Starting phenix.real_space_refine on Fri Jul 3 15:54:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5m_29749/07_2026/8g5m_29749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5m_29749/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g5m_29749/07_2026/8g5m_29749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5m_29749/07_2026/8g5m_29749_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5m_29749/07_2026/8g5m_29749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5m_29749/07_2026/8g5m_29749.map" } 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-dev-6108/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: 3.21, per 1000 atoms: 0.22 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: 1.31 Conformation dependent library (CDL) restraints added in 700.9 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: 2.05 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: 3.12 Time building geometry restraints manager: 1.67 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 - 2.48: 19863 2.48 - 4.96: 701 4.96 - 7.43: 129 7.43 - 9.91: 18 9.91 - 12.39: 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 120.20 107.81 12.39 1.50e+00 4.44e-01 6.82e+01 angle pdb=" C3' C R 15 " pdb=" O3' C R 15 " pdb=" P G R 16 " ideal model delta sigma weight residual 120.20 107.98 12.22 1.50e+00 4.44e-01 6.64e+01 angle pdb=" C3' C R 12 " pdb=" O3' C R 12 " pdb=" P U R 13 " ideal model delta sigma weight residual 120.20 108.36 11.84 1.50e+00 4.44e-01 6.23e+01 angle pdb=" C3' DG T 16 " pdb=" O3' DG T 16 " pdb=" P DC T 17 " ideal model delta sigma weight residual 120.20 108.39 11.81 1.50e+00 4.44e-01 6.20e+01 angle pdb=" C3' U R 11 " pdb=" O3' U R 11 " pdb=" P C R 12 " ideal model delta sigma weight residual 120.20 109.33 10.87 1.50e+00 4.44e-01 5.25e+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: 2165 0.131 - 0.263: 72 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.900 Find NCS groups from input model: 0.170 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- 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= 0.389 Angle : 1.039 12.390 20717 Z= 0.630 Chirality : 0.088 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 / 0.39 (15121) covalent geometry : angle 1.03905 / 0.63 (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 : 0.572 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: 0.5232 time to fit residues: 168.6024 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 : 0.463 ------------------------------------------------------------------------------- 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 ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4296 r_free = 0.4296 target = 0.165546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.116092 restraints weight = 24928.610| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.82 r_work: 0.3500 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15121 Z= 0.260 Angle : 0.809 11.723 20717 Z= 0.416 Chirality : 0.049 0.220 2284 Planarity : 0.006 0.078 2505 Dihedral : 17.702 174.663 2512 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.20 % Favored : 89.74 % Rotamer: Outliers : 5.57 % Allowed : 20.10 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1725 helix: 1.14 (0.22), residues: 592 sheet: 1.10 (0.34), residues: 228 loop : -2.09 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 325 TYR 0.036 0.003 TYR C 291 PHE 0.025 0.002 PHE A 949 TRP 0.038 0.002 TRP A 486 HIS 0.007 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 (15121) covalent geometry : angle 0.80923 / 0.42 (20717) hydrogen bonds : bond 0.05240 / 3.54 ( 551) hydrogen bonds : angle 4.64469 / 3.21 ( 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 282 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 201 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8787 (ttp-110) cc_final: 0.8546 (ptm-80) REVERT: A 480 LYS cc_start: 0.9435 (mmtt) cc_final: 0.8982 (tppt) REVERT: A 490 TRP cc_start: 0.5630 (OUTLIER) cc_final: 0.4732 (m-10) REVERT: A 540 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8010 (mp-120) REVERT: A 541 GLN cc_start: 0.5996 (mp10) cc_final: 0.5548 (mp10) REVERT: A 796 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7801 (ptmm) REVERT: A 985 MET cc_start: 0.8262 (mtp) cc_final: 0.7689 (mtt) REVERT: A 1195 MET cc_start: 0.7335 (ppp) cc_final: 0.7103 (ppp) REVERT: B 134 LYS cc_start: 0.8933 (ptmt) cc_final: 0.8679 (pttt) REVERT: B 321 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8072 (mptt) REVERT: B 328 ARG cc_start: 0.8921 (mtm110) cc_final: 0.8460 (tpm-80) REVERT: B 336 LEU cc_start: 0.8775 (mp) cc_final: 0.8571 (mp) REVERT: B 419 GLU cc_start: 0.8539 (tp30) cc_final: 0.7820 (tp30) REVERT: B 466 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7938 (ttp) REVERT: C 122 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7904 (mmm160) REVERT: C 389 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7543 (mmm160) REVERT: C 400 GLN cc_start: 0.8040 (mt0) cc_final: 0.7629 (mm-40) outliers start: 81 outliers final: 32 residues processed: 258 average time/residue: 0.5049 time to fit residues: 145.6225 Evaluate side-chains 213 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 437 VAL 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 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 466 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 211 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: 6.9990 chunk 116 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 440 ASN A 945 HIS A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN B 454 HIS C 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.165296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.115701 restraints weight = 25103.707| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.80 r_work: 0.3483 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15121 Z= 0.217 Angle : 0.747 12.046 20717 Z= 0.383 Chirality : 0.046 0.225 2284 Planarity : 0.005 0.055 2505 Dihedral : 17.414 174.940 2495 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.38 % Favored : 89.57 % Rotamer: Outliers : 4.89 % Allowed : 21.61 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1725 helix: 1.14 (0.22), residues: 586 sheet: 1.05 (0.35), residues: 221 loop : -2.02 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 802 TYR 0.039 0.002 TYR C 291 PHE 0.026 0.002 PHE A 197 TRP 0.036 0.002 TRP A 484 HIS 0.010 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (15121) covalent geometry : angle 0.74746 / 0.38 (20717) hydrogen bonds : bond 0.04565 / 3.14 ( 551) hydrogen bonds : angle 4.54035 / 3.12 ( 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 260 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 189 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8786 (ttp-110) cc_final: 0.8510 (ptm-80) REVERT: A 465 ASP cc_start: 0.8583 (m-30) cc_final: 0.8338 (m-30) REVERT: A 490 TRP cc_start: 0.5593 (OUTLIER) cc_final: 0.4760 (m-10) REVERT: A 796 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7854 (ptmm) REVERT: A 823 ARG cc_start: 0.7662 (tmt170) cc_final: 0.7390 (tmt-80) REVERT: A 1216 GLU cc_start: 0.5062 (OUTLIER) cc_final: 0.4023 (tm-30) REVERT: B 134 LYS cc_start: 0.8882 (ptmt) cc_final: 0.8605 (pttt) REVERT: B 231 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7863 (mp) REVERT: B 260 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8307 (tp) REVERT: B 321 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8048 (mptt) REVERT: B 328 ARG cc_start: 0.8966 (mtm110) cc_final: 0.8415 (tpm-80) REVERT: B 419 GLU cc_start: 0.8526 (tp30) cc_final: 0.7654 (tp30) REVERT: B 466 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7571 (ttp) REVERT: C 122 ARG cc_start: 0.8296 (tpp-160) cc_final: 0.7917 (mmm160) REVERT: C 238 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.9009 (p) REVERT: C 309 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.8149 (p-80) REVERT: C 321 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.8903 (pmtt) REVERT: C 449 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6730 (mp0) outliers start: 71 outliers final: 31 residues processed: 236 average time/residue: 0.5188 time to fit residues: 137.2774 Evaluate side-chains 210 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 213 VAL 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 566 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 929 THR 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 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 268 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL 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 309 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 321 LYS 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: 3.9990 chunk 160 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 GLN A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS C 400 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.161701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111560 restraints weight = 24881.581| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.80 r_work: 0.3433 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15121 Z= 0.250 Angle : 0.770 11.880 20717 Z= 0.393 Chirality : 0.047 0.210 2284 Planarity : 0.005 0.052 2505 Dihedral : 17.332 171.304 2495 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.72 % Favored : 89.22 % Rotamer: Outliers : 5.30 % Allowed : 22.71 % Favored : 71.99 % 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: -0.82 (0.21), residues: 1725 helix: 0.96 (0.22), residues: 592 sheet: 0.81 (0.34), residues: 232 loop : -2.07 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 389 TYR 0.034 0.003 TYR C 291 PHE 0.026 0.002 PHE A 949 TRP 0.029 0.002 TRP A 484 HIS 0.008 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (15121) covalent geometry : angle 0.77037 / 0.39 (20717) hydrogen bonds : bond 0.04519 / 3.11 ( 551) hydrogen bonds : angle 4.64878 / 3.19 ( 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 257 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 180 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8849 (ttp-110) cc_final: 0.8562 (ptm-80) REVERT: A 480 LYS cc_start: 0.9398 (mmtt) cc_final: 0.8992 (tppt) REVERT: A 484 TRP cc_start: 0.8635 (m-90) cc_final: 0.8161 (m-90) REVERT: A 490 TRP cc_start: 0.5582 (OUTLIER) cc_final: 0.4709 (m-10) REVERT: A 796 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7743 (tmtm) REVERT: B 134 LYS cc_start: 0.8837 (ptmt) cc_final: 0.8535 (pttt) REVERT: B 231 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 321 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8017 (mptt) REVERT: B 328 ARG cc_start: 0.9035 (mtm110) cc_final: 0.8422 (tpm-80) REVERT: B 466 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7503 (ttp) REVERT: C 122 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.7937 (mmm160) REVERT: C 238 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.9055 (p) REVERT: C 309 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8247 (p90) REVERT: C 400 GLN cc_start: 0.8005 (mt0) cc_final: 0.7547 (mm-40) REVERT: C 462 MET cc_start: 0.7866 (mmp) cc_final: 0.7597 (mmp) outliers start: 77 outliers final: 37 residues processed: 235 average time/residue: 0.4940 time to fit residues: 130.5205 Evaluate side-chains 211 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 213 VAL 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 566 LEU 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 1199 THR Chi-restraints excluded: chain B residue 119 VAL 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 268 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 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 139 LEU 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 309 HIS 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 479 ILE 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: 0.6980 chunk 103 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 chunk 102 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 968 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.165646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115765 restraints weight = 24280.665| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.81 r_work: 0.3507 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15121 Z= 0.137 Angle : 0.716 12.135 20717 Z= 0.361 Chirality : 0.044 0.204 2284 Planarity : 0.005 0.060 2505 Dihedral : 17.164 170.448 2494 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.09 % Rotamer: Outliers : 4.27 % Allowed : 23.68 % Favored : 72.06 % 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: -0.52 (0.21), residues: 1725 helix: 1.24 (0.22), residues: 578 sheet: 0.96 (0.34), residues: 231 loop : -1.85 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.027 0.002 TYR C 432 PHE 0.028 0.001 PHE A 949 TRP 0.019 0.001 TRP A 484 HIS 0.022 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (15121) covalent geometry : angle 0.71616 / 0.36 (20717) hydrogen bonds : bond 0.03853 / 2.67 ( 551) hydrogen bonds : angle 4.32682 / 2.98 ( 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 255 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.8523 (ptm-80) REVERT: A 484 TRP cc_start: 0.8480 (m-90) cc_final: 0.8057 (m-90) REVERT: A 490 TRP cc_start: 0.5458 (OUTLIER) cc_final: 0.4476 (m-10) REVERT: A 796 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7992 (ptmm) REVERT: A 812 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7970 (ttt) REVERT: A 1138 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7785 (mmm160) REVERT: A 1216 GLU cc_start: 0.5139 (OUTLIER) cc_final: 0.4396 (tt0) REVERT: B 134 LYS cc_start: 0.8864 (ptmt) cc_final: 0.8540 (pttt) REVERT: B 231 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 260 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8525 (tp) REVERT: B 321 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8036 (mptt) REVERT: B 328 ARG cc_start: 0.8969 (mtm110) cc_final: 0.8407 (tpm-80) REVERT: B 466 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7424 (ttp) REVERT: C 122 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.7920 (mmm160) REVERT: C 224 ILE cc_start: 0.1068 (OUTLIER) cc_final: 0.0195 (pp) REVERT: C 238 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.9015 (p) REVERT: C 432 TYR cc_start: 0.8966 (m-80) cc_final: 0.8759 (m-80) REVERT: C 449 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: C 462 MET cc_start: 0.7899 (mmp) cc_final: 0.7603 (mmp) outliers start: 62 outliers final: 23 residues processed: 236 average time/residue: 0.4960 time to fit residues: 130.5805 Evaluate side-chains 199 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL 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 566 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 812 MET 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 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 224 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 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: 0.9990 chunk 50 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 166 optimal weight: 0.0570 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN 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 = 0.4279 r_free = 0.4279 target = 0.164444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114793 restraints weight = 24407.811| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.76 r_work: 0.3492 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15121 Z= 0.155 Angle : 0.723 11.799 20717 Z= 0.363 Chirality : 0.045 0.195 2284 Planarity : 0.005 0.051 2505 Dihedral : 17.078 170.762 2494 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.49 % Favored : 89.45 % Rotamer: Outliers : 4.75 % Allowed : 24.16 % Favored : 71.09 % 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: -0.54 (0.21), residues: 1725 helix: 1.22 (0.22), residues: 584 sheet: 0.95 (0.34), residues: 231 loop : -1.88 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 102 TYR 0.030 0.002 TYR C 432 PHE 0.028 0.001 PHE A 949 TRP 0.016 0.001 TRP A 113 HIS 0.006 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (15121) covalent geometry : angle 0.72344 / 0.36 (20717) hydrogen bonds : bond 0.03841 / 2.67 ( 551) hydrogen bonds : angle 4.28476 / 2.96 ( 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 241 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8849 (ttp-110) cc_final: 0.8557 (ptm-80) REVERT: A 480 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9001 (tppt) REVERT: A 484 TRP cc_start: 0.8598 (m-90) cc_final: 0.8110 (m-90) REVERT: A 490 TRP cc_start: 0.5476 (OUTLIER) cc_final: 0.4492 (m-10) REVERT: A 796 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8027 (ptmm) REVERT: A 797 MET cc_start: 0.8653 (mtp) cc_final: 0.8443 (mtp) REVERT: A 823 ARG cc_start: 0.7711 (tmt170) cc_final: 0.7380 (tmt-80) REVERT: A 1164 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8516 (t80) REVERT: A 1210 TYR cc_start: 0.7962 (m-80) cc_final: 0.7728 (t80) REVERT: B 134 LYS cc_start: 0.8802 (ptmt) cc_final: 0.8460 (pttt) REVERT: B 231 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8098 (mp) REVERT: B 260 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8475 (tp) REVERT: B 321 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8052 (mptt) REVERT: B 328 ARG cc_start: 0.8955 (mtm110) cc_final: 0.8414 (tpm-80) REVERT: B 346 MET cc_start: 0.8436 (ttt) cc_final: 0.8134 (ttm) REVERT: B 466 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7499 (ttp) REVERT: C 122 ARG cc_start: 0.8332 (tpp-160) cc_final: 0.7940 (mmm160) REVERT: C 238 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.9019 (p) REVERT: C 325 ARG cc_start: 0.5862 (ptm160) cc_final: 0.5444 (ptm-80) REVERT: C 400 GLN cc_start: 0.7975 (mt0) cc_final: 0.7531 (mm-40) REVERT: C 462 MET cc_start: 0.7963 (mmp) cc_final: 0.7674 (mmp) outliers start: 69 outliers final: 31 residues processed: 224 average time/residue: 0.5325 time to fit residues: 133.1655 Evaluate side-chains 200 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 566 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 742 VAL 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 1068 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 119 VAL 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 268 MET Chi-restraints excluded: chain B residue 338 VAL 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 139 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 51 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 176 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.163892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114222 restraints weight = 24207.772| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.74 r_work: 0.3487 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15121 Z= 0.167 Angle : 0.733 14.987 20717 Z= 0.365 Chirality : 0.045 0.191 2284 Planarity : 0.005 0.049 2505 Dihedral : 17.028 170.996 2494 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.67 % Favored : 89.28 % Rotamer: Outliers : 3.85 % Allowed : 24.98 % Favored : 71.16 % 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: -0.55 (0.21), residues: 1725 helix: 1.20 (0.22), residues: 584 sheet: 0.94 (0.34), residues: 231 loop : -1.88 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 102 TYR 0.025 0.002 TYR C 432 PHE 0.028 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 0.00375 / 0.17 (15121) covalent geometry : angle 0.73332 / 0.37 (20717) hydrogen bonds : bond 0.03840 / 2.66 ( 551) hydrogen bonds : angle 4.29282 / 2.97 ( 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 229 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8897 (ttp-110) cc_final: 0.8589 (ptm-80) REVERT: A 484 TRP cc_start: 0.8639 (m-90) cc_final: 0.8152 (m-90) REVERT: A 490 TRP cc_start: 0.5484 (OUTLIER) cc_final: 0.4532 (m-10) REVERT: A 552 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 796 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7766 (tmtm) REVERT: A 1164 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8523 (t80) REVERT: A 1210 TYR cc_start: 0.7923 (m-80) cc_final: 0.7706 (t80) REVERT: A 1216 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.3977 (tm-30) REVERT: B 134 LYS cc_start: 0.8786 (ptmt) cc_final: 0.8432 (pttt) REVERT: B 231 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8098 (mp) REVERT: B 321 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8042 (mptt) REVERT: B 328 ARG cc_start: 0.8986 (mtm110) cc_final: 0.8439 (tpm-80) REVERT: B 346 MET cc_start: 0.8433 (ttt) cc_final: 0.8142 (ttm) REVERT: B 466 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7472 (ttp) REVERT: C 122 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.7974 (mmm160) REVERT: C 155 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: C 238 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.9033 (p) REVERT: C 325 ARG cc_start: 0.5834 (ptm160) cc_final: 0.5540 (ptm-80) REVERT: C 400 GLN cc_start: 0.7998 (mt0) cc_final: 0.7536 (mm-40) REVERT: C 462 MET cc_start: 0.7976 (mmp) cc_final: 0.7708 (mmp) outliers start: 56 outliers final: 31 residues processed: 215 average time/residue: 0.5195 time to fit residues: 124.9127 Evaluate side-chains 201 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 566 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 742 VAL 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 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 338 VAL 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 155 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 315 TYR 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: 0.0980 chunk 83 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.159591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109540 restraints weight = 24610.290| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.72 r_work: 0.3410 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15121 Z= 0.289 Angle : 0.827 13.306 20717 Z= 0.415 Chirality : 0.048 0.189 2284 Planarity : 0.005 0.065 2505 Dihedral : 17.077 171.292 2492 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.07 % Favored : 88.81 % Rotamer: Outliers : 4.13 % Allowed : 25.40 % Favored : 70.47 % 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: -0.95 (0.20), residues: 1725 helix: 0.76 (0.22), residues: 604 sheet: 0.60 (0.35), residues: 229 loop : -2.06 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 102 TYR 0.035 0.003 TYR C 432 PHE 0.032 0.002 PHE A 949 TRP 0.017 0.002 TRP A 113 HIS 0.008 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.29 (15121) covalent geometry : angle 0.82709 / 0.41 (20717) hydrogen bonds : bond 0.04536 / 3.14 ( 551) hydrogen bonds : angle 4.68703 / 3.24 ( 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 224 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8930 (ttp-110) cc_final: 0.8611 (ptm-80) REVERT: A 126 ARG cc_start: 0.7561 (mmm160) cc_final: 0.7134 (tpm170) REVERT: A 480 LYS cc_start: 0.9411 (mmtt) cc_final: 0.9024 (tppt) REVERT: A 484 TRP cc_start: 0.8844 (m-90) cc_final: 0.8437 (m-90) REVERT: A 490 TRP cc_start: 0.5532 (OUTLIER) cc_final: 0.4664 (m-10) REVERT: A 552 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7818 (mm) REVERT: A 796 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7950 (tptp) REVERT: A 823 ARG cc_start: 0.7662 (tmt170) cc_final: 0.7378 (tmt-80) REVERT: A 1210 TYR cc_start: 0.7913 (m-80) cc_final: 0.7674 (t80) REVERT: B 134 LYS cc_start: 0.8758 (ptmt) cc_final: 0.8394 (pttt) REVERT: B 231 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8206 (mp) REVERT: B 321 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8029 (mptt) REVERT: B 328 ARG cc_start: 0.9034 (mtm110) cc_final: 0.8416 (tpm-80) REVERT: B 346 MET cc_start: 0.8420 (ttt) cc_final: 0.8132 (ttm) REVERT: B 466 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7535 (ttp) REVERT: C 122 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.7901 (mmm160) REVERT: C 155 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: C 238 SER cc_start: 0.9307 (OUTLIER) cc_final: 0.9079 (p) REVERT: C 325 ARG cc_start: 0.5888 (ptm160) cc_final: 0.5518 (ptm-80) outliers start: 60 outliers final: 31 residues processed: 213 average time/residue: 0.4992 time to fit residues: 118.7547 Evaluate side-chains 195 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 566 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 742 VAL 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 1199 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 268 MET 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 C residue 87 SER Chi-restraints excluded: chain C residue 155 GLU 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 407 LEU 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: 0.9990 chunk 118 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS C 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.163698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114074 restraints weight = 24412.112| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.74 r_work: 0.3481 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15121 Z= 0.146 Angle : 0.770 14.088 20717 Z= 0.379 Chirality : 0.045 0.220 2284 Planarity : 0.005 0.060 2505 Dihedral : 16.933 171.450 2492 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.43 % Favored : 89.51 % Rotamer: Outliers : 3.17 % Allowed : 26.70 % Favored : 70.13 % 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: -0.63 (0.21), residues: 1725 helix: 1.09 (0.22), residues: 589 sheet: 0.83 (0.34), residues: 231 loop : -1.89 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 102 TYR 0.030 0.002 TYR C 432 PHE 0.030 0.001 PHE A 949 TRP 0.019 0.001 TRP A 113 HIS 0.007 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (15121) covalent geometry : angle 0.76992 / 0.38 (20717) hydrogen bonds : bond 0.03786 / 2.63 ( 551) hydrogen bonds : angle 4.36405 / 3.03 ( 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 218 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8933 (ttp-110) cc_final: 0.8608 (ptm-80) REVERT: A 126 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7217 (tpm170) REVERT: A 484 TRP cc_start: 0.8625 (m-90) cc_final: 0.8200 (m-90) REVERT: A 490 TRP cc_start: 0.5556 (OUTLIER) cc_final: 0.4475 (m-10) REVERT: A 552 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7708 (mm) REVERT: A 796 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7913 (tptp) REVERT: A 823 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7336 (tmt-80) REVERT: A 1210 TYR cc_start: 0.7865 (m-80) cc_final: 0.7578 (t80) REVERT: B 191 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8412 (tp30) REVERT: B 231 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 321 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8032 (mptt) REVERT: B 328 ARG cc_start: 0.8988 (mtm110) cc_final: 0.8391 (tpm-80) REVERT: B 346 MET cc_start: 0.8374 (ttt) cc_final: 0.8118 (ttm) REVERT: B 466 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7455 (ttp) REVERT: C 122 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.7927 (mmm160) REVERT: C 155 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: C 238 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.9045 (p) REVERT: C 258 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8166 (m-70) REVERT: C 325 ARG cc_start: 0.6099 (ptm160) cc_final: 0.5656 (ptm-80) REVERT: C 400 GLN cc_start: 0.7935 (mt0) cc_final: 0.7576 (mm-40) outliers start: 46 outliers final: 26 residues processed: 208 average time/residue: 0.4786 time to fit residues: 111.2758 Evaluate side-chains 193 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 566 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 830 ASP 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 B residue 119 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 VAL 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 155 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 315 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 173 optimal weight: 50.0000 chunk 47 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 89 optimal weight: 0.0570 chunk 50 optimal weight: 20.0000 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.163599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113600 restraints weight = 24825.441| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.85 r_work: 0.3464 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15121 Z= 0.151 Angle : 0.782 13.753 20717 Z= 0.387 Chirality : 0.045 0.179 2284 Planarity : 0.005 0.063 2505 Dihedral : 16.867 171.645 2492 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.26 % Favored : 89.68 % Rotamer: Outliers : 3.03 % Allowed : 27.05 % Favored : 69.92 % 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: -0.61 (0.21), residues: 1725 helix: 1.14 (0.22), residues: 584 sheet: 0.89 (0.35), residues: 225 loop : -1.88 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 102 TYR 0.036 0.002 TYR A 479 PHE 0.031 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 0.00336 / 0.15 (15121) covalent geometry : angle 0.78246 / 0.39 (20717) hydrogen bonds : bond 0.03756 / 2.60 ( 551) hydrogen bonds : angle 4.33969 / 3.02 ( 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 217 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.594 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: 0.8933 (ttp-110) cc_final: 0.8594 (ptm-80) REVERT: A 126 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7209 (tpm170) REVERT: A 484 TRP cc_start: 0.8626 (m-90) cc_final: 0.8189 (m-90) REVERT: A 490 TRP cc_start: 0.5525 (OUTLIER) cc_final: 0.4475 (m-10) REVERT: A 552 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7682 (mm) REVERT: A 796 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7885 (tptp) REVERT: A 823 ARG cc_start: 0.7643 (tmt170) cc_final: 0.7292 (tmt-80) REVERT: A 985 MET cc_start: 0.6442 (mpm) cc_final: 0.6236 (mpm) REVERT: A 1164 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8574 (t80) REVERT: A 1210 TYR cc_start: 0.7807 (m-80) cc_final: 0.7505 (t80) REVERT: B 134 LYS cc_start: 0.8782 (ptmt) cc_final: 0.8370 (pttt) REVERT: B 176 LYS cc_start: 0.8447 (mtpp) cc_final: 0.7795 (tptp) REVERT: B 191 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8388 (tp30) REVERT: B 231 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 321 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8059 (mptt) REVERT: B 328 ARG cc_start: 0.8985 (mtm110) cc_final: 0.8405 (tpm-80) REVERT: B 346 MET cc_start: 0.8362 (ttt) cc_final: 0.8107 (ttm) REVERT: B 419 GLU cc_start: 0.8748 (tp30) cc_final: 0.7967 (tm-30) REVERT: B 466 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7446 (ttp) REVERT: C 122 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.7939 (mmm160) REVERT: C 155 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: C 258 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8147 (m-70) REVERT: C 325 ARG cc_start: 0.6174 (ptm160) cc_final: 0.5733 (ptm-80) REVERT: C 400 GLN cc_start: 0.7957 (mt0) cc_final: 0.7661 (mm-40) outliers start: 44 outliers final: 29 residues processed: 207 average time/residue: 0.5277 time to fit residues: 121.7091 Evaluate side-chains 201 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 310 SER 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 566 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 830 ASP 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 1164 PHE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 VAL 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 155 GLU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 407 LEU 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: 0.9990 chunk 115 optimal weight: 0.0020 chunk 168 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.162307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112500 restraints weight = 24290.970| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.73 r_work: 0.3464 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15121 Z= 0.187 Angle : 0.803 18.850 20717 Z= 0.396 Chirality : 0.046 0.262 2284 Planarity : 0.005 0.065 2505 Dihedral : 16.848 171.861 2492 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.72 % Favored : 89.22 % Rotamer: Outliers : 3.30 % Allowed : 27.05 % Favored : 69.65 % 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: -0.66 (0.21), residues: 1725 helix: 1.14 (0.22), residues: 584 sheet: 0.79 (0.35), residues: 227 loop : -1.94 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 102 TYR 0.024 0.002 TYR C 315 PHE 0.031 0.002 PHE A 949 TRP 0.023 0.001 TRP A 113 HIS 0.010 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (15121) covalent geometry : angle 0.80349 / 0.40 (20717) hydrogen bonds : bond 0.03965 / 2.72 ( 551) hydrogen bonds : angle 4.39905 / 3.06 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6564.00 seconds wall clock time: 112 minutes 23.89 seconds (6743.89 seconds total)