHE cc_start: 0.6671 (t80) cc_final: 0.6311 (t80) REVERT: N 323 PHE cc_start: 0.8287 (p90) cc_final: 0.8041 (p90) outliers start: 96 outliers final: 66 residues processed: 343 average time/residue: 0.2048 time to fit residues: 112.6639 Evaluate side-chains 335 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 145 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 215 VAL 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 447 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 321 HIS 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 26 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 329 THR 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 25 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 94 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 328 GLU Chi-restraints excluded: chain F residue 329 LEU 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 I residue 25 ARG Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN 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 47 MET Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 237 LYS Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain M residue 63 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 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 420 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 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 339 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 330 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 340 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 302 optimal weight: 0.0070 chunk 341 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 ASN N 8 ASN ** N 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095215 restraints weight = 55052.899| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.40 r_work: 0.3020 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 32230 Z= 0.246 Angle : 0.628 9.633 44339 Z= 0.335 Chirality : 0.045 0.214 4841 Planarity : 0.005 0.059 5148 Dihedral : 15.814 162.344 5939 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.21 % Favored : 88.77 % Rotamer: Outliers : 3.97 % Allowed : 28.69 % Favored : 67.34 % 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 aren not related in a simple way. whole: -1.62 (0.14), residues: 3427 helix: 1.07 (0.18), residues: 922 sheet: -0.77 (0.19), residues: 749 loop : -2.51 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 218 TYR 0.014 0.002 TYR N 343 PHE 0.020 0.002 PHE A 282 TRP 0.015 0.002 TRP J 420 HIS 0.010 0.001 HIS J 320 Details of bonding type rmsd covalent geometry : bond 0.00587 (32230) covalent geometry : angle 0.62824 (44339) hydrogen bonds : bond 0.05786 ( 1017) hydrogen bonds : angle 4.73054 ( 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 366 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 249 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: A 206 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8147 (p0) REVERT: A 304 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.7174 (m-70) REVERT: B 53 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8055 (mtp) REVERT: B 76 SER cc_start: 0.6882 (OUTLIER) cc_final: 0.6033 (t) REVERT: E 15 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8133 (p90) REVERT: F 14 ILE cc_start: 0.8595 (mt) cc_final: 0.8265 (tp) REVERT: F 116 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7426 (p0) REVERT: F 151 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7044 (mp) REVERT: F 212 TRP cc_start: 0.6578 (m100) cc_final: 0.5418 (m100) REVERT: F 283 ARG cc_start: 0.6258 (mpp-170) cc_final: 0.5872 (ptt-90) REVERT: F 328 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: I 292 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: J 237 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7578 (mmmt) REVERT: J 247 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7559 (mt-10) REVERT: N 23 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.6634 (t80) REVERT: N 140 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7890 (ttmm) REVERT: N 202 PHE cc_start: 0.6705 (t80) cc_final: 0.6289 (t80) REVERT: N 248 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.6283 (mp10) REVERT: N 266 ASP cc_start: 0.4768 (p0) cc_final: 0.4521 (p0) REVERT: N 323 PHE cc_start: 0.8243 (p90) cc_final: 0.7965 (p90) outliers start: 117 outliers final: 80 residues processed: 340 average time/residue: 0.1944 time to fit residues: 105.5111 Evaluate side-chains 330 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 237 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 SER 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 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 132 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 214 PHE 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 377 MET 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 215 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 329 THR 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 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 116 ASP 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 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 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 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 237 LYS 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 63 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 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 442 LYS 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 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 Chi-restraints excluded: chain N residue 417 GLU 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: 10.0000 chunk 94 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 331 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096031 restraints weight = 54943.020| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.39 r_work: 0.3063 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32230 Z= 0.146 Angle : 0.553 8.541 44339 Z= 0.296 Chirality : 0.041 0.199 4841 Planarity : 0.004 0.059 5148 Dihedral : 15.768 163.232 5935 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.12 % Allowed : 29.67 % Favored : 67.21 % 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 aren not related in a simple way. whole: -1.52 (0.14), residues: 3427 helix: 1.17 (0.18), residues: 924 sheet: -0.71 (0.19), residues: 747 loop : -2.46 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 93 TYR 0.016 0.001 TYR B 79 PHE 0.014 0.001 PHE A 282 TRP 0.015 0.001 TRP J 212 HIS 0.008 0.001 HIS N 379 Details of bonding type rmsd covalent geometry : bond 0.00342 (32230) covalent geometry : angle 0.55285 (44339) hydrogen bonds : bond 0.04388 ( 1017) hydrogen bonds : angle 4.58767 ( 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 336 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 244 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: A 206 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (p0) REVERT: A 304 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.8090 (m90) REVERT: B 53 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: B 76 SER cc_start: 0.6913 (OUTLIER) cc_final: 0.6055 (t) REVERT: B 289 PHE cc_start: 0.8535 (m-80) cc_final: 0.8201 (m-80) REVERT: E 15 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8239 (p90) REVERT: E 234 MET cc_start: 0.8961 (mmt) cc_final: 0.8567 (mmt) REVERT: F 14 ILE cc_start: 0.8656 (mt) cc_final: 0.8321 (tp) REVERT: F 37 GLU cc_start: 0.7073 (pt0) cc_final: 0.6732 (pm20) REVERT: F 116 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7341 (p0) REVERT: F 132 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7563 (tp) REVERT: F 151 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7078 (mp) REVERT: F 212 TRP cc_start: 0.6547 (m100) cc_final: 0.5377 (m100) REVERT: F 238 GLU cc_start: 0.7548 (pm20) cc_final: 0.6401 (tm-30) REVERT: F 283 ARG cc_start: 0.6342 (mpp-170) cc_final: 0.5949 (ptt-90) REVERT: F 328 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: I 292 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8700 (mtpt) REVERT: I 420 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8884 (mt) REVERT: J 237 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7529 (mmmt) REVERT: J 247 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7704 (mt-10) REVERT: N 23 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.6649 (t80) REVERT: N 140 LYS cc_start: 0.8168 (ptmt) cc_final: 0.7872 (ttmm) REVERT: N 177 MET cc_start: 0.4369 (mmp) cc_final: 0.4030 (mmp) REVERT: N 187 ARG cc_start: 0.5650 (mmp80) cc_final: 0.3784 (mtm180) REVERT: N 202 PHE cc_start: 0.6843 (t80) cc_final: 0.6394 (t80) REVERT: N 263 THR cc_start: 0.6655 (p) cc_final: 0.6313 (p) REVERT: N 323 PHE cc_start: 0.8299 (p90) cc_final: 0.8086 (p90) outliers start: 92 outliers final: 70 residues processed: 316 average time/residue: 0.1953 time to fit residues: 99.4592 Evaluate side-chains 320 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 236 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 194 SER 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 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 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 184 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 377 MET 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 215 VAL Chi-restraints excluded: chain E residue 329 THR 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 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 116 ASP Chi-restraints excluded: chain F residue 132 LEU 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 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 F residue 400 TYR 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 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 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 237 LYS Chi-restraints excluded: chain J residue 241 LEU 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 63 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 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 131 ASP Chi-restraints excluded: chain N residue 168 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 254 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 343 optimal weight: 1.9990 chunk 330 optimal weight: 0.0170 chunk 83 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 228 optimal weight: 8.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 353 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 = 0.3802 r_free = 0.3802 target = 0.134675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095553 restraints weight = 54899.949| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.43 r_work: 0.3052 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1791 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= 0.164 Angle : 0.561 9.132 44339 Z= 0.300 Chirality : 0.042 0.199 4841 Planarity : 0.004 0.058 5148 Dihedral : 15.760 162.673 5935 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.32 % Allowed : 29.40 % Favored : 67.28 % 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 aren not related in a simple way. whole: -1.54 (0.14), residues: 3427 helix: 1.15 (0.18), residues: 924 sheet: -0.72 (0.19), residues: 747 loop : -2.47 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 93 TYR 0.016 0.001 TYR B 79 PHE 0.021 0.001 PHE J 211 TRP 0.012 0.001 TRP J 212 HIS 0.008 0.001 HIS N 379 Details of bonding type rmsd covalent geometry : bond 0.00387 (32230) covalent geometry : angle 0.56057 (44339) hydrogen bonds : bond 0.04545 ( 1017) hydrogen bonds : angle 4.58387 ( 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 338 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 240 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: A 206 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8252 (p0) REVERT: A 304 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7121 (m-70) REVERT: B 53 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: B 76 SER cc_start: 0.6973 (OUTLIER) cc_final: 0.6134 (t) REVERT: E 15 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8223 (p90) REVERT: E 234 MET cc_start: 0.8843 (mmt) cc_final: 0.8398 (mmt) REVERT: E 267 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8135 (ttt90) REVERT: F 14 ILE cc_start: 0.8595 (mt) cc_final: 0.8266 (tp) REVERT: F 37 GLU cc_start: 0.7033 (pt0) cc_final: 0.6623 (pm20) REVERT: F 132 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7477 (tp) REVERT: F 151 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7045 (mp) REVERT: F 212 TRP cc_start: 0.6506 (m100) cc_final: 0.5342 (m100) REVERT: F 238 GLU cc_start: 0.7473 (pm20) cc_final: 0.6284 (tm-30) REVERT: F 283 ARG cc_start: 0.6307 (mpp-170) cc_final: 0.5900 (ptt-90) REVERT: F 328 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: I 292 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8676 (mtpt) REVERT: I 420 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8795 (mt) REVERT: J 237 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7538 (mmmt) REVERT: J 247 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7518 (mt-10) REVERT: N 23 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.6622 (t80) REVERT: N 140 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7874 (ttmm) REVERT: N 202 PHE cc_start: 0.6745 (t80) cc_final: 0.6337 (t80) REVERT: N 248 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.6285 (mp10) REVERT: N 323 PHE cc_start: 0.8290 (p90) cc_final: 0.8084 (p90) outliers start: 98 outliers final: 76 residues processed: 317 average time/residue: 0.1934 time to fit residues: 98.3716 Evaluate side-chains 325 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 234 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 194 SER 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 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 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 132 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 377 MET 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 215 VAL Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 329 THR 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 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 132 LEU 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 349 TYR 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 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 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 237 LYS Chi-restraints excluded: chain J residue 241 LEU 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 63 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 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 74 ASP Chi-restraints excluded: chain N residue 86 LEU 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 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 307 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 272 optimal weight: 0.0070 chunk 94 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 155 optimal weight: 0.9980 chunk 335 optimal weight: 8.9990 chunk 292 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN F 242 HIS ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 353 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 = 0.3849 r_free = 0.3849 target = 0.138373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099209 restraints weight = 55040.281| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.42 r_work: 0.3111 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32230 Z= 0.105 Angle : 0.524 8.903 44339 Z= 0.279 Chirality : 0.040 0.197 4841 Planarity : 0.003 0.056 5148 Dihedral : 15.667 162.668 5935 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.54 % Allowed : 30.45 % 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 aren not related in a simple way. whole: -1.35 (0.14), residues: 3427 helix: 1.23 (0.18), residues: 942 sheet: -0.54 (0.19), residues: 774 loop : -2.40 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 93 TYR 0.017 0.001 TYR B 79 PHE 0.022 0.001 PHE J 211 TRP 0.011 0.001 TRP J 212 HIS 0.009 0.001 HIS N 379 Details of bonding type rmsd covalent geometry : bond 0.00230 (32230) covalent geometry : angle 0.52442 (44339) hydrogen bonds : bond 0.03346 ( 1017) hydrogen bonds : angle 4.41420 ( 2755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7585.31 seconds wall clock time: 130 minutes 24.04 seconds (7824.04 seconds total)