Starting phenix.real_space_refine on Thu Aug 6 10:58:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5m_29749/08_2026/8g5m_29749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5m_29749/08_2026/8g5m_29749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5m_29749/08_2026/8g5m_29749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5m_29749/08_2026/8g5m_29749.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5m_29749/08_2026/8g5m_29749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5m_29749/08_2026/8g5m_29749_neut.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 78 5.16 5 C 9168 2.51 5 N 2588 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14673 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7224 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 61, 'TRANS': 870} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 7, 'ARG:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 167 Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3253 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3230 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 479 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 18} Chain: "T" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 487 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 2.52, per 1000 atoms: 0.17 Number of scatterers: 14673 At special positions: 0 Unit cell: (108.979, 102.374, 143.654, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 46 15.00 O 2793 8.00 N 2588 7.00 C 9168 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: 0.78 Conformation dependent library (CDL) restraints added in 440.3 milliseconds 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 36.2% alpha, 11.3% beta 21 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 135 through 159 removed outlier: 4.118A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.571A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.568A pdb=" N VAL A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 278 No H-bonds generated for 'chain 'A' and resid 277 through 278' Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.617A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.043A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.980A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.234A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 477' Processing helix chain 'A' and resid 540 through 552 removed outlier: 3.903A pdb=" N MET A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.941A pdb=" N LEU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.850A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 803 removed outlier: 3.710A pdb=" N ASN A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.576A pdb=" N GLU A 873 " --> pdb=" O VAL A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 946 through 956 Processing helix chain 'A' and resid 958 through 969 Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.547A pdb=" N ARG A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A1098 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 3.581A pdb=" N LYS A1167 " --> pdb=" O MET A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 197 removed outlier: 4.668A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.616A pdb=" N LEU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.911A pdb=" N GLN B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.974A pdb=" N LEU B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASN B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.790A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.501A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 3.568A pdb=" N TRP C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.668A pdb=" N MET C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 395 through 409 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 470 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.896A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA A 212 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 813 through 815 Processing sheet with id=AA3, first strand: chain 'A' and resid 884 through 889 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.302A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.878A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.066A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.237A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.145A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR C 444 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU C 452 " --> pdb=" O THR C 444 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2308 1.31 - 1.43: 4265 1.43 - 1.56: 8334 1.56 - 1.69: 92 1.69 - 1.82: 122 Bond restraints: 15121 Sorted by residual: bond pdb=" C PRO A 563 " pdb=" O PRO A 563 " ideal model delta sigma weight residual 1.238 1.179 0.059 1.36e-02 5.41e+03 1.90e+01 bond pdb=" P DT T 24 " pdb=" O5' DT T 24 " ideal model delta sigma weight residual 1.593 1.629 -0.036 1.00e-02 1.00e+04 1.33e+01 bond pdb=" N SER A 764 " pdb=" CA SER A 764 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.75e+00 bond pdb=" N GLU C 419 " pdb=" CA GLU C 419 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.35e+00 bond pdb=" P DG T 23 " pdb=" O5' DG T 23 " ideal model delta sigma weight residual 1.593 1.623 -0.030 1.00e-02 1.00e+04 9.08e+00 ... (remaining 15116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 19809 2.38 - 4.76: 742 4.76 - 7.13: 137 7.13 - 9.51: 23 9.51 - 11.89: 6 Bond angle restraints: 20717 Sorted by residual: angle pdb=" C3' DC T 15 " pdb=" O3' DC T 15 " pdb=" P DG T 16 " ideal model delta sigma weight residual 119.70 107.81 11.89 1.20e+00 6.94e-01 9.82e+01 angle pdb=" C3' C R 15 " pdb=" O3' C R 15 " pdb=" P G R 16 " ideal model delta sigma weight residual 119.70 107.98 11.72 1.20e+00 6.94e-01 9.54e+01 angle pdb=" C3' C R 12 " pdb=" O3' C R 12 " pdb=" P U R 13 " ideal model delta sigma weight residual 119.70 108.36 11.34 1.20e+00 6.94e-01 8.94e+01 angle pdb=" C3' DG T 16 " pdb=" O3' DG T 16 " pdb=" P DC T 17 " ideal model delta sigma weight residual 119.70 108.39 11.31 1.20e+00 6.94e-01 8.88e+01 angle pdb=" C3' U R 11 " pdb=" O3' U R 11 " pdb=" P C R 12 " ideal model delta sigma weight residual 119.70 109.33 10.37 1.20e+00 6.94e-01 7.46e+01 ... (remaining 20712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 8543 34.54 - 69.08: 442 69.08 - 103.62: 26 103.62 - 138.16: 0 138.16 - 172.69: 3 Dihedral angle restraints: 9014 sinusoidal: 3981 harmonic: 5033 Sorted by residual: dihedral pdb=" CD ARG B 257 " pdb=" NE ARG B 257 " pdb=" CZ ARG B 257 " pdb=" NH1 ARG B 257 " ideal model delta sinusoidal sigma weight residual 0.00 -73.22 73.22 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CD ARG C 203 " pdb=" NE ARG C 203 " pdb=" CZ ARG C 203 " pdb=" NH1 ARG C 203 " ideal model delta sinusoidal sigma weight residual 0.00 68.03 -68.03 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CD ARG C 328 " pdb=" NE ARG C 328 " pdb=" CZ ARG C 328 " pdb=" NH1 ARG C 328 " ideal model delta sinusoidal sigma weight residual 0.00 67.12 -67.12 1 1.00e+01 1.00e-02 5.87e+01 ... (remaining 9011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2178 0.131 - 0.263: 59 0.263 - 0.394: 2 0.394 - 0.526: 33 0.526 - 0.657: 12 Chirality restraints: 2284 Sorted by residual: chirality pdb=" P DG T 3 " pdb=" OP1 DG T 3 " pdb=" OP2 DG T 3 " pdb=" O5' DG T 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DA T 4 " pdb=" OP1 DA T 4 " pdb=" OP2 DA T 4 " pdb=" O5' DA T 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DC T 25 " pdb=" OP1 DC T 25 " pdb=" OP2 DC T 25 " pdb=" O5' DC T 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.21e+00 ... (remaining 2281 not shown) Planarity restraints: 2505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 257 " 1.052 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG B 257 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 257 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 257 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 257 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 203 " 1.020 9.50e-02 1.11e+02 4.57e-01 1.26e+02 pdb=" NE ARG C 203 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 203 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 203 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 203 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 328 " 1.014 9.50e-02 1.11e+02 4.55e-01 1.25e+02 pdb=" NE ARG C 328 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 328 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 328 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 328 " 0.023 2.00e-02 2.50e+03 ... (remaining 2502 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 410 2.67 - 3.23: 14515 3.23 - 3.79: 23269 3.79 - 4.34: 30513 4.34 - 4.90: 49258 Nonbonded interactions: 117965 Sorted by model distance: nonbonded pdb=" ND2 ASN A 440 " pdb=" SD MET A1206 " model vdw 2.115 3.480 nonbonded pdb=" O ARG A 579 " pdb=" CG LEU A 580 " model vdw 2.119 3.470 nonbonded pdb=" NH1 ARG A 275 " pdb=" OE1 GLN A 281 " model vdw 2.146 3.120 nonbonded pdb=" O ASN A 970 " pdb=" ND1 HIS A 971 " model vdw 2.147 3.120 nonbonded pdb=" O ARG B 328 " pdb=" NE ARG B 328 " model vdw 2.154 3.120 ... (remaining 117960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 66 through 146 or (resid 147 and (name N or name CA or nam \ e C or name O or name CB )) or resid 148 through 170 or (resid 171 through 176 a \ nd (name N or name CA or name C or name O or name CB )) or resid 177 through 222 \ or (resid 223 and (name N or name CA or name C or name O or name CB )) or resid \ 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) or r \ esid 226 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 355 or resid 368 through 485)) selection = (chain 'C' and (resid 66 or (resid 67 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 153 or (resid 154 \ and (name N or name CA or name C or name O or name CB )) or resid 155 through 16 \ 0 or resid 170 through 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 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 : 0.006 0.059 15121 Z= 0.397 Angle : 1.029 11.890 20717 Z= 0.639 Chirality : 0.087 0.657 2284 Planarity : 0.023 0.471 2505 Dihedral : 18.453 172.694 5764 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.03 % Favored : 89.91 % Rotamer: Outliers : 1.31 % Allowed : 23.12 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1725 helix: 1.32 (0.24), residues: 575 sheet: 1.10 (0.36), residues: 209 loop : -2.09 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 546 TYR 0.021 0.001 TYR B 432 PHE 0.026 0.001 PHE A 539 TRP 0.025 0.001 TRP A 113 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.40 (15121) covalent geometry : angle 1.02889 / 0.64 (20717) hydrogen bonds : bond 0.14754 / 10.37 ( 551) hydrogen bonds : angle 6.87891 / 4.86 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 279 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 TRP cc_start: 0.8733 (m100) cc_final: 0.8358 (m-90) REVERT: A 740 ASN cc_start: 0.5277 (OUTLIER) cc_final: 0.4853 (t0) REVERT: A 969 PHE cc_start: 0.7787 (m-10) cc_final: 0.6557 (m-80) REVERT: B 321 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8407 (mptt) REVERT: B 466 MET cc_start: 0.8207 (ttp) cc_final: 0.7935 (tmt) outliers start: 19 outliers final: 9 residues processed: 290 average time/residue: 0.4447 time to fit residues: 143.1526 Evaluate side-chains 210 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 144 GLN A 270 ASN A 388 ASN A 404 HIS A 408 GLN A 540 GLN A 550 GLN A 618 HIS A 894 GLN ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 133 HIS B 158 GLN B 258 HIS B 397 GLN C 250 GLN C 292 ASN C 309 HIS C 400 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.166093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.116789 restraints weight = 24919.561| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.82 r_work: 0.3509 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15121 Z= 0.260 Angle : 0.802 11.552 20717 Z= 0.410 Chirality : 0.050 0.399 2284 Planarity : 0.006 0.074 2505 Dihedral : 17.577 170.818 2512 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.20 % Favored : 89.74 % Rotamer: Outliers : 5.30 % Allowed : 20.99 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1725 helix: 1.18 (0.22), residues: 592 sheet: 1.11 (0.34), residues: 228 loop : -2.09 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 325 TYR 0.034 0.002 TYR C 291 PHE 0.026 0.002 PHE A 949 TRP 0.033 0.002 TRP A 486 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 (15121) covalent geometry : angle 0.80198 / 0.41 (20717) hydrogen bonds : bond 0.05332 / 3.62 ( 551) hydrogen bonds : angle 4.63485 / 3.20 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 200 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8552 (ptm-80) REVERT: A 465 ASP cc_start: 0.8602 (m-30) cc_final: 0.8398 (m-30) REVERT: A 480 LYS cc_start: 0.9436 (mmtt) cc_final: 0.8990 (tppt) REVERT: A 490 TRP cc_start: 0.5604 (OUTLIER) cc_final: 0.4768 (m-10) REVERT: A 540 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7985 (mp-120) REVERT: A 541 GLN cc_start: 0.5936 (mp10) cc_final: 0.5459 (mp10) REVERT: A 796 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7792 (ptmm) REVERT: A 1195 MET cc_start: 0.7331 (ppp) cc_final: 0.7058 (ppp) REVERT: B 134 LYS cc_start: 0.8939 (ptmt) cc_final: 0.8691 (pttt) REVERT: B 231 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 321 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8083 (mptt) REVERT: B 328 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8461 (tpm-80) REVERT: B 336 LEU cc_start: 0.8758 (mp) cc_final: 0.8548 (mp) REVERT: B 419 GLU cc_start: 0.8494 (tp30) cc_final: 0.7592 (tp30) REVERT: C 122 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7902 (mmm160) REVERT: C 389 ARG cc_start: 0.7789 (mmm160) cc_final: 0.7550 (mmm160) REVERT: C 400 GLN cc_start: 0.8034 (mt0) cc_final: 0.7633 (mm110) outliers start: 77 outliers final: 31 residues processed: 254 average time/residue: 0.4334 time to fit residues: 122.6146 Evaluate side-chains 216 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 945 HIS Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 176 optimal weight: 50.0000 chunk 164 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 0.0670 chunk 166 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 140 optimal weight: 0.0370 chunk 149 optimal weight: 0.8980 chunk 133 optimal weight: 0.0040 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 945 HIS A 959 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS C 77 HIS C 309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.170673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.121766 restraints weight = 25013.080| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.85 r_work: 0.3587 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15121 Z= 0.144 Angle : 0.727 12.369 20717 Z= 0.366 Chirality : 0.046 0.384 2284 Planarity : 0.005 0.055 2505 Dihedral : 17.185 170.750 2495 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.33 % Favored : 90.61 % Rotamer: Outliers : 4.06 % Allowed : 21.82 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1725 helix: 1.28 (0.22), residues: 590 sheet: 1.20 (0.34), residues: 227 loop : -1.91 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 802 TYR 0.026 0.002 TYR C 432 PHE 0.021 0.001 PHE A 197 TRP 0.032 0.001 TRP A 484 HIS 0.009 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (15121) covalent geometry : angle 0.72670 / 0.37 (20717) hydrogen bonds : bond 0.04286 / 2.93 ( 551) hydrogen bonds : angle 4.34322 / 2.99 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 205 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8767 (ttp-110) cc_final: 0.8498 (ptm-80) REVERT: A 484 TRP cc_start: 0.8576 (m-90) cc_final: 0.8375 (m-90) REVERT: A 490 TRP cc_start: 0.5535 (OUTLIER) cc_final: 0.4549 (m-10) REVERT: A 796 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7759 (ptmm) REVERT: A 812 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8014 (ttt) REVERT: A 959 GLN cc_start: 0.7314 (mp10) cc_final: 0.7056 (mm-40) REVERT: A 985 MET cc_start: 0.7689 (mpp) cc_final: 0.6543 (mpp) REVERT: A 1195 MET cc_start: 0.7177 (ppp) cc_final: 0.6872 (ppp) REVERT: A 1216 GLU cc_start: 0.4619 (OUTLIER) cc_final: 0.3647 (tm-30) REVERT: B 134 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8629 (pttt) REVERT: B 231 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 321 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8045 (mptt) REVERT: B 328 ARG cc_start: 0.8901 (mtm110) cc_final: 0.8404 (tpm-80) REVERT: B 419 GLU cc_start: 0.8551 (tp30) cc_final: 0.7572 (tm-30) REVERT: B 466 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7780 (ttp) REVERT: C 122 ARG cc_start: 0.8356 (tpp-160) cc_final: 0.7904 (mmm160) REVERT: C 238 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8816 (p) REVERT: C 309 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.8096 (p90) REVERT: C 321 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.8986 (pmtt) REVERT: C 400 GLN cc_start: 0.7981 (mt0) cc_final: 0.7559 (mm110) REVERT: C 449 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6622 (mp0) outliers start: 59 outliers final: 25 residues processed: 245 average time/residue: 0.4260 time to fit residues: 117.2692 Evaluate side-chains 214 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 945 HIS Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 11 optimal weight: 0.0010 chunk 160 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 159 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 90 GLN A 398 GLN A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.169277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120192 restraints weight = 24712.864| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.83 r_work: 0.3560 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15121 Z= 0.137 Angle : 0.712 12.318 20717 Z= 0.355 Chirality : 0.046 0.383 2284 Planarity : 0.005 0.055 2505 Dihedral : 17.054 168.262 2495 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.51 % Favored : 90.43 % Rotamer: Outliers : 3.79 % Allowed : 23.40 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1725 helix: 1.36 (0.23), residues: 578 sheet: 1.22 (0.34), residues: 227 loop : -1.83 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 802 TYR 0.026 0.002 TYR C 432 PHE 0.025 0.001 PHE A 949 TRP 0.017 0.001 TRP A 486 HIS 0.023 0.001 HIS A 945 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (15121) covalent geometry : angle 0.71204 / 0.36 (20717) hydrogen bonds : bond 0.03980 / 2.74 ( 551) hydrogen bonds : angle 4.25436 / 2.94 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8788 (ttp-110) cc_final: 0.8509 (ptm-80) REVERT: A 484 TRP cc_start: 0.8576 (m-90) cc_final: 0.8127 (m-90) REVERT: A 490 TRP cc_start: 0.5571 (OUTLIER) cc_final: 0.4518 (m-10) REVERT: A 796 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7766 (ptmm) REVERT: A 959 GLN cc_start: 0.7425 (mp10) cc_final: 0.7122 (mm-40) REVERT: A 985 MET cc_start: 0.7700 (mpp) cc_final: 0.6752 (mpp) REVERT: A 1216 GLU cc_start: 0.4642 (OUTLIER) cc_final: 0.3690 (tm-30) REVERT: B 134 LYS cc_start: 0.8895 (ptmt) cc_final: 0.8595 (pttt) REVERT: B 231 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7743 (mp) REVERT: B 321 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8058 (mptt) REVERT: B 328 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8443 (tpm-80) REVERT: B 346 MET cc_start: 0.8354 (ttt) cc_final: 0.8085 (ttm) REVERT: B 419 GLU cc_start: 0.8829 (tp30) cc_final: 0.7715 (tm-30) REVERT: B 466 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7806 (ttp) REVERT: C 122 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.7919 (mmm160) REVERT: C 238 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8856 (p) REVERT: C 346 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7799 (mtp) REVERT: C 449 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6659 (mp0) outliers start: 55 outliers final: 24 residues processed: 232 average time/residue: 0.4293 time to fit residues: 111.5968 Evaluate side-chains 206 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 103 optimal weight: 0.0010 chunk 112 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS C 400 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.168572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.119274 restraints weight = 24614.571| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.85 r_work: 0.3560 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15121 Z= 0.139 Angle : 0.710 12.222 20717 Z= 0.353 Chirality : 0.045 0.384 2284 Planarity : 0.005 0.053 2505 Dihedral : 16.939 166.398 2494 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.51 % Favored : 90.43 % Rotamer: Outliers : 4.06 % Allowed : 23.33 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1725 helix: 1.38 (0.23), residues: 584 sheet: 1.18 (0.34), residues: 227 loop : -1.83 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 802 TYR 0.037 0.002 TYR C 432 PHE 0.028 0.001 PHE A 949 TRP 0.017 0.001 TRP A 113 HIS 0.008 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15121) covalent geometry : angle 0.71033 / 0.35 (20717) hydrogen bonds : bond 0.03809 / 2.64 ( 551) hydrogen bonds : angle 4.18586 / 2.89 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8800 (ttp-110) cc_final: 0.8512 (ptm-80) REVERT: A 484 TRP cc_start: 0.8574 (m-90) cc_final: 0.7999 (m-90) REVERT: A 490 TRP cc_start: 0.5521 (OUTLIER) cc_final: 0.4484 (m-10) REVERT: A 796 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7931 (ptmm) REVERT: A 802 ARG cc_start: 0.9270 (ttm-80) cc_final: 0.9048 (ttm110) REVERT: A 985 MET cc_start: 0.7693 (mpp) cc_final: 0.7176 (mpp) REVERT: A 1138 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7516 (mmm160) REVERT: A 1210 TYR cc_start: 0.7936 (m-80) cc_final: 0.7706 (t80) REVERT: A 1216 GLU cc_start: 0.4615 (OUTLIER) cc_final: 0.3675 (tm-30) REVERT: B 134 LYS cc_start: 0.8873 (ptmt) cc_final: 0.8538 (pttt) REVERT: B 191 GLU cc_start: 0.8717 (tp30) cc_final: 0.8443 (tp30) REVERT: B 231 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7754 (mp) REVERT: B 321 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8028 (mptt) REVERT: B 328 ARG cc_start: 0.8929 (mtm110) cc_final: 0.8425 (tpm-80) REVERT: B 346 MET cc_start: 0.8366 (ttt) cc_final: 0.8124 (ttm) REVERT: B 466 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7904 (ttp) REVERT: C 122 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.7885 (mmm160) REVERT: C 238 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8896 (p) REVERT: C 325 ARG cc_start: 0.6027 (ptm160) cc_final: 0.5374 (ptm160) REVERT: C 400 GLN cc_start: 0.7959 (mt0) cc_final: 0.7527 (mm-40) REVERT: C 449 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: C 462 MET cc_start: 0.7857 (mmp) cc_final: 0.7611 (mmp) outliers start: 59 outliers final: 28 residues processed: 232 average time/residue: 0.4075 time to fit residues: 106.2712 Evaluate side-chains 206 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 175 optimal weight: 30.0000 chunk 137 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 103 optimal weight: 0.0970 chunk 117 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS C 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.169546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120010 restraints weight = 24681.128| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.85 r_work: 0.3576 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15121 Z= 0.128 Angle : 0.709 12.279 20717 Z= 0.350 Chirality : 0.045 0.385 2284 Planarity : 0.004 0.050 2505 Dihedral : 16.860 165.362 2494 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.51 % Favored : 90.43 % Rotamer: Outliers : 3.65 % Allowed : 24.78 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1725 helix: 1.38 (0.22), residues: 584 sheet: 1.18 (0.33), residues: 227 loop : -1.80 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 802 TYR 0.034 0.001 TYR C 432 PHE 0.026 0.001 PHE A 949 TRP 0.016 0.001 TRP A 113 HIS 0.007 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (15121) covalent geometry : angle 0.70915 / 0.35 (20717) hydrogen bonds : bond 0.03672 / 2.54 ( 551) hydrogen bonds : angle 4.12947 / 2.86 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8848 (ttp-110) cc_final: 0.8538 (ptm-80) REVERT: A 484 TRP cc_start: 0.8575 (m-90) cc_final: 0.8005 (m-90) REVERT: A 490 TRP cc_start: 0.5478 (OUTLIER) cc_final: 0.4462 (m-10) REVERT: A 796 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7862 (ptmm) REVERT: A 812 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8005 (ttt) REVERT: A 1136 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: A 1210 TYR cc_start: 0.7899 (m-80) cc_final: 0.7671 (t80) REVERT: A 1216 GLU cc_start: 0.4607 (OUTLIER) cc_final: 0.3675 (tm-30) REVERT: B 134 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8516 (pttt) REVERT: B 321 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8029 (mptt) REVERT: B 328 ARG cc_start: 0.8921 (mtm110) cc_final: 0.8557 (tpm170) REVERT: B 346 MET cc_start: 0.8331 (ttt) cc_final: 0.8123 (ttm) REVERT: B 466 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7956 (ttp) REVERT: C 122 ARG cc_start: 0.8307 (tpp-160) cc_final: 0.7861 (mmm160) REVERT: C 238 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8902 (p) REVERT: C 400 GLN cc_start: 0.7977 (mt0) cc_final: 0.7524 (mm-40) REVERT: C 449 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: C 462 MET cc_start: 0.7866 (mmp) cc_final: 0.7626 (mmp) outliers start: 53 outliers final: 29 residues processed: 228 average time/residue: 0.3849 time to fit residues: 98.6070 Evaluate side-chains 207 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 115 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 chunk 51 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 176 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 305 ASN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.167685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118556 restraints weight = 24233.355| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.74 r_work: 0.3539 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15121 Z= 0.149 Angle : 0.745 15.084 20717 Z= 0.363 Chirality : 0.046 0.386 2284 Planarity : 0.004 0.050 2505 Dihedral : 16.823 164.292 2494 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.62 % Favored : 90.32 % Rotamer: Outliers : 3.72 % Allowed : 24.78 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1725 helix: 1.41 (0.23), residues: 584 sheet: 1.06 (0.34), residues: 216 loop : -1.82 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 325 TYR 0.040 0.002 TYR C 432 PHE 0.028 0.001 PHE A 949 TRP 0.018 0.001 TRP A 113 HIS 0.007 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (15121) covalent geometry : angle 0.74451 / 0.36 (20717) hydrogen bonds : bond 0.03733 / 2.59 ( 551) hydrogen bonds : angle 4.17230 / 2.89 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.8518 (ptm-80) REVERT: A 484 TRP cc_start: 0.8644 (m-90) cc_final: 0.8023 (m-90) REVERT: A 490 TRP cc_start: 0.5522 (OUTLIER) cc_final: 0.4518 (m-10) REVERT: A 796 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7918 (ptmm) REVERT: A 1136 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: A 1202 ASN cc_start: 0.5126 (OUTLIER) cc_final: 0.4740 (t0) REVERT: A 1210 TYR cc_start: 0.7900 (m-80) cc_final: 0.7671 (t80) REVERT: B 321 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8035 (mptt) REVERT: B 328 ARG cc_start: 0.8936 (mtm110) cc_final: 0.8545 (tpm170) REVERT: B 346 MET cc_start: 0.8365 (ttt) cc_final: 0.8156 (ttm) REVERT: B 419 GLU cc_start: 0.8798 (tp30) cc_final: 0.7746 (tm-30) REVERT: B 466 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7999 (ttp) REVERT: C 122 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.7886 (mmm160) REVERT: C 238 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8927 (p) REVERT: C 325 ARG cc_start: 0.5898 (ptm160) cc_final: 0.5425 (ptm160) REVERT: C 329 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8762 (mppt) REVERT: C 400 GLN cc_start: 0.8002 (mt0) cc_final: 0.7557 (mm110) REVERT: C 462 MET cc_start: 0.7886 (mmp) cc_final: 0.7631 (mmp) outliers start: 54 outliers final: 30 residues processed: 224 average time/residue: 0.4746 time to fit residues: 118.7773 Evaluate side-chains 203 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 110 optimal weight: 0.0060 chunk 83 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 173 optimal weight: 50.0000 chunk 157 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.0070 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN C 77 HIS C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.166714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.117142 restraints weight = 24453.665| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.76 r_work: 0.3519 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15121 Z= 0.161 Angle : 0.758 14.917 20717 Z= 0.370 Chirality : 0.046 0.388 2284 Planarity : 0.005 0.060 2505 Dihedral : 16.774 163.328 2494 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.68 % Favored : 90.26 % Rotamer: Outliers : 3.44 % Allowed : 25.60 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1725 helix: 1.34 (0.23), residues: 585 sheet: 1.03 (0.34), residues: 216 loop : -1.84 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 328 TYR 0.022 0.002 TYR A 479 PHE 0.030 0.001 PHE A 949 TRP 0.019 0.001 TRP A 113 HIS 0.008 0.001 HIS C 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15121) covalent geometry : angle 0.75834 / 0.37 (20717) hydrogen bonds : bond 0.03778 / 2.61 ( 551) hydrogen bonds : angle 4.19861 / 2.92 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8867 (ttp-110) cc_final: 0.8557 (ptm-80) REVERT: A 480 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9003 (tppt) REVERT: A 484 TRP cc_start: 0.8710 (m-90) cc_final: 0.8158 (m-90) REVERT: A 490 TRP cc_start: 0.5445 (OUTLIER) cc_final: 0.4547 (m-10) REVERT: A 796 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7956 (ptmm) REVERT: A 823 ARG cc_start: 0.7791 (tmt170) cc_final: 0.7282 (tmt-80) REVERT: A 954 ILE cc_start: 0.8115 (tt) cc_final: 0.7857 (pp) REVERT: A 1136 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 1202 ASN cc_start: 0.5260 (OUTLIER) cc_final: 0.4840 (t0) REVERT: A 1210 TYR cc_start: 0.7933 (m-80) cc_final: 0.7688 (t80) REVERT: A 1216 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.3990 (tm-30) REVERT: B 176 LYS cc_start: 0.8409 (mtpp) cc_final: 0.7754 (tptp) REVERT: B 321 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8025 (mptt) REVERT: B 328 ARG cc_start: 0.8959 (mtm110) cc_final: 0.8533 (tpm170) REVERT: B 346 MET cc_start: 0.8385 (ttt) cc_final: 0.8172 (ttm) REVERT: B 419 GLU cc_start: 0.8811 (tp30) cc_final: 0.7613 (tm-30) REVERT: B 466 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8001 (ttp) REVERT: C 122 ARG cc_start: 0.8302 (tpp-160) cc_final: 0.7897 (mmm160) REVERT: C 238 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8957 (p) REVERT: C 325 ARG cc_start: 0.6171 (ptm160) cc_final: 0.5516 (ptm-80) REVERT: C 329 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8588 (mppt) REVERT: C 400 GLN cc_start: 0.7990 (mt0) cc_final: 0.7534 (mm-40) outliers start: 50 outliers final: 30 residues processed: 211 average time/residue: 0.4286 time to fit residues: 101.1322 Evaluate side-chains 206 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 422 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.166636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.116260 restraints weight = 24867.724| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.89 r_work: 0.3526 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15121 Z= 0.135 Angle : 0.761 15.764 20717 Z= 0.368 Chirality : 0.046 0.388 2284 Planarity : 0.004 0.047 2505 Dihedral : 16.721 162.801 2494 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.51 % Favored : 90.43 % Rotamer: Outliers : 3.51 % Allowed : 25.81 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1725 helix: 1.35 (0.22), residues: 584 sheet: 1.09 (0.34), residues: 221 loop : -1.78 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 802 TYR 0.016 0.001 TYR C 315 PHE 0.029 0.001 PHE A 949 TRP 0.020 0.001 TRP A 113 HIS 0.007 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15121) covalent geometry : angle 0.76112 / 0.37 (20717) hydrogen bonds : bond 0.03595 / 2.49 ( 551) hydrogen bonds : angle 4.14548 / 2.89 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8546 (tp30) cc_final: 0.8190 (mp0) REVERT: A 94 MET cc_start: 0.7763 (tmt) cc_final: 0.7009 (tmm) REVERT: A 101 ARG cc_start: 0.8869 (ttp-110) cc_final: 0.8551 (ptm-80) REVERT: A 480 LYS cc_start: 0.9430 (mmtt) cc_final: 0.9042 (tppt) REVERT: A 484 TRP cc_start: 0.8651 (m-90) cc_final: 0.8155 (m-90) REVERT: A 490 TRP cc_start: 0.5363 (OUTLIER) cc_final: 0.4381 (m-10) REVERT: A 796 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7944 (ptmm) REVERT: A 1136 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: A 1206 MET cc_start: 0.4036 (mpt) cc_final: 0.1570 (OUTLIER) REVERT: A 1210 TYR cc_start: 0.7923 (m-80) cc_final: 0.7654 (t80) REVERT: A 1216 GLU cc_start: 0.4966 (OUTLIER) cc_final: 0.3979 (tm-30) REVERT: B 176 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7744 (tptp) REVERT: B 321 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8029 (mptt) REVERT: B 328 ARG cc_start: 0.8997 (mtm110) cc_final: 0.8540 (tpm170) REVERT: B 346 MET cc_start: 0.8334 (ttt) cc_final: 0.8131 (ttm) REVERT: B 419 GLU cc_start: 0.8820 (tp30) cc_final: 0.8343 (mp0) REVERT: B 466 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: C 122 ARG cc_start: 0.8330 (tpp-160) cc_final: 0.7902 (mmm160) REVERT: C 238 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8953 (p) REVERT: C 325 ARG cc_start: 0.5971 (ptm160) cc_final: 0.5739 (ptm-80) REVERT: C 400 GLN cc_start: 0.8022 (mt0) cc_final: 0.7573 (mm110) outliers start: 51 outliers final: 34 residues processed: 219 average time/residue: 0.4136 time to fit residues: 101.0579 Evaluate side-chains 209 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 173 optimal weight: 50.0000 chunk 47 optimal weight: 0.4980 chunk 171 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 354 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 249 ASN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.167239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.117752 restraints weight = 24424.270| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.76 r_work: 0.3541 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15121 Z= 0.152 Angle : 0.787 15.873 20717 Z= 0.383 Chirality : 0.046 0.388 2284 Planarity : 0.004 0.047 2505 Dihedral : 16.692 162.407 2494 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Rotamer: Outliers : 3.10 % Allowed : 26.29 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1725 helix: 1.34 (0.23), residues: 585 sheet: 1.00 (0.34), residues: 216 loop : -1.79 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 802 TYR 0.020 0.001 TYR A 479 PHE 0.029 0.001 PHE A 949 TRP 0.020 0.001 TRP A 113 HIS 0.006 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15121) covalent geometry : angle 0.78663 / 0.38 (20717) hydrogen bonds : bond 0.03648 / 2.52 ( 551) hydrogen bonds : angle 4.15805 / 2.91 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8605 (tp30) cc_final: 0.8235 (mp0) REVERT: A 94 MET cc_start: 0.7908 (tmt) cc_final: 0.7385 (tmm) REVERT: A 101 ARG cc_start: 0.8872 (ttp-110) cc_final: 0.8549 (ptm-80) REVERT: A 480 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9034 (tppt) REVERT: A 484 TRP cc_start: 0.8681 (m-90) cc_final: 0.8148 (m-90) REVERT: A 490 TRP cc_start: 0.5344 (OUTLIER) cc_final: 0.4392 (m-10) REVERT: A 552 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7676 (mm) REVERT: A 796 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7927 (ptmm) REVERT: A 823 ARG cc_start: 0.7655 (tmt170) cc_final: 0.7079 (tmt-80) REVERT: A 959 GLN cc_start: 0.6868 (mp10) cc_final: 0.6409 (mm-40) REVERT: A 1136 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: A 1206 MET cc_start: 0.4057 (mpt) cc_final: 0.1600 (OUTLIER) REVERT: A 1210 TYR cc_start: 0.7879 (m-80) cc_final: 0.7624 (t80) REVERT: A 1216 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.4061 (tt0) REVERT: B 176 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7745 (tptp) REVERT: B 321 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8039 (mptt) REVERT: B 328 ARG cc_start: 0.8977 (mtm110) cc_final: 0.8529 (tpm170) REVERT: B 346 MET cc_start: 0.8366 (ttt) cc_final: 0.8165 (ttm) REVERT: B 419 GLU cc_start: 0.8849 (tp30) cc_final: 0.8338 (mp0) REVERT: B 466 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8010 (ttp) REVERT: C 122 ARG cc_start: 0.8317 (tpp-160) cc_final: 0.7936 (mmm160) REVERT: C 238 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8960 (p) REVERT: C 321 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.8969 (pmtt) REVERT: C 325 ARG cc_start: 0.6214 (ptm160) cc_final: 0.5675 (ptm-80) outliers start: 45 outliers final: 32 residues processed: 208 average time/residue: 0.4231 time to fit residues: 98.5000 Evaluate side-chains 208 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 176 optimal weight: 50.0000 chunk 156 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS C 400 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.166413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.116841 restraints weight = 24267.519| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.75 r_work: 0.3483 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15121 Z= 0.163 Angle : 0.787 16.384 20717 Z= 0.383 Chirality : 0.047 0.388 2284 Planarity : 0.005 0.069 2505 Dihedral : 16.675 162.695 2494 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Rotamer: Outliers : 3.10 % Allowed : 26.50 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1725 helix: 1.33 (0.23), residues: 584 sheet: 0.98 (0.34), residues: 216 loop : -1.82 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 328 TYR 0.017 0.002 TYR C 291 PHE 0.029 0.001 PHE A 949 TRP 0.021 0.001 TRP A 113 HIS 0.006 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15121) covalent geometry : angle 0.78664 / 0.38 (20717) hydrogen bonds : bond 0.03674 / 2.53 ( 551) hydrogen bonds : angle 4.17834 / 2.92 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5609.61 seconds wall clock time: 95 minutes 54.88 seconds (5754.88 seconds total)