Starting phenix.real_space_refine on Sun Nov 17 23:43:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5m_29749/11_2024/8g5m_29749_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5m_29749/11_2024/8g5m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5m_29749/11_2024/8g5m_29749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5m_29749/11_2024/8g5m_29749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5m_29749/11_2024/8g5m_29749_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5m_29749/11_2024/8g5m_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.54, per 1000 atoms: 0.65 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: 4.29 Conformation dependent library (CDL) restraints added in 1.9 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: 5.40 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: 5.44 Time building geometry restraints manager: 4.71 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: 2.220 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: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.340 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.170 ------------------------------------------------------------------------------- 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= 0.393 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 *********************** 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 : 1.523 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: 1.2373 time to fit residues: 399.6230 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 : 1.733 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 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= 0.305 Angle : 0.763 12.950 20717 Z= 0.384 Chirality : 0.046 0.194 2284 Planarity : 0.005 0.059 2505 Dihedral : 17.516 172.303 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 *********************** 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 : 1.637 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 480 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8818 (tppt) REVERT: A 484 TRP cc_start: 0.8560 (m-90) cc_final: 0.8276 (m-90) REVERT: A 490 TRP cc_start: 0.5463 (OUTLIER) cc_final: 0.4828 (m-10) REVERT: A 540 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7621 (mp-120) REVERT: A 541 GLN cc_start: 0.6362 (mp10) cc_final: 0.6071 (mp10) REVERT: B 69 LEU cc_start: 0.8709 (mp) cc_final: 0.8501 (tp) REVERT: B 321 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8376 (mptt) REVERT: B 419 GLU cc_start: 0.8091 (tp30) cc_final: 0.7521 (tp30) REVERT: C 309 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7728 (p90) REVERT: C 325 ARG cc_start: 0.6833 (ptm160) cc_final: 0.6511 (ptm-80) outliers start: 68 outliers final: 26 residues processed: 252 average time/residue: 1.2379 time to fit residues: 346.9111 Evaluate side-chains 211 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 173 optimal weight: 50.0000 chunk 143 optimal weight: 30.0000 chunk 159 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15121 Z= 0.230 Angle : 0.721 12.458 20717 Z= 0.359 Chirality : 0.044 0.191 2284 Planarity : 0.005 0.055 2505 Dihedral : 17.193 171.576 2495 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.68 % Favored : 90.26 % Rotamer: Outliers : 4.47 % Allowed : 22.16 % Favored : 73.37 % 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: -0.44 (0.21), residues: 1725 helix: 1.35 (0.22), residues: 586 sheet: 1.09 (0.35), residues: 221 loop : -1.87 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 486 HIS 0.011 0.001 HIS C 309 PHE 0.024 0.001 PHE A 197 TYR 0.025 0.002 TYR C 291 ARG 0.008 0.001 ARG C 122 *********************** 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 261 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8370 (mmt) cc_final: 0.7866 (mmt) REVERT: A 465 ASP cc_start: 0.8311 (m-30) cc_final: 0.8109 (m-30) REVERT: A 490 TRP cc_start: 0.5445 (OUTLIER) cc_final: 0.4712 (m-10) REVERT: A 540 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7385 (mp-120) REVERT: A 985 MET cc_start: 0.7773 (mmm) cc_final: 0.7431 (mmm) REVERT: A 1216 GLU cc_start: 0.4839 (OUTLIER) cc_final: 0.3974 (tt0) REVERT: B 69 LEU cc_start: 0.8732 (mp) cc_final: 0.8524 (tp) REVERT: B 321 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8344 (mptt) REVERT: B 419 GLU cc_start: 0.8223 (tp30) cc_final: 0.7778 (tp30) REVERT: C 325 ARG cc_start: 0.6755 (ptm160) cc_final: 0.6388 (ptm-80) outliers start: 65 outliers final: 28 residues processed: 244 average time/residue: 1.0607 time to fit residues: 291.4005 Evaluate side-chains 205 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 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 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 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 84 HIS A 984 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS C 309 HIS C 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 15121 Z= 0.191 Angle : 0.708 12.523 20717 Z= 0.350 Chirality : 0.043 0.188 2284 Planarity : 0.005 0.051 2505 Dihedral : 17.035 172.310 2494 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.39 % Favored : 90.55 % Rotamer: Outliers : 3.23 % Allowed : 23.88 % Favored : 72.88 % 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: -0.39 (0.21), residues: 1725 helix: 1.41 (0.22), residues: 586 sheet: 1.11 (0.34), residues: 221 loop : -1.84 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 484 HIS 0.010 0.001 HIS C 309 PHE 0.022 0.001 PHE A 949 TYR 0.033 0.002 TYR C 432 ARG 0.012 0.001 ARG C 122 *********************** 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 243 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TRP cc_start: 0.5392 (OUTLIER) cc_final: 0.4608 (m-10) REVERT: A 812 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7963 (ttt) REVERT: A 1216 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.3783 (tm-30) REVERT: B 321 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8313 (mptt) REVERT: B 419 GLU cc_start: 0.8231 (tp30) cc_final: 0.7770 (tm-30) outliers start: 47 outliers final: 26 residues processed: 228 average time/residue: 1.1428 time to fit residues: 291.7144 Evaluate side-chains 201 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 812 MET 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 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 127 optimal weight: 0.0070 chunk 70 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 153 optimal weight: 0.0980 chunk 43 optimal weight: 0.0040 overall best weight: 0.2610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN 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** C 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15121 Z= 0.174 Angle : 0.701 12.483 20717 Z= 0.345 Chirality : 0.043 0.185 2284 Planarity : 0.005 0.061 2505 Dihedral : 16.893 172.969 2494 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.39 % Favored : 90.55 % Rotamer: Outliers : 3.85 % Allowed : 24.57 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.21), residues: 1725 helix: 1.52 (0.23), residues: 582 sheet: 1.13 (0.34), residues: 222 loop : -1.84 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 484 HIS 0.007 0.001 HIS A 945 PHE 0.026 0.001 PHE A 949 TYR 0.034 0.001 TYR C 432 ARG 0.016 0.000 ARG C 122 *********************** 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 262 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TRP cc_start: 0.5322 (OUTLIER) cc_final: 0.4486 (m-10) REVERT: A 812 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7919 (ttt) REVERT: A 1206 MET cc_start: 0.5442 (mpt) cc_final: 0.2550 (ttm) REVERT: A 1216 GLU cc_start: 0.4639 (OUTLIER) cc_final: 0.3648 (tm-30) REVERT: B 191 GLU cc_start: 0.7877 (tp30) cc_final: 0.7637 (tp30) REVERT: B 321 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8325 (mptt) REVERT: B 419 GLU cc_start: 0.8369 (tp30) cc_final: 0.7795 (tm-30) REVERT: C 407 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8598 (mp) outliers start: 56 outliers final: 26 residues processed: 245 average time/residue: 1.0819 time to fit residues: 299.5663 Evaluate side-chains 203 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1056 GLU 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 73 CYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 315 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.0470 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 305 ASN C 77 HIS C 85 GLN C 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15121 Z= 0.274 Angle : 0.749 13.961 20717 Z= 0.366 Chirality : 0.045 0.183 2284 Planarity : 0.005 0.047 2505 Dihedral : 16.877 173.302 2494 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.09 % Rotamer: Outliers : 3.65 % Allowed : 25.46 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.21), residues: 1725 helix: 1.39 (0.23), residues: 585 sheet: 0.99 (0.34), residues: 216 loop : -1.85 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 484 HIS 0.010 0.001 HIS C 96 PHE 0.028 0.002 PHE A 949 TYR 0.032 0.002 TYR C 432 ARG 0.006 0.000 ARG A 101 *********************** 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 233 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TRP cc_start: 0.5410 (OUTLIER) cc_final: 0.4715 (m-10) REVERT: A 1216 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.3930 (tm-30) REVERT: B 191 GLU cc_start: 0.7885 (tp30) cc_final: 0.7676 (tp30) REVERT: B 321 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8342 (mptt) REVERT: B 419 GLU cc_start: 0.8425 (tp30) cc_final: 0.7858 (tm-30) REVERT: B 466 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7464 (ttt) REVERT: C 325 ARG cc_start: 0.6618 (ptm160) cc_final: 0.6235 (ptm-80) REVERT: C 407 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 53 outliers final: 29 residues processed: 220 average time/residue: 1.1196 time to fit residues: 275.7445 Evaluate side-chains 200 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1056 GLU 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 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 C residue 238 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 440 ASN A 493 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15121 Z= 0.222 Angle : 0.738 13.539 20717 Z= 0.361 Chirality : 0.044 0.182 2284 Planarity : 0.004 0.045 2505 Dihedral : 16.810 173.442 2494 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.57 % Favored : 90.38 % Rotamer: Outliers : 3.92 % Allowed : 26.02 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.21), residues: 1725 helix: 1.30 (0.22), residues: 592 sheet: 0.96 (0.34), residues: 222 loop : -1.81 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 484 HIS 0.006 0.001 HIS C 96 PHE 0.028 0.001 PHE A 949 TYR 0.032 0.002 TYR C 432 ARG 0.006 0.000 ARG A 823 *********************** 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 243 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TRP cc_start: 0.5287 (OUTLIER) cc_final: 0.4528 (m-10) REVERT: A 493 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.4353 (tm130) REVERT: A 796 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8212 (tptp) REVERT: A 1216 GLU cc_start: 0.5085 (OUTLIER) cc_final: 0.4192 (tt0) REVERT: B 191 GLU cc_start: 0.7811 (tp30) cc_final: 0.7544 (tp30) REVERT: B 321 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8335 (mptt) REVERT: B 419 GLU cc_start: 0.8421 (tp30) cc_final: 0.8182 (mp0) REVERT: B 466 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7490 (ttt) REVERT: C 325 ARG cc_start: 0.6620 (ptm160) cc_final: 0.6236 (ptm-80) REVERT: C 407 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8612 (mp) outliers start: 57 outliers final: 28 residues processed: 228 average time/residue: 1.1864 time to fit residues: 302.1465 Evaluate side-chains 203 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 594 LEU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1056 GLU 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 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain 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 315 TYR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 134 optimal weight: 0.0070 chunk 155 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 264 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** C 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3479 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= 0.198 Angle : 0.746 13.537 20717 Z= 0.364 Chirality : 0.044 0.182 2284 Planarity : 0.004 0.046 2505 Dihedral : 16.747 173.619 2494 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.57 % Favored : 90.38 % Rotamer: Outliers : 3.10 % Allowed : 27.32 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.21), residues: 1725 helix: 1.38 (0.22), residues: 585 sheet: 0.97 (0.34), residues: 216 loop : -1.83 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 484 HIS 0.006 0.001 HIS C 96 PHE 0.029 0.001 PHE A 949 TYR 0.034 0.002 TYR C 432 ARG 0.006 0.000 ARG C 122 *********************** 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 226 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TRP cc_start: 0.5199 (OUTLIER) cc_final: 0.4290 (m-10) REVERT: A 796 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8212 (tptp) REVERT: A 1216 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.4116 (tt0) REVERT: B 191 GLU cc_start: 0.7810 (tp30) cc_final: 0.7491 (tp30) REVERT: B 321 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8331 (mptt) REVERT: B 466 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7466 (ttt) REVERT: C 407 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8593 (mp) outliers start: 45 outliers final: 27 residues processed: 210 average time/residue: 1.1312 time to fit residues: 269.4409 Evaluate side-chains 205 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1056 GLU 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 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 758 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15121 Z= 0.258 Angle : 0.776 13.151 20717 Z= 0.380 Chirality : 0.045 0.194 2284 Planarity : 0.004 0.045 2505 Dihedral : 16.753 173.794 2494 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.20 % Favored : 89.74 % Rotamer: Outliers : 3.44 % Allowed : 27.39 % Favored : 69.17 % 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: -0.50 (0.21), residues: 1725 helix: 1.31 (0.22), residues: 590 sheet: 0.91 (0.34), residues: 216 loop : -1.86 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 484 HIS 0.011 0.001 HIS A 420 PHE 0.030 0.002 PHE A 949 TYR 0.029 0.002 TYR C 432 ARG 0.006 0.000 ARG A 126 *********************** 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 225 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6907 (mmm160) cc_final: 0.6505 (tpm170) REVERT: A 480 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8774 (tppt) REVERT: A 490 TRP cc_start: 0.5303 (OUTLIER) cc_final: 0.4491 (m-10) REVERT: A 796 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8225 (tptp) REVERT: A 1216 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.4356 (tt0) REVERT: B 260 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8431 (tp) REVERT: B 321 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8335 (mptt) REVERT: B 466 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7476 (ttt) REVERT: B 483 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7976 (tptp) REVERT: C 325 ARG cc_start: 0.6693 (ptm-80) cc_final: 0.6358 (ptm-80) REVERT: C 407 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8582 (mp) outliers start: 50 outliers final: 24 residues processed: 210 average time/residue: 1.1502 time to fit residues: 270.1124 Evaluate side-chains 197 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 TRP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 315 TYR 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 102 optimal weight: 0.0980 chunk 79 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 86 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 149 optimal weight: 0.0050 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 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** C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15121 Z= 0.196 Angle : 0.774 13.238 20717 Z= 0.376 Chirality : 0.044 0.196 2284 Planarity : 0.004 0.046 2505 Dihedral : 16.679 173.879 2494 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.45 % Favored : 90.49 % Rotamer: Outliers : 2.27 % Allowed : 28.97 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.22), residues: 585 sheet: 0.88 (0.34), residues: 218 loop : -1.76 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 484 HIS 0.005 0.001 HIS A 298 PHE 0.029 0.001 PHE A 949 TYR 0.030 0.001 TYR C 432 ARG 0.005 0.000 ARG A 126 ********************** 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 209 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6844 (mmm160) cc_final: 0.6512 (tpm170) REVERT: A 480 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8757 (tppt) REVERT: A 490 TRP cc_start: 0.5258 (OUTLIER) cc_final: 0.4376 (m-10) REVERT: A 544 MET cc_start: 0.8505 (tmm) cc_final: 0.8294 (tmm) REVERT: A 796 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8169 (tptp) REVERT: A 823 ARG cc_start: 0.7397 (tmt170) cc_final: 0.7096 (tmt170) REVERT: A 1216 GLU cc_start: 0.4877 (OUTLIER) cc_final: 0.4081 (tt0) REVERT: B 321 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8343 (mptt) REVERT: B 466 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7488 (ttt) REVERT: B 483 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7912 (tptp) REVERT: C 407 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8536 (mp) outliers start: 33 outliers final: 23 residues processed: 198 average time/residue: 1.1019 time to fit residues: 244.3713 Evaluate side-chains 198 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 594 LEU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 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 B residue 483 LYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 315 TYR 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 43 optimal weight: 0.0270 chunk 129 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 ASN ** 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 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.168171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.118437 restraints weight = 24635.516| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.85 r_work: 0.3540 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15121 Z= 0.203 Angle : 0.787 19.331 20717 Z= 0.380 Chirality : 0.044 0.185 2284 Planarity : 0.004 0.045 2505 Dihedral : 16.602 174.008 2494 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.68 % Favored : 90.26 % Rotamer: Outliers : 2.13 % Allowed : 29.46 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.44 (0.21), residues: 1725 helix: 1.26 (0.22), residues: 591 sheet: 1.00 (0.34), residues: 216 loop : -1.76 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 484 HIS 0.007 0.001 HIS A 420 PHE 0.029 0.001 PHE A 949 TYR 0.022 0.001 TYR C 315 ARG 0.005 0.000 ARG A 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5698.63 seconds wall clock time: 105 minutes 10.36 seconds (6310.36 seconds total)