Starting phenix.real_space_refine on Wed May 28 15:33:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jt2_61790/05_2025/9jt2_61790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jt2_61790/05_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_61790/05_2025/9jt2_61790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jt2_61790/05_2025/9jt2_61790.map" model { file = "/net/cci-nas-00/data/ceres_data/9jt2_61790/05_2025/9jt2_61790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jt2_61790/05_2025/9jt2_61790.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.22, per 1000 atoms: 0.62 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: 7.71 Conformation dependent library (CDL) restraints added in 3.7 seconds 6854 Ramachandran restraints generated. 3427 Oldfield, 0 Emsley, 3427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6406 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 36 sheets defined 29.3% alpha, 16.0% beta 61 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 10.48 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: 10.91 Time building geometry restraints manager: 8.88 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: 9.210 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: 1.150 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 72.270 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP B 204 HIS 0.006 0.001 HIS N 379 PHE 0.026 0.001 PHE J 403 TYR 0.030 0.001 TYR M 266 ARG 0.012 0.000 ARG N 218 Details of bonding type rmsd hydrogen bonds : bond 0.14608 ( 1017) hydrogen bonds : angle 6.31040 ( 2755) covalent geometry : bond 0.00311 (32230) covalent geometry : angle 0.69264 (44339) *********************** 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 : 3.513 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: 0.4537 time to fit residues: 207.3055 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 : 3.155 ------------------------------------------------------------------------------- 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 295 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 141 optimal weight: 0.0000 chunk 274 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 317 optimal weight: 7.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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 280 GLN M 392 HIS M 424 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094147 restraints weight = 54934.086| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.50 r_work: 0.3027 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1188 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= 0.266 Angle : 0.652 10.527 44339 Z= 0.351 Chirality : 0.045 0.270 4841 Planarity : 0.005 0.073 5148 Dihedral : 16.077 159.464 5955 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.33 % Favored : 89.61 % Rotamer: Outliers : 4.48 % Allowed : 28.79 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.14), residues: 3427 helix: 0.43 (0.18), residues: 910 sheet: -0.92 (0.19), residues: 765 loop : -2.70 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 212 HIS 0.011 0.001 HIS M 74 PHE 0.022 0.002 PHE A 282 TYR 0.018 0.002 TYR N 343 ARG 0.007 0.001 ARG F 283 Details of bonding type rmsd hydrogen bonds : bond 0.06010 ( 1017) hydrogen bonds : angle 5.10353 ( 2755) covalent geometry : bond 0.00637 (32230) covalent geometry : angle 0.65187 (44339) *********************** 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 372 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 240 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8029 (p0) REVERT: A 304 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7217 (m-70) REVERT: B 289 PHE cc_start: 0.8327 (m-80) cc_final: 0.8076 (m-80) REVERT: E 15 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8379 (p90) REVERT: E 267 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8331 (ttt90) REVERT: F 14 ILE cc_start: 0.8548 (mt) cc_final: 0.8284 (tp) REVERT: F 66 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: F 328 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: I 25 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8502 (mtt180) REVERT: J 187 ARG cc_start: 0.7247 (ppt170) cc_final: 0.6923 (ptt-90) REVERT: M 74 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.7078 (p90) REVERT: M 300 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8837 (m) REVERT: N 23 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7381 (t80) REVERT: N 187 ARG cc_start: 0.5104 (OUTLIER) cc_final: 0.3899 (mtt90) REVERT: N 344 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.5658 (p90) REVERT: N 353 GLN cc_start: 0.5674 (OUTLIER) cc_final: 0.4712 (pm20) outliers start: 132 outliers final: 76 residues processed: 341 average time/residue: 0.4384 time to fit residues: 241.0453 Evaluate side-chains 321 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 232 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 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 25 THR Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 358 LEU 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 267 ARG Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 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 402 MET 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 156 GLU Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 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 347 ASN 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 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 421 CYS 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 330 MET Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 344 TYR Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 328 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 347 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** M 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097210 restraints weight = 55073.038| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.50 r_work: 0.3074 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1161 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= 0.130 Angle : 0.538 8.272 44339 Z= 0.292 Chirality : 0.041 0.208 4841 Planarity : 0.004 0.066 5148 Dihedral : 15.891 160.756 5944 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.49 % Allowed : 29.47 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3427 helix: 0.81 (0.18), residues: 915 sheet: -0.87 (0.19), residues: 770 loop : -2.61 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 212 HIS 0.007 0.001 HIS N 379 PHE 0.012 0.001 PHE I 342 TYR 0.017 0.001 TYR N 178 ARG 0.007 0.000 ARG N 218 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 1017) hydrogen bonds : angle 4.76983 ( 2755) covalent geometry : bond 0.00297 (32230) covalent geometry : angle 0.53849 (44339) *********************** 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 365 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 262 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 206 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8002 (p0) REVERT: B 62 LYS cc_start: 0.8335 (mttm) cc_final: 0.8085 (mmtt) REVERT: B 122 ARG cc_start: 0.8437 (mtm180) cc_final: 0.7950 (mtp180) REVERT: B 289 PHE cc_start: 0.8286 (m-80) cc_final: 0.7979 (m-80) REVERT: E 244 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.6706 (mtt-85) REVERT: F 14 ILE cc_start: 0.8544 (mt) cc_final: 0.8275 (tp) REVERT: F 37 GLU cc_start: 0.7077 (pt0) cc_final: 0.6792 (pm20) REVERT: F 238 GLU cc_start: 0.7392 (pm20) cc_final: 0.6215 (tm-30) REVERT: F 328 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: I 420 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8741 (mt) REVERT: J 177 MET cc_start: 0.8148 (tmm) cc_final: 0.7906 (tmm) REVERT: M 300 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8844 (m) REVERT: N 23 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7590 (t80) REVERT: N 35 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7290 (mtm-85) REVERT: N 53 MET cc_start: 0.8140 (mmm) cc_final: 0.7886 (mmm) REVERT: N 187 ARG cc_start: 0.5072 (OUTLIER) cc_final: 0.3793 (mtt90) REVERT: N 344 TYR cc_start: 0.7228 (p90) cc_final: 0.5589 (p90) REVERT: N 353 GLN cc_start: 0.5771 (OUTLIER) cc_final: 0.4685 (pm20) outliers start: 103 outliers final: 57 residues processed: 340 average time/residue: 0.4264 time to fit residues: 230.5293 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 : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL 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 214 PHE 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 244 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 59 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 276 THR 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 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 130 ILE Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 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 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 353 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 310 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 197 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- 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** F 257 GLN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092785 restraints weight = 55177.437| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.43 r_work: 0.3004 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 32230 Z= 0.259 Angle : 0.637 10.395 44339 Z= 0.343 Chirality : 0.045 0.230 4841 Planarity : 0.005 0.065 5148 Dihedral : 15.996 161.195 5939 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.12 % Favored : 88.85 % Rotamer: Outliers : 5.46 % Allowed : 27.70 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3427 helix: 0.73 (0.18), residues: 914 sheet: -1.05 (0.19), residues: 748 loop : -2.67 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 212 HIS 0.009 0.001 HIS N 379 PHE 0.019 0.002 PHE A 282 TYR 0.016 0.002 TYR I 413 ARG 0.006 0.000 ARG J 187 Details of bonding type rmsd hydrogen bonds : bond 0.05963 ( 1017) hydrogen bonds : angle 4.93745 ( 2755) covalent geometry : bond 0.00617 (32230) covalent geometry : angle 0.63694 (44339) *********************** 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 404 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 243 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: A 206 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 207 ASP cc_start: 0.7905 (t70) cc_final: 0.7696 (t0) REVERT: A 304 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.7324 (m-70) REVERT: B 76 SER cc_start: 0.6904 (OUTLIER) cc_final: 0.6020 (t) REVERT: B 122 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8139 (mtp180) REVERT: E 15 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8465 (p90) REVERT: E 244 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.6940 (mtt-85) REVERT: E 267 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8276 (ttt90) REVERT: F 37 GLU cc_start: 0.7202 (pt0) cc_final: 0.6740 (pm20) REVERT: F 151 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6929 (mp) REVERT: F 212 TRP cc_start: 0.6646 (m100) cc_final: 0.5472 (m100) REVERT: F 328 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: I 292 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8722 (mtpt) REVERT: J 187 ARG cc_start: 0.7586 (ppt170) cc_final: 0.6970 (ptt-90) REVERT: N 23 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7230 (t80) REVERT: N 35 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7429 (mtm-85) REVERT: N 53 MET cc_start: 0.8162 (mmm) cc_final: 0.7786 (mmm) REVERT: N 55 ARG cc_start: 0.8041 (mmt180) cc_final: 0.7699 (mmp-170) REVERT: N 169 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6787 (mm) REVERT: N 178 TYR cc_start: 0.4604 (t80) cc_final: 0.4299 (t80) REVERT: N 187 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.3962 (mtt90) REVERT: N 353 GLN cc_start: 0.5943 (OUTLIER) cc_final: 0.5722 (pm20) outliers start: 161 outliers final: 96 residues processed: 372 average time/residue: 0.4337 time to fit residues: 258.6256 Evaluate side-chains 338 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 227 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 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 59 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 427 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 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 402 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 369 GLU Chi-restraints excluded: chain 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 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 347 ASN Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 96 ILE 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 264 SER Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 442 LYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 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 252 SER Chi-restraints excluded: chain N residue 330 MET Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 344 TYR Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 111 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 336 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 264 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 230 optimal weight: 0.0670 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 242 HIS E 118 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098087 restraints weight = 54611.121| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.48 r_work: 0.3089 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32230 Z= 0.107 Angle : 0.528 7.896 44339 Z= 0.286 Chirality : 0.041 0.331 4841 Planarity : 0.004 0.060 5148 Dihedral : 15.868 162.065 5939 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.36 % Allowed : 30.04 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3427 helix: 0.98 (0.18), residues: 922 sheet: -0.79 (0.19), residues: 771 loop : -2.57 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 212 HIS 0.007 0.001 HIS N 379 PHE 0.011 0.001 PHE M 282 TYR 0.014 0.001 TYR N 291 ARG 0.006 0.000 ARG F 283 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1017) hydrogen bonds : angle 4.62895 ( 2755) covalent geometry : bond 0.00231 (32230) covalent geometry : angle 0.52787 (44339) *********************** 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 360 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 261 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: A 206 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8125 (p0) REVERT: A 304 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7896 (m90) REVERT: B 53 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: B 76 SER cc_start: 0.6945 (OUTLIER) cc_final: 0.6096 (t) REVERT: B 126 ILE cc_start: 0.8591 (mt) cc_final: 0.8374 (mm) REVERT: F 37 GLU cc_start: 0.7069 (pt0) cc_final: 0.6657 (pm20) REVERT: F 212 TRP cc_start: 0.6335 (m100) cc_final: 0.5343 (m100) REVERT: F 238 GLU cc_start: 0.7439 (pm20) cc_final: 0.6142 (tm-30) REVERT: F 283 ARG cc_start: 0.5923 (mpp-170) cc_final: 0.5683 (ptt-90) REVERT: F 328 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: I 292 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8567 (mtpt) REVERT: I 420 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8739 (mt) REVERT: J 177 MET cc_start: 0.8243 (tmm) cc_final: 0.7935 (tmm) REVERT: J 187 ARG cc_start: 0.7532 (ppt170) cc_final: 0.6914 (ptt-90) REVERT: J 247 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7327 (mt-10) REVERT: J 328 GLU cc_start: 0.7735 (pt0) cc_final: 0.7528 (pt0) REVERT: M 442 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9074 (mtmm) REVERT: N 23 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7616 (t80) REVERT: N 53 MET cc_start: 0.8173 (mmm) cc_final: 0.7782 (mmm) REVERT: N 55 ARG cc_start: 0.7881 (mmt180) cc_final: 0.7526 (mmp-170) REVERT: N 140 LYS cc_start: 0.8082 (ptmt) cc_final: 0.7798 (ttmm) REVERT: N 187 ARG cc_start: 0.5229 (OUTLIER) cc_final: 0.3714 (mtt90) REVERT: N 248 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6288 (mp10) REVERT: N 323 PHE cc_start: 0.8283 (p90) cc_final: 0.8066 (p90) outliers start: 99 outliers final: 62 residues processed: 333 average time/residue: 0.4450 time to fit residues: 235.3847 Evaluate side-chains 320 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 246 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU 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 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 76 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 285 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 38 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 215 VAL 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 59 VAL Chi-restraints excluded: chain F residue 94 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 402 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN 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 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 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 J residue 424 LYS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 418 LEU Chi-restraints excluded: chain M residue 442 LYS Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 248 GLN Chi-restraints excluded: chain N residue 344 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 58 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 chunk 169 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093540 restraints weight = 55351.250| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.44 r_work: 0.3018 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32230 Z= 0.225 Angle : 0.604 9.943 44339 Z= 0.325 Chirality : 0.044 0.210 4841 Planarity : 0.005 0.060 5148 Dihedral : 15.919 161.483 5939 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.09 % Favored : 88.88 % Rotamer: Outliers : 5.02 % Allowed : 28.45 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3427 helix: 0.91 (0.18), residues: 922 sheet: -0.95 (0.19), residues: 755 loop : -2.60 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 212 HIS 0.009 0.001 HIS N 379 PHE 0.019 0.002 PHE A 282 TYR 0.013 0.001 TYR M 266 ARG 0.006 0.000 ARG N 218 Details of bonding type rmsd hydrogen bonds : bond 0.05417 ( 1017) hydrogen bonds : angle 4.77266 ( 2755) covalent geometry : bond 0.00541 (32230) covalent geometry : angle 0.60440 (44339) *********************** 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 386 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 238 time to evaluate : 3.307 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: A 198 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: A 206 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8227 (p0) REVERT: A 304 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7178 (m-70) REVERT: B 53 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8096 (mtp) REVERT: B 76 SER cc_start: 0.6889 (OUTLIER) cc_final: 0.6029 (t) REVERT: E 244 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.6708 (mtt-85) REVERT: F 81 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7046 (tt) REVERT: F 121 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: F 151 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6903 (mp) REVERT: F 212 TRP cc_start: 0.6461 (m100) cc_final: 0.5350 (m100) REVERT: F 328 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: I 292 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8675 (mtpt) REVERT: J 237 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7610 (mmmt) REVERT: J 247 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7352 (mt-10) REVERT: N 23 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7134 (t80) REVERT: N 53 MET cc_start: 0.8141 (mmm) cc_final: 0.7792 (mmm) REVERT: N 187 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.3843 (mtt90) REVERT: N 248 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6334 (mp10) REVERT: N 323 PHE cc_start: 0.8304 (p90) cc_final: 0.8055 (p90) outliers start: 148 outliers final: 95 residues processed: 352 average time/residue: 0.4310 time to fit residues: 246.3617 Evaluate side-chains 337 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 226 time to evaluate : 3.480 ------------------------------------------------------------------------------- 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 198 GLN Chi-restraints excluded: chain A residue 201 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 132 LEU 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 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 280 GLN 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 81 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 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 J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 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 J residue 424 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 77 MET Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 211 ILE Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 421 CYS Chi-restraints excluded: chain M residue 442 LYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 187 ARG Chi-restraints excluded: chain N residue 237 LYS Chi-restraints excluded: chain N residue 248 GLN Chi-restraints excluded: chain N residue 339 THR Chi-restraints excluded: chain N residue 344 TYR Chi-restraints excluded: chain N residue 417 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 75 optimal weight: 0.0020 chunk 297 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 242 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095607 restraints weight = 54826.035| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.37 r_work: 0.3057 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32230 Z= 0.143 Angle : 0.550 8.729 44339 Z= 0.297 Chirality : 0.041 0.189 4841 Planarity : 0.004 0.060 5148 Dihedral : 15.883 162.546 5939 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 4.20 % Allowed : 29.09 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3427 helix: 1.07 (0.18), residues: 918 sheet: -0.84 (0.19), residues: 749 loop : -2.55 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 212 HIS 0.010 0.001 HIS M 74 PHE 0.017 0.001 PHE J 211 TYR 0.013 0.001 TYR N 291 ARG 0.006 0.000 ARG I 120 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 1017) hydrogen bonds : angle 4.65861 ( 2755) covalent geometry : bond 0.00332 (32230) covalent geometry : angle 0.55041 (44339) *********************** 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 367 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 243 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: A 198 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: A 206 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8261 (p0) REVERT: A 304 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.8008 (m90) REVERT: B 53 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: B 76 SER cc_start: 0.6820 (OUTLIER) cc_final: 0.5937 (t) REVERT: B 79 TYR cc_start: 0.7315 (t80) cc_final: 0.6946 (t80) REVERT: E 15 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8212 (p90) REVERT: F 81 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7089 (tt) REVERT: F 121 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6995 (pt0) REVERT: F 151 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6969 (mp) REVERT: F 212 TRP cc_start: 0.6561 (m100) cc_final: 0.5442 (m100) REVERT: F 238 GLU cc_start: 0.7501 (pm20) cc_final: 0.6182 (tm-30) REVERT: F 328 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: F 367 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.6903 (mmtt) REVERT: I 25 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8584 (mtt180) REVERT: I 292 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8746 (mtpt) REVERT: I 420 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8883 (mt) REVERT: J 204 TRP cc_start: 0.6391 (p-90) cc_final: 0.6078 (p-90) REVERT: J 237 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7550 (mmmt) REVERT: J 247 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7481 (mt-10) REVERT: J 328 GLU cc_start: 0.7976 (pt0) cc_final: 0.7742 (pt0) REVERT: J 402 MET cc_start: 0.8378 (mtt) cc_final: 0.8096 (mtp) REVERT: M 345 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: N 23 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7527 (t80) REVERT: N 53 MET cc_start: 0.8155 (mmm) cc_final: 0.7757 (mmm) REVERT: N 55 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7660 (mmp-170) REVERT: N 248 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.6364 (mp10) REVERT: N 323 PHE cc_start: 0.8358 (p90) cc_final: 0.8158 (p90) outliers start: 124 outliers final: 84 residues processed: 341 average time/residue: 0.4104 time to fit residues: 224.3726 Evaluate side-chains 336 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 233 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 201 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 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 320 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 38 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 223 ILE 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 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 121 GLU 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 367 LYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 402 MET 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 156 GLU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 277 SER 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 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 J residue 401 LEU Chi-restraints excluded: chain J residue 424 LYS 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 307 MET Chi-restraints excluded: chain M residue 345 GLU Chi-restraints excluded: chain M residue 376 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 31 ASP Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN 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 Chi-restraints excluded: chain N residue 344 TYR Chi-restraints excluded: chain N residue 345 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 177 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 331 optimal weight: 6.9990 chunk 286 optimal weight: 0.5980 chunk 255 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 121 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 317 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 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 = 0.3814 r_free = 0.3814 target = 0.135741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096891 restraints weight = 55209.344| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.39 r_work: 0.3072 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32230 Z= 0.122 Angle : 0.532 8.602 44339 Z= 0.286 Chirality : 0.041 0.187 4841 Planarity : 0.004 0.057 5148 Dihedral : 15.795 162.242 5935 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.04 % Allowed : 29.23 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3427 helix: 1.13 (0.18), residues: 927 sheet: -0.76 (0.19), residues: 770 loop : -2.52 (0.13), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 212 HIS 0.015 0.001 HIS J 320 PHE 0.016 0.001 PHE J 211 TYR 0.015 0.001 TYR M 266 ARG 0.007 0.000 ARG J 319 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 1017) hydrogen bonds : angle 4.54969 ( 2755) covalent geometry : bond 0.00279 (32230) covalent geometry : angle 0.53169 (44339) *********************** 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 367 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 248 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: A 198 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7527 (tp40) REVERT: A 206 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8269 (p0) REVERT: A 304 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7115 (m-70) REVERT: B 43 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8408 (mm) REVERT: B 53 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8052 (mtp) REVERT: B 76 SER cc_start: 0.6764 (OUTLIER) cc_final: 0.5934 (t) REVERT: B 79 TYR cc_start: 0.7352 (t80) cc_final: 0.6893 (t80) REVERT: B 204 TRP cc_start: 0.7180 (p90) cc_final: 0.6642 (p90) REVERT: E 15 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8191 (p90) REVERT: E 267 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8178 (ttt90) REVERT: F 14 ILE cc_start: 0.8552 (mt) cc_final: 0.8195 (tp) REVERT: F 121 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6960 (pt0) REVERT: F 212 TRP cc_start: 0.6441 (m100) cc_final: 0.5375 (m100) REVERT: F 238 GLU cc_start: 0.7593 (pm20) cc_final: 0.6319 (tm-30) REVERT: F 328 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: I 25 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8537 (mtt180) REVERT: I 292 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8716 (mtpt) REVERT: I 420 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8829 (mt) REVERT: J 237 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7598 (mmmt) REVERT: J 247 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7431 (mt-10) REVERT: J 328 GLU cc_start: 0.7893 (pt0) cc_final: 0.7658 (pt0) REVERT: J 402 MET cc_start: 0.8261 (mtt) cc_final: 0.8005 (mtp) REVERT: M 345 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: N 23 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7464 (t80) REVERT: N 53 MET cc_start: 0.8132 (mmm) cc_final: 0.7721 (mmm) REVERT: N 55 ARG cc_start: 0.7990 (mmt180) cc_final: 0.7600 (mmp-170) REVERT: N 187 ARG cc_start: 0.5577 (mmp80) cc_final: 0.3761 (mtm180) REVERT: N 323 PHE cc_start: 0.8298 (p90) cc_final: 0.8047 (p90) outliers start: 119 outliers final: 89 residues processed: 341 average time/residue: 0.4315 time to fit residues: 239.8491 Evaluate side-chains 345 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 239 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 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 43 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 132 LEU 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 285 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 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 267 ARG Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 329 THR 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 121 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 SER 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 210 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 277 SER 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 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 96 VAL 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 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 424 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 211 ILE Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 345 GLU 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 9 GLN Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN 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 344 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 8 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 303 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 312 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096603 restraints weight = 55044.522| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.40 r_work: 0.3065 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32230 Z= 0.132 Angle : 0.541 8.505 44339 Z= 0.290 Chirality : 0.041 0.190 4841 Planarity : 0.004 0.057 5148 Dihedral : 15.771 162.366 5935 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.14 % Allowed : 29.13 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3427 helix: 1.15 (0.18), residues: 927 sheet: -0.74 (0.19), residues: 780 loop : -2.51 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 204 HIS 0.010 0.001 HIS J 320 PHE 0.015 0.001 PHE J 211 TYR 0.014 0.001 TYR M 266 ARG 0.006 0.000 ARG I 120 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1017) hydrogen bonds : angle 4.52341 ( 2755) covalent geometry : bond 0.00307 (32230) covalent geometry : angle 0.54059 (44339) *********************** 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 360 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 238 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: A 206 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8236 (p0) REVERT: A 304 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7112 (m-70) REVERT: B 43 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8363 (mm) REVERT: B 53 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8013 (mtp) REVERT: B 76 SER cc_start: 0.6759 (OUTLIER) cc_final: 0.5926 (t) REVERT: B 200 LYS cc_start: 0.5702 (OUTLIER) cc_final: 0.5345 (mptt) REVERT: B 204 TRP cc_start: 0.7119 (p90) cc_final: 0.6569 (p90) REVERT: E 15 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8224 (p90) REVERT: E 267 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8197 (ttt90) REVERT: F 14 ILE cc_start: 0.8499 (mt) cc_final: 0.8225 (tp) REVERT: F 121 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6970 (pt0) REVERT: F 212 TRP cc_start: 0.6435 (m100) cc_final: 0.5378 (m100) REVERT: F 238 GLU cc_start: 0.7639 (pm20) cc_final: 0.6400 (tm-30) REVERT: F 328 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: F 367 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.6782 (mmtt) REVERT: I 25 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8543 (mtt180) REVERT: I 292 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8735 (mtpt) REVERT: I 420 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8842 (mt) REVERT: J 237 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7537 (mmmt) REVERT: J 328 GLU cc_start: 0.7887 (pt0) cc_final: 0.7641 (pt0) REVERT: J 402 MET cc_start: 0.8223 (mtt) cc_final: 0.7970 (mtp) REVERT: M 345 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: N 23 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7310 (t80) REVERT: N 53 MET cc_start: 0.8134 (mmm) cc_final: 0.7782 (mmm) REVERT: N 187 ARG cc_start: 0.5605 (mmp80) cc_final: 0.3801 (mtm180) REVERT: N 323 PHE cc_start: 0.8293 (p90) cc_final: 0.8017 (p90) outliers start: 122 outliers final: 94 residues processed: 333 average time/residue: 0.4120 time to fit residues: 221.2730 Evaluate side-chains 343 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 231 time to evaluate : 3.111 ------------------------------------------------------------------------------- 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 201 TRP Chi-restraints excluded: chain A residue 205 ILE 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 40 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 132 LEU 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 200 LYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 223 ILE 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 329 THR 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 121 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 SER 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 210 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 277 SER 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 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 96 VAL 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 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 424 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 194 SER Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 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 345 GLU 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 9 GLN Chi-restraints excluded: chain N residue 23 PHE Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN 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 344 TYR Chi-restraints excluded: chain N residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 292 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 323 optimal weight: 0.0030 chunk 334 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- 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 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094382 restraints weight = 55102.953| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.39 r_work: 0.3037 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32230 Z= 0.186 Angle : 0.584 9.429 44339 Z= 0.313 Chirality : 0.043 0.197 4841 Planarity : 0.004 0.058 5148 Dihedral : 15.820 162.778 5935 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 3.93 % Allowed : 29.26 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3427 helix: 1.09 (0.18), residues: 923 sheet: -0.84 (0.19), residues: 745 loop : -2.53 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 212 HIS 0.009 0.001 HIS J 320 PHE 0.016 0.001 PHE A 282 TYR 0.013 0.001 TYR M 266 ARG 0.007 0.000 ARG N 218 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 1017) hydrogen bonds : angle 4.64438 ( 2755) covalent geometry : bond 0.00441 (32230) covalent geometry : angle 0.58436 (44339) ********************** 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 350 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 234 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: A 198 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7557 (tp40) REVERT: A 206 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (p0) REVERT: A 304 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.8011 (m90) REVERT: B 43 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 76 SER cc_start: 0.6868 (OUTLIER) cc_final: 0.5976 (t) REVERT: B 200 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.5381 (mptt) REVERT: B 204 TRP cc_start: 0.6950 (p90) cc_final: 0.6532 (p90) REVERT: B 242 HIS cc_start: 0.6910 (t-90) cc_final: 0.6692 (t-170) REVERT: E 15 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8320 (p90) REVERT: E 267 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8198 (ttt90) REVERT: F 14 ILE cc_start: 0.8552 (mt) cc_final: 0.8275 (tp) REVERT: F 121 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7061 (pt0) REVERT: F 151 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6986 (mp) REVERT: F 212 TRP cc_start: 0.6550 (m100) cc_final: 0.5450 (m100) REVERT: F 238 GLU cc_start: 0.7565 (pm20) cc_final: 0.6397 (tm-30) REVERT: F 328 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: I 25 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8601 (mtt180) REVERT: I 292 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8781 (mtpt) REVERT: I 420 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8911 (mt) REVERT: J 328 GLU cc_start: 0.7965 (pt0) cc_final: 0.7725 (pt0) REVERT: J 402 MET cc_start: 0.8312 (mtt) cc_final: 0.8062 (mtp) REVERT: M 345 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: N 23 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7222 (t80) REVERT: N 323 PHE cc_start: 0.8339 (p90) cc_final: 0.8073 (p90) outliers start: 116 outliers final: 95 residues processed: 328 average time/residue: 0.4135 time to fit residues: 218.3545 Evaluate side-chains 340 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 228 time to evaluate : 3.114 ------------------------------------------------------------------------------- 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 198 GLN Chi-restraints excluded: chain A residue 201 TRP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 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 43 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 132 LEU 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 200 LYS 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 E residue 15 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 223 ILE 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 329 THR 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 121 GLU 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 283 ARG Chi-restraints excluded: chain F residue 291 TYR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 349 TYR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 SER 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 210 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 277 SER 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 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain J residue 235 ASN Chi-restraints excluded: chain J residue 241 LEU Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain J residue 424 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 194 SER Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 211 ILE Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 282 PHE Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 345 GLU 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 31 ASP Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 93 ASN 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 344 TYR Chi-restraints excluded: chain N residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 161 optimal weight: 0.0020 chunk 321 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 266 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.0790 ------------------------------------------------------------------------------- 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** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096644 restraints weight = 54527.592| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.40 r_work: 0.3066 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32230 Z= 0.124 Angle : 0.546 8.565 44339 Z= 0.292 Chirality : 0.041 0.192 4841 Planarity : 0.004 0.057 5148 Dihedral : 15.770 162.924 5931 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.83 % Allowed : 29.37 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3427 helix: 1.20 (0.18), residues: 924 sheet: -0.78 (0.19), residues: 757 loop : -2.47 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 204 HIS 0.009 0.001 HIS J 320 PHE 0.021 0.001 PHE J 211 TYR 0.017 0.001 TYR N 277 ARG 0.006 0.000 ARG N 218 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 1017) hydrogen bonds : angle 4.52624 ( 2755) covalent geometry : bond 0.00285 (32230) covalent geometry : angle 0.54581 (44339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18513.74 seconds wall clock time: 320 minutes 21.76 seconds (19221.76 seconds total)