Starting phenix.real_space_refine on Fri Jun 13 10:42:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5m_29749/06_2025/8g5m_29749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5m_29749/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5m_29749/06_2025/8g5m_29749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5m_29749/06_2025/8g5m_29749.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5m_29749/06_2025/8g5m_29749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5m_29749/06_2025/8g5m_29749_neut.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} 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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 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: 11.42, per 1000 atoms: 0.78 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: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.77 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: 4.84 Time building geometry restraints manager: 4.34 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.850 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.290 ------------------------------------------------------------------------------- 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 : 7.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.001 TRP A 113 HIS 0.005 0.001 HIS B 258 PHE 0.026 0.001 PHE A 539 TYR 0.021 0.001 TYR B 432 ARG 0.021 0.001 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.14754 ( 551) hydrogen bonds : angle 6.87891 ( 1512) covalent geometry : bond 0.00606 (15121) covalent geometry : angle 1.04079 (20717) *********************** 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 : 1.418 Fit side-chains 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: 0.4854 (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: 1.1110 time to fit residues: 358.1825 Evaluate side-chains 213 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 149 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 540 GLN A 550 GLN A 618 HIS A 894 GLN A 945 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 133 HIS B 158 GLN B 258 HIS B 397 GLN C 250 GLN C 292 ASN C 309 HIS C 422 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.168726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.119486 restraints weight = 24904.144| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.86 r_work: 0.3551 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15121 Z= 0.207 Angle : 0.763 12.950 20717 Z= 0.384 Chirality : 0.046 0.194 2284 Planarity : 0.005 0.059 2505 Dihedral : 17.517 172.304 2512 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.57 % Favored : 90.38 % Rotamer: Outliers : 4.68 % Allowed : 20.58 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1725 helix: 1.41 (0.22), residues: 592 sheet: 1.08 (0.34), residues: 232 loop : -2.02 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 486 HIS 0.008 0.001 HIS C 309 PHE 0.021 0.002 PHE A 949 TYR 0.029 0.002 TYR C 432 ARG 0.008 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 551) hydrogen bonds : angle 4.47773 ( 1512) covalent geometry : bond 0.00467 (15121) covalent geometry : angle 0.76323 (20717) *********************** 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 274 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 1.672 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 97 GLU cc_start: 0.8993 (mp0) cc_final: 0.8786 (tm-30) REVERT: A 465 ASP cc_start: 0.8563 (m-30) cc_final: 0.8363 (m-30) REVERT: A 480 LYS cc_start: 0.9440 (mmtt) cc_final: 0.8988 (tppt) REVERT: A 490 TRP cc_start: 0.5593 (OUTLIER) cc_final: 0.4753 (m-10) REVERT: A 540 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8003 (mp-120) REVERT: A 541 GLN cc_start: 0.5994 (mp10) cc_final: 0.5620 (mp10) REVERT: A 796 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7766 (ptmm) REVERT: A 1207 GLU cc_start: 0.7997 (pm20) cc_final: 0.7778 (pm20) REVERT: B 134 LYS cc_start: 0.8954 (ptmt) cc_final: 0.8718 (pttt) REVERT: B 231 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7640 (mp) REVERT: B 321 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8096 (mptt) REVERT: B 328 ARG cc_start: 0.8928 (mtm110) cc_final: 0.8438 (tpm-80) REVERT: B 419 GLU cc_start: 0.8469 (tp30) cc_final: 0.7667 (tp30) REVERT: C 122 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7656 (mmm160) REVERT: C 235 THR cc_start: 0.9093 (m) cc_final: 0.8826 (t) REVERT: C 309 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8099 (p90) REVERT: C 325 ARG cc_start: 0.6310 (ptm160) cc_final: 0.5875 (ptm-80) REVERT: C 449 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6698 (mp0) outliers start: 68 outliers final: 26 residues processed: 252 average time/residue: 1.1184 time to fit residues: 314.1624 Evaluate side-chains 217 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 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 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 1074 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 39 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 0.0670 chunk 145 optimal weight: 0.6980 chunk 58 optimal weight: 0.0030 chunk 105 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 540 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS C 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.170084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121567 restraints weight = 24477.585| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.79 r_work: 0.3590 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15121 Z= 0.133 Angle : 0.703 12.611 20717 Z= 0.349 Chirality : 0.044 0.191 2284 Planarity : 0.005 0.054 2505 Dihedral : 17.150 171.587 2495 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.67 % Rotamer: Outliers : 4.27 % Allowed : 22.23 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1725 helix: 1.44 (0.22), residues: 582 sheet: 1.18 (0.34), residues: 233 loop : -1.84 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 484 HIS 0.009 0.001 HIS C 309 PHE 0.022 0.001 PHE A 197 TYR 0.024 0.001 TYR C 432 ARG 0.008 0.000 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 551) hydrogen bonds : angle 4.20187 ( 1512) covalent geometry : bond 0.00282 (15121) covalent geometry : angle 0.70340 (20717) *********************** 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 262 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 1.446 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 105 GLU cc_start: 0.9591 (tm-30) cc_final: 0.9374 (pp20) REVERT: A 393 MET cc_start: 0.8461 (mmt) cc_final: 0.8218 (mmt) REVERT: A 465 ASP cc_start: 0.8547 (m-30) cc_final: 0.8331 (m-30) REVERT: A 484 TRP cc_start: 0.8652 (m-90) cc_final: 0.8284 (m-90) REVERT: A 490 TRP cc_start: 0.5491 (OUTLIER) cc_final: 0.4450 (m-10) REVERT: A 740 ASN cc_start: 0.5159 (OUTLIER) cc_final: 0.4624 (t0) REVERT: A 796 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7781 (ptmm) REVERT: A 812 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7993 (ttt) REVERT: A 985 MET cc_start: 0.8256 (mmm) cc_final: 0.7424 (mmm) REVERT: A 1216 GLU cc_start: 0.4609 (OUTLIER) cc_final: 0.3659 (tm-30) REVERT: B 134 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8661 (pttt) REVERT: B 231 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7675 (mp) REVERT: B 321 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8058 (mptt) REVERT: B 328 ARG cc_start: 0.8918 (mtm110) cc_final: 0.8403 (tpm-80) REVERT: B 346 MET cc_start: 0.8299 (ttt) cc_final: 0.8034 (ttm) REVERT: B 419 GLU cc_start: 0.8601 (tp30) cc_final: 0.7660 (tm-30) REVERT: B 466 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7905 (ttp) REVERT: C 122 ARG cc_start: 0.8322 (tpp-160) cc_final: 0.7911 (mmm160) REVERT: C 238 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 321 LYS cc_start: 0.9512 (ttmm) cc_final: 0.8980 (pmtt) REVERT: C 325 ARG cc_start: 0.6314 (ptm160) cc_final: 0.5830 (ptm-80) REVERT: C 432 TYR cc_start: 0.8899 (m-80) cc_final: 0.8696 (m-80) REVERT: C 449 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6691 (mp0) outliers start: 62 outliers final: 23 residues processed: 243 average time/residue: 1.0271 time to fit residues: 281.0705 Evaluate side-chains 209 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 945 HIS Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 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 238 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU 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 128 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 127 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS C 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.120000 restraints weight = 24629.740| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.84 r_work: 0.3553 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15121 Z= 0.146 Angle : 0.698 12.542 20717 Z= 0.346 Chirality : 0.044 0.189 2284 Planarity : 0.005 0.051 2505 Dihedral : 17.006 172.487 2494 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.74 % Favored : 90.20 % Rotamer: Outliers : 3.79 % Allowed : 23.19 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1725 helix: 1.45 (0.22), residues: 584 sheet: 1.15 (0.34), residues: 222 loop : -1.84 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 620 HIS 0.006 0.001 HIS C 309 PHE 0.023 0.001 PHE A 949 TYR 0.025 0.002 TYR A 479 ARG 0.009 0.000 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 551) hydrogen bonds : angle 4.12967 ( 1512) covalent geometry : bond 0.00322 (15121) covalent geometry : angle 0.69840 (20717) *********************** 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 254 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 1.614 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: 0.8877 (ptm-80) cc_final: 0.8406 (ppt170) REVERT: A 484 TRP cc_start: 0.8631 (m-90) cc_final: 0.8150 (m-90) REVERT: A 490 TRP cc_start: 0.5516 (OUTLIER) cc_final: 0.4580 (m-10) REVERT: A 540 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8005 (mp-120) REVERT: A 740 ASN cc_start: 0.5302 (OUTLIER) cc_final: 0.4794 (t0) REVERT: A 796 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7860 (ptmm) REVERT: A 1207 GLU cc_start: 0.7823 (pm20) cc_final: 0.7523 (pm20) REVERT: A 1216 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.3710 (tm-30) REVERT: B 134 LYS cc_start: 0.8874 (ptmt) cc_final: 0.8543 (pttt) REVERT: B 229 LYS cc_start: 0.6735 (pttp) cc_final: 0.6506 (pttm) REVERT: B 231 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7741 (mp) REVERT: B 321 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8042 (mptt) REVERT: B 328 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8430 (tpm-80) REVERT: B 346 MET cc_start: 0.8329 (ttt) cc_final: 0.8094 (ttm) REVERT: B 419 GLU cc_start: 0.8758 (tp30) cc_final: 0.7708 (tm-30) REVERT: B 466 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7902 (ttp) REVERT: C 122 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7910 (mmm160) REVERT: C 238 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8911 (p) REVERT: C 314 MET cc_start: 0.8759 (ttm) cc_final: 0.8551 (ttm) outliers start: 55 outliers final: 29 residues processed: 237 average time/residue: 1.0048 time to fit residues: 268.5083 Evaluate side-chains 205 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 540 GLN 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 939 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 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 139 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL 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 75 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 153 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 147 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.169656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.119976 restraints weight = 24846.510| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.89 r_work: 0.3555 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15121 Z= 0.128 Angle : 0.691 12.415 20717 Z= 0.340 Chirality : 0.043 0.185 2284 Planarity : 0.004 0.054 2505 Dihedral : 16.889 173.025 2494 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.72 % Rotamer: Outliers : 3.58 % Allowed : 24.43 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1725 helix: 1.45 (0.22), residues: 584 sheet: 1.12 (0.34), residues: 222 loop : -1.78 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 620 HIS 0.006 0.001 HIS C 309 PHE 0.027 0.001 PHE A 949 TYR 0.021 0.001 TYR C 432 ARG 0.008 0.000 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 551) hydrogen bonds : angle 4.03257 ( 1512) covalent geometry : bond 0.00273 (15121) covalent geometry : angle 0.69081 (20717) *********************** 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 240 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.581 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 484 TRP cc_start: 0.8592 (m-90) cc_final: 0.8036 (m-90) REVERT: A 490 TRP cc_start: 0.5408 (OUTLIER) cc_final: 0.4383 (m-10) REVERT: A 540 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7945 (mp-120) REVERT: A 740 ASN cc_start: 0.5303 (OUTLIER) cc_final: 0.4764 (t0) REVERT: A 796 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7851 (ptmm) REVERT: A 812 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8030 (ttt) REVERT: A 1207 GLU cc_start: 0.7834 (pm20) cc_final: 0.7614 (pm20) REVERT: A 1210 TYR cc_start: 0.7919 (m-80) cc_final: 0.7690 (t80) REVERT: A 1216 GLU cc_start: 0.4744 (OUTLIER) cc_final: 0.3748 (tm-30) REVERT: B 191 GLU cc_start: 0.8703 (tp30) cc_final: 0.8436 (tp30) REVERT: B 231 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7742 (mp) REVERT: B 321 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8032 (mptt) REVERT: B 328 ARG cc_start: 0.8964 (mtm110) cc_final: 0.8538 (tpm170) REVERT: B 419 GLU cc_start: 0.8813 (tp30) cc_final: 0.7764 (tm-30) REVERT: B 466 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7894 (ttp) REVERT: C 122 ARG cc_start: 0.8342 (tpp-160) cc_final: 0.7915 (mmm160) REVERT: C 238 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8936 (p) REVERT: C 321 LYS cc_start: 0.9516 (ttmm) cc_final: 0.8980 (pmtt) REVERT: C 325 ARG cc_start: 0.6036 (ptm160) cc_final: 0.5784 (ptm160) REVERT: C 407 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 432 TYR cc_start: 0.8860 (m-80) cc_final: 0.8634 (m-80) REVERT: C 449 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: C 462 MET cc_start: 0.7811 (mmp) cc_final: 0.7540 (mmp) outliers start: 52 outliers final: 24 residues processed: 228 average time/residue: 1.0155 time to fit residues: 260.9852 Evaluate side-chains 202 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 540 GLN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 812 MET 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 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 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 99 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 87 optimal weight: 0.0870 chunk 72 optimal weight: 30.0000 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 493 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 223 GLN C 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.168330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118651 restraints weight = 24762.731| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.87 r_work: 0.3530 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3149 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= 0.150 Angle : 0.708 13.872 20717 Z= 0.346 Chirality : 0.044 0.183 2284 Planarity : 0.004 0.046 2505 Dihedral : 16.824 173.345 2494 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.62 % Favored : 90.32 % Rotamer: Outliers : 3.99 % Allowed : 25.33 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1725 helix: 1.41 (0.23), residues: 590 sheet: 1.02 (0.34), residues: 222 loop : -1.79 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 113 HIS 0.006 0.001 HIS C 96 PHE 0.027 0.001 PHE A 949 TYR 0.022 0.002 TYR A 479 ARG 0.006 0.000 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 551) hydrogen bonds : angle 4.08932 ( 1512) covalent geometry : bond 0.00337 (15121) covalent geometry : angle 0.70792 (20717) *********************** 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 235 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8684 (mmp) cc_final: 0.8305 (pmm) REVERT: A 484 TRP cc_start: 0.8671 (m-90) cc_final: 0.8173 (m-90) REVERT: A 490 TRP cc_start: 0.5507 (OUTLIER) cc_final: 0.4542 (m-10) REVERT: A 493 GLN cc_start: 0.5899 (OUTLIER) cc_final: 0.5592 (tm130) REVERT: A 540 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7920 (mp-120) REVERT: A 740 ASN cc_start: 0.5461 (OUTLIER) cc_final: 0.4915 (t0) REVERT: A 796 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7923 (ptmm) REVERT: A 823 ARG cc_start: 0.7650 (tmt170) cc_final: 0.7316 (tmt-80) REVERT: A 1136 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: A 1207 GLU cc_start: 0.7886 (pm20) cc_final: 0.7643 (pm20) REVERT: A 1210 TYR cc_start: 0.7879 (m-80) cc_final: 0.7662 (t80) REVERT: A 1216 GLU cc_start: 0.4893 (OUTLIER) cc_final: 0.3827 (tm-30) REVERT: B 176 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7740 (tptp) REVERT: B 191 GLU cc_start: 0.8681 (tp30) cc_final: 0.8414 (tp30) REVERT: B 231 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 321 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8062 (mptt) REVERT: B 328 ARG cc_start: 0.9037 (mtm110) cc_final: 0.8548 (tpm170) REVERT: B 419 GLU cc_start: 0.8789 (tp30) cc_final: 0.7767 (tm-30) REVERT: B 466 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7963 (ttp) REVERT: C 122 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.7986 (mmm160) REVERT: C 238 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8976 (p) REVERT: C 321 LYS cc_start: 0.9516 (ttmm) cc_final: 0.8998 (pmtt) REVERT: C 462 MET cc_start: 0.7885 (mmp) cc_final: 0.7631 (mmp) outliers start: 58 outliers final: 26 residues processed: 223 average time/residue: 1.3522 time to fit residues: 341.7837 Evaluate side-chains 208 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 493 GLN Chi-restraints excluded: chain A residue 540 GLN 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 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 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 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 398 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 77 HIS C 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.165616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115800 restraints weight = 24775.384| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.84 r_work: 0.3479 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15121 Z= 0.208 Angle : 0.755 13.415 20717 Z= 0.371 Chirality : 0.045 0.183 2284 Planarity : 0.005 0.045 2505 Dihedral : 16.846 173.490 2494 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.14 % Favored : 89.80 % Rotamer: Outliers : 4.06 % Allowed : 25.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1725 helix: 1.34 (0.22), residues: 585 sheet: 0.86 (0.33), residues: 233 loop : -1.86 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 113 HIS 0.008 0.001 HIS A 298 PHE 0.029 0.002 PHE A 949 TYR 0.023 0.002 TYR C 291 ARG 0.009 0.001 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 551) hydrogen bonds : angle 4.27122 ( 1512) covalent geometry : bond 0.00479 (15121) covalent geometry : angle 0.75495 (20717) *********************** 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 237 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8729 (mmp) cc_final: 0.8344 (pmm) REVERT: A 101 ARG cc_start: 0.8856 (ptm-80) cc_final: 0.8454 (ppt170) REVERT: A 126 ARG cc_start: 0.7484 (mmm160) cc_final: 0.7139 (tpm170) REVERT: A 383 LYS cc_start: 0.8266 (mmmt) cc_final: 0.8018 (mmmt) REVERT: A 484 TRP cc_start: 0.8748 (m-90) cc_final: 0.8226 (m-90) REVERT: A 490 TRP cc_start: 0.5377 (OUTLIER) cc_final: 0.4448 (m-10) REVERT: A 540 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7925 (mp-120) REVERT: A 740 ASN cc_start: 0.5536 (OUTLIER) cc_final: 0.5014 (t0) REVERT: A 796 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7774 (tmtm) REVERT: A 823 ARG cc_start: 0.7644 (tmt170) cc_final: 0.7365 (tmt170) REVERT: A 1075 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7791 (tt) REVERT: A 1136 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: A 1207 GLU cc_start: 0.7897 (pm20) cc_final: 0.7668 (pm20) REVERT: A 1216 GLU cc_start: 0.5114 (OUTLIER) cc_final: 0.4301 (tt0) REVERT: B 176 LYS cc_start: 0.8450 (mtpp) cc_final: 0.7790 (tptp) REVERT: B 191 GLU cc_start: 0.8711 (tp30) cc_final: 0.8400 (tp30) REVERT: B 231 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 321 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8024 (mptt) REVERT: B 328 ARG cc_start: 0.9067 (mtm110) cc_final: 0.8553 (tpm170) REVERT: B 419 GLU cc_start: 0.8809 (tp30) cc_final: 0.7706 (tm-30) REVERT: B 466 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7505 (ttt) REVERT: C 122 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.7939 (mmm160) REVERT: C 238 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.9034 (p) REVERT: C 258 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.8162 (m-70) REVERT: C 321 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.8996 (pmtt) REVERT: C 325 ARG cc_start: 0.5889 (ptm160) cc_final: 0.5506 (ptm160) REVERT: C 432 TYR cc_start: 0.8914 (m-80) cc_final: 0.8634 (m-80) outliers start: 59 outliers final: 26 residues processed: 223 average time/residue: 1.1068 time to fit residues: 275.7911 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 : 1.587 ------------------------------------------------------------------------------- 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 540 GLN 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 1075 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 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 238 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 337 SER 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 64 optimal weight: 5.9990 chunk 133 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 0.0050 chunk 13 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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 440 ASN A 493 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.167609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.117989 restraints weight = 24603.398| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.84 r_work: 0.3513 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3520 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= 0.142 Angle : 0.732 13.449 20717 Z= 0.358 Chirality : 0.044 0.182 2284 Planarity : 0.004 0.045 2505 Dihedral : 16.729 173.602 2492 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.74 % Favored : 90.20 % Rotamer: Outliers : 3.65 % Allowed : 26.63 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1725 helix: 1.38 (0.23), residues: 584 sheet: 0.91 (0.34), residues: 224 loop : -1.78 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 113 HIS 0.005 0.001 HIS C 309 PHE 0.029 0.001 PHE A 949 TYR 0.019 0.002 TYR A 479 ARG 0.007 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 551) hydrogen bonds : angle 4.13785 ( 1512) covalent geometry : bond 0.00318 (15121) covalent geometry : angle 0.73241 (20717) *********************** 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 231 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8868 (ptm-80) cc_final: 0.8468 (ppt170) REVERT: A 126 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7159 (tpm170) REVERT: A 383 LYS cc_start: 0.8257 (mmmt) cc_final: 0.8024 (mmmt) REVERT: A 393 MET cc_start: 0.8566 (mmt) cc_final: 0.8306 (mmt) REVERT: A 484 TRP cc_start: 0.8659 (m-90) cc_final: 0.8159 (m-90) REVERT: A 490 TRP cc_start: 0.5413 (OUTLIER) cc_final: 0.4362 (m-10) REVERT: A 540 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7935 (mp-120) REVERT: A 552 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 740 ASN cc_start: 0.5472 (OUTLIER) cc_final: 0.4926 (t0) REVERT: A 796 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7723 (tmtm) REVERT: A 1136 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: A 1206 MET cc_start: 0.4309 (mpt) cc_final: 0.1597 (ttp) REVERT: A 1207 GLU cc_start: 0.7914 (pm20) cc_final: 0.7614 (pm20) REVERT: A 1216 GLU cc_start: 0.5010 (OUTLIER) cc_final: 0.4193 (tt0) REVERT: B 176 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7807 (tptp) REVERT: B 231 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 321 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8039 (mptt) REVERT: B 328 ARG cc_start: 0.9066 (mtm110) cc_final: 0.8551 (tpm170) REVERT: B 419 GLU cc_start: 0.8754 (tp30) cc_final: 0.8332 (mp0) REVERT: B 466 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7911 (ttp) REVERT: C 122 ARG cc_start: 0.8429 (tpp-160) cc_final: 0.7977 (mmm160) REVERT: C 258 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8168 (m-70) REVERT: C 407 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 432 TYR cc_start: 0.8885 (m-80) cc_final: 0.8552 (m-80) outliers start: 53 outliers final: 25 residues processed: 216 average time/residue: 1.0393 time to fit residues: 252.2794 Evaluate side-chains 201 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 540 GLN 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 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 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 134 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 758 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.165816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115725 restraints weight = 24565.423| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.85 r_work: 0.3487 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15121 Z= 0.173 Angle : 0.765 13.368 20717 Z= 0.374 Chirality : 0.044 0.181 2284 Planarity : 0.004 0.044 2505 Dihedral : 16.713 173.832 2492 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.43 % Favored : 89.51 % Rotamer: Outliers : 3.30 % Allowed : 27.32 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1725 helix: 1.34 (0.22), residues: 584 sheet: 0.83 (0.35), residues: 221 loop : -1.81 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 113 HIS 0.009 0.001 HIS C 309 PHE 0.030 0.001 PHE A 949 TYR 0.020 0.002 TYR C 291 ARG 0.008 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 551) hydrogen bonds : angle 4.22863 ( 1512) covalent geometry : bond 0.00396 (15121) covalent geometry : angle 0.76517 (20717) *********************** 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 216 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.8287 (mmmt) cc_final: 0.8053 (mmmt) REVERT: A 484 TRP cc_start: 0.8739 (m-90) cc_final: 0.8255 (m-90) REVERT: A 490 TRP cc_start: 0.5431 (OUTLIER) cc_final: 0.4484 (m-10) REVERT: A 540 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7957 (mp-120) REVERT: A 552 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7635 (mm) REVERT: A 740 ASN cc_start: 0.5492 (OUTLIER) cc_final: 0.4942 (t0) REVERT: A 796 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7738 (tmtm) REVERT: A 985 MET cc_start: 0.7471 (mmm) cc_final: 0.7034 (mpp) REVERT: A 1136 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: A 1207 GLU cc_start: 0.7926 (pm20) cc_final: 0.7656 (pm20) REVERT: A 1216 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.4300 (tt0) REVERT: B 176 LYS cc_start: 0.8392 (mtpp) cc_final: 0.7727 (tptp) REVERT: B 231 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8050 (mp) REVERT: B 321 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8036 (mptt) REVERT: B 328 ARG cc_start: 0.9075 (mtm110) cc_final: 0.8550 (tpm170) REVERT: B 419 GLU cc_start: 0.8754 (tp30) cc_final: 0.8322 (mp0) REVERT: B 466 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7469 (ttt) REVERT: C 122 ARG cc_start: 0.8460 (tpp-160) cc_final: 0.7979 (mmm160) REVERT: C 258 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8173 (m-70) REVERT: C 309 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.8233 (p90) REVERT: C 325 ARG cc_start: 0.5979 (ptm160) cc_final: 0.5518 (ptm160) REVERT: C 407 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8127 (mp) REVERT: C 432 TYR cc_start: 0.8896 (m-80) cc_final: 0.8610 (m-80) outliers start: 48 outliers final: 25 residues processed: 205 average time/residue: 1.0953 time to fit residues: 250.7439 Evaluate side-chains 200 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 540 GLN 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 1068 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 268 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 354 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.167559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117509 restraints weight = 24590.423| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.87 r_work: 0.3510 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15121 Z= 0.139 Angle : 0.745 13.198 20717 Z= 0.365 Chirality : 0.044 0.192 2284 Planarity : 0.005 0.071 2505 Dihedral : 16.647 173.872 2492 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.74 % Favored : 90.20 % Rotamer: Outliers : 2.96 % Allowed : 27.74 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1725 helix: 1.36 (0.22), residues: 584 sheet: 0.88 (0.34), residues: 218 loop : -1.76 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 113 HIS 0.010 0.001 HIS C 309 PHE 0.030 0.001 PHE A 949 TYR 0.018 0.001 TYR A 479 ARG 0.016 0.001 ARG C 328 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 551) hydrogen bonds : angle 4.12524 ( 1512) covalent geometry : bond 0.00310 (15121) covalent geometry : angle 0.74505 (20717) ********************** 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: 43 poor density : 172 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8322 (tpt) cc_final: 0.8112 (tmt) REVERT: A 101 ARG cc_start: 0.8850 (ptm-80) cc_final: 0.8461 (ppt170) REVERT: A 145 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8702 (tmmm) REVERT: A 383 LYS cc_start: 0.8240 (mmmt) cc_final: 0.8018 (mmmt) REVERT: A 480 LYS cc_start: 0.9417 (mmtt) cc_final: 0.9014 (tppt) REVERT: A 484 TRP cc_start: 0.8640 (m-90) cc_final: 0.8128 (m-90) REVERT: A 490 TRP cc_start: 0.5428 (OUTLIER) cc_final: 0.4369 (m-10) REVERT: A 540 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7969 (mp-120) REVERT: A 552 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7511 (mm) REVERT: A 740 ASN cc_start: 0.5415 (OUTLIER) cc_final: 0.4842 (t0) REVERT: A 796 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7651 (tmtm) REVERT: A 1136 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: A 1207 GLU cc_start: 0.7945 (pm20) cc_final: 0.7634 (pm20) REVERT: A 1209 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7675 (mtt180) REVERT: A 1216 GLU cc_start: 0.4921 (OUTLIER) cc_final: 0.4197 (tt0) REVERT: B 176 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7703 (tptp) REVERT: B 191 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8327 (tp30) REVERT: B 321 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8007 (mptt) REVERT: B 328 ARG cc_start: 0.9104 (mtm110) cc_final: 0.8535 (tpm170) REVERT: B 466 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7904 (ttp) REVERT: B 483 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7165 (tptp) REVERT: C 122 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.7934 (mmm160) REVERT: C 155 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 258 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8127 (m-70) REVERT: C 407 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 432 TYR cc_start: 0.8847 (m-80) cc_final: 0.8470 (m-80) outliers start: 43 outliers final: 21 residues processed: 207 average time/residue: 1.1181 time to fit residues: 259.4019 Evaluate side-chains 197 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 145 LYS 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 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 540 GLN 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 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 135 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.167016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116831 restraints weight = 24677.781| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.87 r_work: 0.3504 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3822 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= 0.145 Angle : 0.750 13.190 20717 Z= 0.366 Chirality : 0.044 0.181 2284 Planarity : 0.005 0.057 2505 Dihedral : 16.569 174.002 2492 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Rotamer: Outliers : 2.82 % Allowed : 27.94 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1725 helix: 1.34 (0.22), residues: 590 sheet: 0.91 (0.35), residues: 212 loop : -1.78 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 113 HIS 0.016 0.001 HIS A 618 PHE 0.029 0.001 PHE A 949 TYR 0.016 0.001 TYR C 291 ARG 0.017 0.001 ARG C 328 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 551) hydrogen bonds : angle 4.13141 ( 1512) covalent geometry : bond 0.00328 (15121) covalent geometry : angle 0.74966 (20717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14982.72 seconds wall clock time: 257 minutes 40.08 seconds (15460.08 seconds total)