Starting phenix.real_space_refine on Sat Aug 23 21:51:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5m_29749/08_2025/8g5m_29749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5m_29749/08_2025/8g5m_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_29749/08_2025/8g5m_29749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5m_29749/08_2025/8g5m_29749_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5m_29749/08_2025/8g5m_29749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5m_29749/08_2025/8g5m_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14673 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7224 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 61, 'TRANS': 870} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 7, 'ARG:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 167 Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3253 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3230 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 479 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 18} Chain: "T" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 487 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 2.92, per 1000 atoms: 0.20 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: 1.20 Conformation dependent library (CDL) restraints added in 524.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 36.2% alpha, 11.3% beta 21 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 135 through 159 removed outlier: 4.118A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.571A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.568A pdb=" N VAL A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 278 No H-bonds generated for 'chain 'A' and resid 277 through 278' Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.617A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.043A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.980A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.234A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 477' Processing helix chain 'A' and resid 540 through 552 removed outlier: 3.903A pdb=" N MET A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.941A pdb=" N LEU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.850A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 803 removed outlier: 3.710A pdb=" N ASN A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.576A pdb=" N GLU A 873 " --> pdb=" O VAL A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 946 through 956 Processing helix chain 'A' and resid 958 through 969 Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.547A pdb=" N ARG A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A1098 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 3.581A pdb=" N LYS A1167 " --> pdb=" O MET A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 197 removed outlier: 4.668A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.616A pdb=" N LEU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.911A pdb=" N GLN B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.974A pdb=" N LEU B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASN B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.790A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.501A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 3.568A pdb=" N TRP C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.668A pdb=" N MET C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 395 through 409 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 470 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.896A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA A 212 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 813 through 815 Processing sheet with id=AA3, first strand: chain 'A' and resid 884 through 889 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.302A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.878A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.066A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.237A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.145A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR C 444 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU C 452 " --> pdb=" O THR C 444 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.44 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=" 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=" N VAL B 338 " pdb=" CA VAL B 338 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.22e-02 6.72e+03 8.88e+00 bond pdb=" N ILE C 231 " pdb=" CA ILE C 231 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.63e+00 ... (remaining 15116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 19862 2.48 - 4.96: 702 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 - 0.129: 2163 0.129 - 0.259: 74 0.259 - 0.388: 2 0.388 - 0.517: 30 0.517 - 0.647: 15 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 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+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 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.69e+00 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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.91e+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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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= 0.364 Angle : 1.041 12.390 20717 Z= 0.614 Chirality : 0.087 0.647 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 aren 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 covalent geometry : bond 0.00606 (15121) covalent geometry : angle 1.04079 (20717) hydrogen bonds : bond 0.14754 ( 551) hydrogen bonds : angle 6.87891 ( 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 : 0.470 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: 0.4594 time to fit residues: 147.6689 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 : 0.467 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 144 GLN A 388 ASN A 404 HIS A 408 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 85 GLN C 250 GLN C 292 ASN C 400 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.163632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.113564 restraints weight = 24915.555| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.85 r_work: 0.3463 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15121 Z= 0.271 Angle : 0.827 13.101 20717 Z= 0.418 Chirality : 0.048 0.203 2284 Planarity : 0.006 0.059 2505 Dihedral : 17.571 172.416 2512 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.32 % Favored : 89.62 % Rotamer: Outliers : 5.64 % Allowed : 19.89 % Favored : 74.47 % 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 aren not related in a simple way. whole: -0.68 (0.21), residues: 1725 helix: 1.16 (0.22), residues: 593 sheet: 1.06 (0.34), residues: 230 loop : -2.10 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 328 TYR 0.040 0.003 TYR C 291 PHE 0.022 0.002 PHE C 403 TRP 0.035 0.002 TRP A 486 HIS 0.009 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00611 (15121) covalent geometry : angle 0.82684 (20717) hydrogen bonds : bond 0.04775 ( 551) hydrogen bonds : angle 4.65801 ( 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 287 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 205 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8785 (ttp-110) cc_final: 0.8525 (ptm-80) REVERT: A 465 ASP cc_start: 0.8566 (m-30) cc_final: 0.8345 (m-30) REVERT: A 480 LYS cc_start: 0.9444 (mmtt) cc_final: 0.8992 (tppt) REVERT: A 484 TRP cc_start: 0.8604 (m-90) cc_final: 0.8342 (m-90) REVERT: A 490 TRP cc_start: 0.5642 (OUTLIER) cc_final: 0.4700 (m-10) REVERT: A 540 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: A 541 GLN cc_start: 0.6020 (mp10) cc_final: 0.5463 (mp10) REVERT: A 796 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7857 (ptmm) REVERT: A 823 ARG cc_start: 0.7566 (tmt170) cc_final: 0.7318 (tmt170) REVERT: A 1207 GLU cc_start: 0.7988 (pm20) cc_final: 0.7773 (pm20) REVERT: B 69 LEU cc_start: 0.8732 (mp) cc_final: 0.8531 (tp) REVERT: B 134 LYS cc_start: 0.8906 (ptmt) cc_final: 0.8673 (pttt) REVERT: B 191 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8560 (tp30) REVERT: B 321 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8051 (mptt) REVERT: B 328 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8460 (tpm-80) REVERT: B 419 GLU cc_start: 0.8598 (tp30) cc_final: 0.7760 (tp30) REVERT: B 466 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7682 (ttp) REVERT: C 122 ARG cc_start: 0.8265 (tpp-160) cc_final: 0.7928 (mmm160) REVERT: C 325 ARG cc_start: 0.6269 (ptm160) cc_final: 0.5832 (ptm-80) REVERT: C 389 ARG cc_start: 0.7770 (mmm160) cc_final: 0.7554 (mmm160) REVERT: C 462 MET cc_start: 0.7889 (mmp) cc_final: 0.7676 (mmp) outliers start: 82 outliers final: 35 residues processed: 261 average time/residue: 0.4971 time to fit residues: 144.5769 Evaluate side-chains 214 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 945 HIS Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 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 238 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 176 optimal weight: 20.0000 chunk 164 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 270 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 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS C 400 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.165086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115189 restraints weight = 25132.404| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.85 r_work: 0.3499 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15121 Z= 0.169 Angle : 0.717 11.986 20717 Z= 0.359 Chirality : 0.045 0.192 2284 Planarity : 0.005 0.052 2505 Dihedral : 17.227 171.573 2495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.91 % Favored : 90.03 % Rotamer: Outliers : 4.75 % Allowed : 22.51 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1725 helix: 1.28 (0.22), residues: 590 sheet: 1.08 (0.34), residues: 229 loop : -1.94 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 802 TYR 0.027 0.002 TYR C 432 PHE 0.023 0.001 PHE A 197 TRP 0.020 0.001 TRP A 486 HIS 0.008 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00380 (15121) covalent geometry : angle 0.71713 (20717) hydrogen bonds : bond 0.03988 ( 551) hydrogen bonds : angle 4.39690 ( 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: 69 poor density : 191 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8802 (ttp-110) cc_final: 0.8520 (ptm-80) REVERT: A 484 TRP cc_start: 0.8489 (m-90) cc_final: 0.8219 (m-90) REVERT: A 490 TRP cc_start: 0.5596 (OUTLIER) cc_final: 0.4696 (m-10) REVERT: A 796 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7945 (ptmm) REVERT: A 1216 GLU cc_start: 0.5110 (OUTLIER) cc_final: 0.4124 (tm-30) REVERT: B 69 LEU cc_start: 0.8803 (mp) cc_final: 0.8603 (tp) REVERT: B 134 LYS cc_start: 0.8865 (ptmt) cc_final: 0.8569 (pttt) REVERT: B 191 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8354 (tp30) REVERT: B 229 LYS cc_start: 0.6764 (pttp) cc_final: 0.6533 (pttm) REVERT: B 231 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 260 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 321 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8043 (mptt) REVERT: B 328 ARG cc_start: 0.9013 (mtm110) cc_final: 0.8438 (tpm-80) REVERT: B 419 GLU cc_start: 0.8626 (tp30) cc_final: 0.7938 (tp30) REVERT: B 466 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7468 (ttp) REVERT: C 113 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: C 122 ARG cc_start: 0.8374 (tpp-160) cc_final: 0.7959 (mmm160) REVERT: C 238 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.9008 (p) REVERT: C 309 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.8131 (p-80) REVERT: C 321 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.8981 (pmtt) REVERT: C 346 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7864 (mtp) REVERT: C 400 GLN cc_start: 0.8062 (mt0) cc_final: 0.7631 (mm-40) REVERT: C 449 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: C 462 MET cc_start: 0.7885 (mmp) cc_final: 0.7652 (mmp) outliers start: 69 outliers final: 25 residues processed: 235 average time/residue: 0.5289 time to fit residues: 137.8390 Evaluate side-chains 207 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 945 HIS Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 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 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 113 GLU 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 346 MET Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 11 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.164185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114405 restraints weight = 24796.154| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.83 r_work: 0.3470 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3103 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= 0.180 Angle : 0.729 12.168 20717 Z= 0.364 Chirality : 0.045 0.187 2284 Planarity : 0.005 0.050 2505 Dihedral : 17.117 172.295 2494 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.67 % Favored : 89.28 % Rotamer: Outliers : 4.34 % Allowed : 23.88 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.21), residues: 1725 helix: 1.25 (0.22), residues: 591 sheet: 0.91 (0.34), residues: 230 loop : -1.92 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 325 TYR 0.026 0.002 TYR C 432 PHE 0.024 0.002 PHE A 197 TRP 0.029 0.001 TRP A 620 HIS 0.008 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00410 (15121) covalent geometry : angle 0.72880 (20717) hydrogen bonds : bond 0.03868 ( 551) hydrogen bonds : angle 4.37321 ( 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 255 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7981 (tp30) cc_final: 0.7776 (tp30) REVERT: A 101 ARG cc_start: 0.8829 (ttp-110) cc_final: 0.8533 (ptm-80) REVERT: A 484 TRP cc_start: 0.8486 (m-90) cc_final: 0.8260 (m-90) REVERT: A 490 TRP cc_start: 0.5492 (OUTLIER) cc_final: 0.4578 (m-10) REVERT: A 740 ASN cc_start: 0.5525 (OUTLIER) cc_final: 0.5100 (t0) REVERT: A 796 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8045 (ptmm) REVERT: A 823 ARG cc_start: 0.7733 (tmt170) cc_final: 0.7403 (tmt-80) REVERT: A 877 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7858 (mpp) REVERT: A 1207 GLU cc_start: 0.7764 (pm20) cc_final: 0.7429 (pm20) REVERT: A 1216 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.4114 (tm-30) REVERT: B 69 LEU cc_start: 0.8798 (mp) cc_final: 0.8597 (tp) REVERT: B 134 LYS cc_start: 0.8835 (ptmt) cc_final: 0.8504 (pttt) REVERT: B 191 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8299 (tp30) REVERT: B 231 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7959 (mp) REVERT: B 321 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8052 (mptt) REVERT: B 328 ARG cc_start: 0.9000 (mtm110) cc_final: 0.8428 (tpm-80) REVERT: B 346 MET cc_start: 0.8416 (ttt) cc_final: 0.8127 (ttm) REVERT: B 466 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7472 (ttp) REVERT: C 113 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: C 122 ARG cc_start: 0.8357 (tpp-160) cc_final: 0.7959 (mmm160) REVERT: C 238 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.9013 (p) REVERT: C 309 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.8191 (p-80) REVERT: C 321 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.9012 (pmtt) REVERT: C 400 GLN cc_start: 0.8057 (mt0) cc_final: 0.7619 (mm-40) REVERT: C 407 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8340 (mp) outliers start: 63 outliers final: 25 residues processed: 233 average time/residue: 0.4887 time to fit residues: 126.9747 Evaluate side-chains 206 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1074 VAL 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 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 113 GLU 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 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 110 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 103 optimal weight: 0.0570 chunk 112 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN 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 = 0.4306 r_free = 0.4306 target = 0.166245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.116897 restraints weight = 24646.670| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.82 r_work: 0.3514 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3248 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= 0.136 Angle : 0.711 11.900 20717 Z= 0.352 Chirality : 0.044 0.185 2284 Planarity : 0.004 0.049 2505 Dihedral : 16.925 172.888 2492 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.74 % Favored : 90.20 % Rotamer: Outliers : 3.92 % Allowed : 24.78 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1725 helix: 1.34 (0.22), residues: 585 sheet: 0.97 (0.34), residues: 228 loop : -1.83 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 102 TYR 0.026 0.001 TYR C 432 PHE 0.028 0.001 PHE A 949 TRP 0.022 0.001 TRP A 620 HIS 0.008 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00296 (15121) covalent geometry : angle 0.71054 (20717) hydrogen bonds : bond 0.03528 ( 551) hydrogen bonds : angle 4.19003 ( 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 253 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.570 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: 0.8889 (ttp-110) cc_final: 0.8578 (ptm-80) REVERT: A 484 TRP cc_start: 0.8391 (m-90) cc_final: 0.8165 (m-90) REVERT: A 490 TRP cc_start: 0.5426 (OUTLIER) cc_final: 0.4363 (m-10) REVERT: A 740 ASN cc_start: 0.5419 (OUTLIER) cc_final: 0.4968 (t0) REVERT: A 796 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7999 (ptmm) REVERT: A 985 MET cc_start: 0.7789 (pp-130) cc_final: 0.7574 (ppp) REVERT: A 1207 GLU cc_start: 0.7813 (pm20) cc_final: 0.7573 (pm20) REVERT: A 1216 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.3982 (tm-30) REVERT: B 69 LEU cc_start: 0.8907 (mp) cc_final: 0.8616 (tp) REVERT: B 134 LYS cc_start: 0.8782 (ptmt) cc_final: 0.8431 (pttt) REVERT: B 231 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 321 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8054 (mptt) REVERT: B 328 ARG cc_start: 0.9020 (mtm110) cc_final: 0.8433 (tpm-80) REVERT: B 346 MET cc_start: 0.8350 (ttt) cc_final: 0.8105 (ttm) REVERT: B 466 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7207 (ttp) REVERT: C 113 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: C 122 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.7985 (mmm160) REVERT: C 238 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.9019 (p) REVERT: C 309 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.8144 (p-80) REVERT: C 325 ARG cc_start: 0.6080 (ptm160) cc_final: 0.5614 (ptm-80) REVERT: C 407 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 432 TYR cc_start: 0.8944 (m-80) cc_final: 0.8728 (m-80) REVERT: C 449 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6780 (mp0) outliers start: 57 outliers final: 21 residues processed: 236 average time/residue: 0.5263 time to fit residues: 138.8388 Evaluate side-chains 202 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 740 ASN 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 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 231 ILE 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 468 ILE Chi-restraints excluded: chain C residue 113 GLU 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 309 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 393 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 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: 10.0000 chunk 137 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 117 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 984 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.164894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114867 restraints weight = 24750.108| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.83 r_work: 0.3507 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15121 Z= 0.154 Angle : 0.726 11.690 20717 Z= 0.359 Chirality : 0.044 0.183 2284 Planarity : 0.005 0.052 2505 Dihedral : 16.852 173.260 2492 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.20 % Favored : 89.74 % Rotamer: Outliers : 4.20 % Allowed : 24.78 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.21), residues: 1725 helix: 1.33 (0.22), residues: 590 sheet: 0.84 (0.34), residues: 227 loop : -1.82 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 102 TYR 0.023 0.002 TYR A 479 PHE 0.027 0.001 PHE A 949 TRP 0.018 0.001 TRP A 113 HIS 0.008 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00347 (15121) covalent geometry : angle 0.72584 (20717) hydrogen bonds : bond 0.03607 ( 551) hydrogen bonds : angle 4.20399 ( 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 243 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7267 (tpm170) REVERT: A 189 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8952 (pp) REVERT: A 484 TRP cc_start: 0.8487 (m-90) cc_final: 0.8242 (m-90) REVERT: A 490 TRP cc_start: 0.5480 (OUTLIER) cc_final: 0.4487 (m-10) REVERT: A 740 ASN cc_start: 0.5517 (OUTLIER) cc_final: 0.5038 (t0) REVERT: A 796 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7801 (tmtm) REVERT: A 1136 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: A 1207 GLU cc_start: 0.7828 (pm20) cc_final: 0.7583 (pm20) REVERT: A 1210 TYR cc_start: 0.7933 (m-80) cc_final: 0.7626 (t80) REVERT: A 1216 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.3967 (tm-30) REVERT: B 69 LEU cc_start: 0.8875 (mp) cc_final: 0.8672 (tp) REVERT: B 176 LYS cc_start: 0.8390 (mtpp) cc_final: 0.7761 (tptp) REVERT: B 191 GLU cc_start: 0.8722 (tp30) cc_final: 0.8516 (tp30) REVERT: B 231 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 321 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8048 (mptt) REVERT: B 328 ARG cc_start: 0.9032 (mtm110) cc_final: 0.8570 (tpm170) REVERT: B 346 MET cc_start: 0.8393 (ttt) cc_final: 0.8120 (ttm) REVERT: B 466 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7439 (ttp) REVERT: C 113 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: C 122 ARG cc_start: 0.8428 (tpp-160) cc_final: 0.7945 (mmm160) REVERT: C 258 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.8161 (m-70) REVERT: C 309 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.8147 (p-80) REVERT: C 325 ARG cc_start: 0.6105 (ptm160) cc_final: 0.5614 (ptm-80) REVERT: C 400 GLN cc_start: 0.8028 (mt0) cc_final: 0.7608 (mm-40) REVERT: C 407 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8295 (mp) outliers start: 61 outliers final: 29 residues processed: 231 average time/residue: 0.4332 time to fit residues: 112.2088 Evaluate side-chains 204 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 189 ILE 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 594 LEU Chi-restraints excluded: chain A residue 740 ASN 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 1136 GLU 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 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 113 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 258 HIS 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 407 LEU 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: 3.9990 chunk 122 optimal weight: 0.0060 chunk 51 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 176 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 758 ASN A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.165956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115985 restraints weight = 24430.679| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.85 r_work: 0.3493 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15121 Z= 0.158 Angle : 0.735 11.093 20717 Z= 0.363 Chirality : 0.044 0.182 2284 Planarity : 0.004 0.046 2505 Dihedral : 16.812 173.475 2492 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.09 % Favored : 89.86 % Rotamer: Outliers : 4.13 % Allowed : 25.46 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1725 helix: 1.30 (0.22), residues: 590 sheet: 0.84 (0.34), residues: 233 loop : -1.79 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 102 TYR 0.031 0.002 TYR C 432 PHE 0.027 0.001 PHE A 949 TRP 0.020 0.001 TRP A 113 HIS 0.008 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00358 (15121) covalent geometry : angle 0.73513 (20717) hydrogen bonds : bond 0.03603 ( 551) hydrogen bonds : angle 4.22325 ( 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 234 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 0.354 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 126 ARG cc_start: 0.7661 (mmm160) cc_final: 0.7390 (tpm170) REVERT: A 484 TRP cc_start: 0.8502 (m-90) cc_final: 0.8145 (m-90) REVERT: A 490 TRP cc_start: 0.5511 (OUTLIER) cc_final: 0.4516 (m-10) REVERT: A 552 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7657 (mm) REVERT: A 740 ASN cc_start: 0.5394 (OUTLIER) cc_final: 0.4896 (t0) REVERT: A 796 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7695 (tptt) REVERT: A 823 ARG cc_start: 0.7643 (tmt170) cc_final: 0.7363 (tmt-80) REVERT: A 1136 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: A 1207 GLU cc_start: 0.7810 (pm20) cc_final: 0.7586 (pm20) REVERT: A 1210 TYR cc_start: 0.7906 (m-80) cc_final: 0.7575 (t80) REVERT: A 1216 GLU cc_start: 0.5025 (OUTLIER) cc_final: 0.4353 (tt0) REVERT: B 176 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7787 (tptp) REVERT: B 191 GLU cc_start: 0.8725 (tp30) cc_final: 0.8435 (tp30) REVERT: B 231 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 321 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8027 (mptt) REVERT: B 328 ARG cc_start: 0.9105 (mtm110) cc_final: 0.8588 (tpm170) REVERT: B 346 MET cc_start: 0.8412 (ttt) cc_final: 0.8174 (ttm) REVERT: B 466 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7413 (ttp) REVERT: C 113 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: C 122 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.7954 (mmm160) REVERT: C 258 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8169 (m-70) REVERT: C 325 ARG cc_start: 0.6020 (ptm160) cc_final: 0.5568 (ptm-80) REVERT: C 400 GLN cc_start: 0.7977 (mt0) cc_final: 0.7526 (mm-40) REVERT: C 407 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 432 TYR cc_start: 0.8927 (m-80) cc_final: 0.8702 (m-80) outliers start: 60 outliers final: 26 residues processed: 220 average time/residue: 0.4398 time to fit residues: 107.7133 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 : 0.522 ------------------------------------------------------------------------------- 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 594 LEU Chi-restraints excluded: chain A residue 740 ASN 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 1136 GLU 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 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 468 ILE Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 407 LEU 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: 1.9990 chunk 83 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 50.0000 chunk 157 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 309 HIS C 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.161007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.110948 restraints weight = 24813.619| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.79 r_work: 0.3404 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15121 Z= 0.281 Angle : 0.830 14.026 20717 Z= 0.410 Chirality : 0.048 0.181 2284 Planarity : 0.005 0.050 2505 Dihedral : 16.897 173.606 2492 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.72 % Favored : 89.16 % Rotamer: Outliers : 3.99 % Allowed : 26.50 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.21), residues: 1725 helix: 0.98 (0.22), residues: 600 sheet: 0.67 (0.35), residues: 222 loop : -1.94 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 102 TYR 0.029 0.002 TYR C 432 PHE 0.030 0.002 PHE A 949 TRP 0.019 0.002 TRP A 113 HIS 0.011 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00648 (15121) covalent geometry : angle 0.82999 (20717) hydrogen bonds : bond 0.04362 ( 551) hydrogen bonds : angle 4.60557 ( 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 228 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TRP cc_start: 0.5658 (OUTLIER) cc_final: 0.4814 (m-10) REVERT: A 552 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 740 ASN cc_start: 0.5422 (OUTLIER) cc_final: 0.4782 (t0) REVERT: A 796 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8006 (tptp) REVERT: A 1136 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: A 1207 GLU cc_start: 0.7900 (pm20) cc_final: 0.7625 (pm20) REVERT: A 1210 TYR cc_start: 0.7945 (m-80) cc_final: 0.7603 (t80) REVERT: B 231 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8212 (mp) REVERT: B 321 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8011 (mptt) REVERT: B 328 ARG cc_start: 0.9115 (mtm110) cc_final: 0.8449 (tpm-80) REVERT: B 466 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7513 (ttp) REVERT: C 113 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 122 ARG cc_start: 0.8348 (tpp-160) cc_final: 0.7874 (mmm160) REVERT: C 258 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8092 (m-70) REVERT: C 325 ARG cc_start: 0.5924 (ptm160) cc_final: 0.5591 (ptm-80) REVERT: C 400 GLN cc_start: 0.7982 (mt0) cc_final: 0.7538 (mm-40) REVERT: C 407 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8296 (mp) outliers start: 58 outliers final: 28 residues processed: 212 average time/residue: 0.4404 time to fit residues: 103.5948 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 : 0.382 ------------------------------------------------------------------------------- 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 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 596 MET Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 742 VAL 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 1136 GLU 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 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 113 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 258 HIS 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 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: 3.9990 chunk 118 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.0670 chunk 151 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 264 GLN ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN C 309 HIS C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.164179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114448 restraints weight = 24700.942| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.85 r_work: 0.3492 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15121 Z= 0.144 Angle : 0.777 14.525 20717 Z= 0.378 Chirality : 0.044 0.194 2284 Planarity : 0.005 0.059 2505 Dihedral : 16.746 173.733 2492 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Rotamer: Outliers : 2.75 % Allowed : 28.36 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.21), residues: 1725 helix: 1.18 (0.22), residues: 591 sheet: 0.86 (0.34), residues: 231 loop : -1.83 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 102 TYR 0.024 0.001 TYR C 432 PHE 0.028 0.001 PHE A 949 TRP 0.021 0.001 TRP A 484 HIS 0.019 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00317 (15121) covalent geometry : angle 0.77739 (20717) hydrogen bonds : bond 0.03602 ( 551) hydrogen bonds : angle 4.27246 ( 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: 40 poor density : 178 time to evaluate : 0.585 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 383 LYS cc_start: 0.8233 (mmmt) cc_final: 0.8012 (mmmt) REVERT: A 490 TRP cc_start: 0.5554 (OUTLIER) cc_final: 0.4489 (m-10) REVERT: A 552 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7604 (mm) REVERT: A 740 ASN cc_start: 0.5361 (OUTLIER) cc_final: 0.4753 (t0) REVERT: A 796 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7906 (tptp) REVERT: A 1136 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: A 1207 GLU cc_start: 0.7863 (pm20) cc_final: 0.7548 (pm20) REVERT: A 1210 TYR cc_start: 0.7799 (m-80) cc_final: 0.7447 (t80) REVERT: B 176 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7484 (tptp) REVERT: B 229 LYS cc_start: 0.6699 (pttp) cc_final: 0.6447 (pttp) REVERT: B 231 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 321 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8038 (mptt) REVERT: B 328 ARG cc_start: 0.9089 (mtm110) cc_final: 0.8546 (tpm170) REVERT: B 346 MET cc_start: 0.8399 (ttt) cc_final: 0.8187 (ttm) REVERT: B 466 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7466 (ttp) REVERT: C 113 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: C 122 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.7921 (mmm160) REVERT: C 258 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8143 (m-70) REVERT: C 325 ARG cc_start: 0.5986 (ptm160) cc_final: 0.5510 (ptm-80) REVERT: C 400 GLN cc_start: 0.7972 (mt0) cc_final: 0.7498 (mm-40) REVERT: C 407 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8278 (mp) outliers start: 40 outliers final: 21 residues processed: 209 average time/residue: 0.5691 time to fit residues: 131.9823 Evaluate side-chains 198 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 354 ASN Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 742 VAL 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 1136 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 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 468 ILE Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 258 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 155 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 173 optimal weight: 50.0000 chunk 47 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 89 optimal weight: 0.0020 chunk 50 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 264 GLN ** A 984 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 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.165451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115618 restraints weight = 24721.728| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.87 r_work: 0.3516 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15121 Z= 0.137 Angle : 0.777 14.617 20717 Z= 0.376 Chirality : 0.044 0.212 2284 Planarity : 0.005 0.059 2505 Dihedral : 16.604 174.081 2492 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.14 % Favored : 89.80 % Rotamer: Outliers : 2.27 % Allowed : 28.77 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.21), residues: 1725 helix: 1.23 (0.22), residues: 591 sheet: 0.91 (0.34), residues: 225 loop : -1.79 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 102 TYR 0.032 0.002 TYR C 432 PHE 0.033 0.001 PHE B 145 TRP 0.030 0.001 TRP A 484 HIS 0.009 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00304 (15121) covalent geometry : angle 0.77654 (20717) hydrogen bonds : bond 0.03462 ( 551) hydrogen bonds : angle 4.18087 ( 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 215 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7832 (mmmt) REVERT: A 387 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 490 TRP cc_start: 0.5478 (OUTLIER) cc_final: 0.4390 (m-10) REVERT: A 552 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7544 (mm) REVERT: A 740 ASN cc_start: 0.5408 (OUTLIER) cc_final: 0.4797 (t0) REVERT: A 796 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7664 (tptt) REVERT: A 1136 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: A 1207 GLU cc_start: 0.7870 (pm20) cc_final: 0.7632 (pm20) REVERT: A 1210 TYR cc_start: 0.7749 (m-80) cc_final: 0.7381 (t80) REVERT: B 176 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7524 (tptp) REVERT: B 231 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8076 (mp) REVERT: B 321 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8039 (mptt) REVERT: B 328 ARG cc_start: 0.9075 (mtm110) cc_final: 0.8532 (tpm170) REVERT: B 346 MET cc_start: 0.8391 (ttt) cc_final: 0.8189 (ttm) REVERT: B 466 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7170 (ttp) REVERT: C 113 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 122 ARG cc_start: 0.8448 (tpp-160) cc_final: 0.7964 (mmm160) REVERT: C 258 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8162 (m-70) REVERT: C 325 ARG cc_start: 0.6030 (ptm160) cc_final: 0.5561 (ptm-80) REVERT: C 400 GLN cc_start: 0.7934 (mt0) cc_final: 0.7471 (mm-40) REVERT: C 407 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8276 (mp) REVERT: C 432 TYR cc_start: 0.8804 (m-80) cc_final: 0.8518 (m-80) REVERT: C 462 MET cc_start: 0.8034 (mmp) cc_final: 0.7665 (mmp) outliers start: 33 outliers final: 17 residues processed: 204 average time/residue: 0.5576 time to fit residues: 126.6540 Evaluate side-chains 192 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 742 VAL 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 1136 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 338 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 258 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 176 optimal weight: 20.0000 chunk 156 optimal weight: 0.0020 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 ASN ** A 983 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 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.165038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.115052 restraints weight = 24653.585| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.90 r_work: 0.3505 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15121 Z= 0.145 Angle : 0.786 17.627 20717 Z= 0.378 Chirality : 0.045 0.226 2284 Planarity : 0.005 0.063 2505 Dihedral : 16.543 174.273 2492 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.97 % Favored : 89.97 % Rotamer: Outliers : 2.41 % Allowed : 28.91 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.21), residues: 1725 helix: 1.26 (0.22), residues: 593 sheet: 0.84 (0.34), residues: 227 loop : -1.78 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 102 TYR 0.016 0.001 TYR C 315 PHE 0.029 0.001 PHE A 949 TRP 0.041 0.001 TRP A 484 HIS 0.007 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00325 (15121) covalent geometry : angle 0.78647 (20717) hydrogen bonds : bond 0.03478 ( 551) hydrogen bonds : angle 4.16597 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6414.98 seconds wall clock time: 109 minutes 50.07 seconds (6590.07 seconds total)