Starting phenix.real_space_refine on Wed Mar 4 15:41:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5n_29750/03_2026/8g5n_29750_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5n_29750/03_2026/8g5n_29750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5n_29750/03_2026/8g5n_29750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5n_29750/03_2026/8g5n_29750.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5n_29750/03_2026/8g5n_29750_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5n_29750/03_2026/8g5n_29750_neut.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 38 5.49 5 S 79 5.16 5 C 9099 2.51 5 N 2536 2.21 5 O 2733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14485 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7217 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 61, 'TRANS': 857} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3247 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3224 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Time building chain proxies: 3.20, per 1000 atoms: 0.22 Number of scatterers: 14485 At special positions: 0 Unit cell: (105.677, 104.851, 146.131, 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 79 16.00 P 38 15.00 O 2733 8.00 N 2536 7.00 C 9099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 806.1 milliseconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 37.9% alpha, 11.4% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.811A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix removed outlier: 3.984A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.610A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.502A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 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: 3.996A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 471 removed outlier: 3.539A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.571A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 481 " --> pdb=" O ARG A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.917A pdb=" N SER A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.784A pdb=" N GLU A 775 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 803 WARNING: missing atoms! removed outlier: 5.065A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.520A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.565A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.776A pdb=" N ARG A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 3.715A pdb=" N TYR A1221 " --> pdb=" O LEU A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 174 through 178 removed outlier: 4.207A pdb=" N THR B 177 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.717A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.785A 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 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.561A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.971A pdb=" N GLN B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.979A pdb=" N LEU B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.933A 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: 3.913A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.505A pdb=" N PHE B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 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 120 through 123 Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.338A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.077A 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 307 through 314 removed outlier: 4.548A pdb=" N LEU C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.849A 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 removed outlier: 3.544A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 4.022A pdb=" N LEU C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 419 " --> pdb=" O GLY C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.724A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.848A pdb=" N PHE C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.843A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 213 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 215 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.684A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.891A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.723A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.745A 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: 3.909A 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: 7.350A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.738A 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: 5.977A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB1, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB2, first strand: chain 'C' and resid 413 through 414 removed outlier: 7.538A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3790 1.33 - 1.46: 3172 1.46 - 1.58: 7760 1.58 - 1.70: 77 1.70 - 1.82: 125 Bond restraints: 14924 Sorted by residual: bond pdb=" C3' G R 20 " pdb=" C2' G R 20 " ideal model delta sigma weight residual 1.525 1.622 -0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" C3' C R 16 " pdb=" C2' C R 16 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.50e-02 4.44e+03 2.34e+01 bond pdb=" CG PRO A 772 " pdb=" CD PRO A 772 " ideal model delta sigma weight residual 1.503 1.382 0.121 3.40e-02 8.65e+02 1.27e+01 bond pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 ... (remaining 14919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 20029 3.34 - 6.69: 343 6.69 - 10.03: 36 10.03 - 13.38: 8 13.38 - 16.72: 1 Bond angle restraints: 20417 Sorted by residual: angle pdb=" CA PRO A 772 " pdb=" N PRO A 772 " pdb=" CD PRO A 772 " ideal model delta sigma weight residual 112.00 95.28 16.72 1.40e+00 5.10e-01 1.43e+02 angle pdb=" C3' G R 21 " pdb=" O3' G R 21 " pdb=" P G R 22 " ideal model delta sigma weight residual 120.20 107.20 13.00 1.50e+00 4.44e-01 7.51e+01 angle pdb=" C3' U R 9 " pdb=" O3' U R 9 " pdb=" P G R 10 " ideal model delta sigma weight residual 120.20 107.30 12.90 1.50e+00 4.44e-01 7.39e+01 angle pdb=" C3' DT T 9 " pdb=" O3' DT T 9 " pdb=" P DC T 10 " ideal model delta sigma weight residual 120.20 108.61 11.59 1.50e+00 4.44e-01 5.97e+01 angle pdb=" C3' C R 18 " pdb=" O3' C R 18 " pdb=" P G R 19 " ideal model delta sigma weight residual 120.20 108.68 11.52 1.50e+00 4.44e-01 5.89e+01 ... (remaining 20412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7625 17.89 - 35.78: 867 35.78 - 53.66: 278 53.66 - 71.55: 91 71.55 - 89.44: 20 Dihedral angle restraints: 8881 sinusoidal: 3881 harmonic: 5000 Sorted by residual: dihedral pdb=" CD ARG C 325 " pdb=" NE ARG C 325 " pdb=" CZ ARG C 325 " pdb=" NH1 ARG C 325 " ideal model delta sinusoidal sigma weight residual 0.00 -64.03 64.03 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" C5' G R 20 " pdb=" C4' G R 20 " pdb=" C3' G R 20 " pdb=" O3' G R 20 " ideal model delta sinusoidal sigma weight residual 147.00 103.33 43.67 1 8.00e+00 1.56e-02 4.15e+01 dihedral pdb=" CD ARG C 344 " pdb=" NE ARG C 344 " pdb=" CZ ARG C 344 " pdb=" NH1 ARG C 344 " ideal model delta sinusoidal sigma weight residual 0.00 48.96 -48.96 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 8878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2141 0.127 - 0.255: 55 0.255 - 0.382: 2 0.382 - 0.510: 29 0.510 - 0.637: 8 Chirality restraints: 2235 Sorted by residual: chirality pdb=" P DT T 5 " pdb=" OP1 DT T 5 " pdb=" OP2 DT T 5 " pdb=" O5' DT T 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P G R 6 " pdb=" OP1 G R 6 " pdb=" OP2 G R 6 " pdb=" O5' G R 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" P DA T 6 " pdb=" OP1 DA T 6 " pdb=" OP2 DA T 6 " pdb=" O5' DA T 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.61e+00 ... (remaining 2232 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 325 " 0.988 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG C 325 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG C 325 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 325 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 325 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 344 " -0.815 9.50e-02 1.11e+02 3.66e-01 8.12e+01 pdb=" NE ARG C 344 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG C 344 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 344 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 344 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 597 " 0.616 9.50e-02 1.11e+02 2.76e-01 4.66e+01 pdb=" NE ARG A 597 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 597 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 597 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 597 " 0.020 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 78 2.48 - 3.08: 10403 3.08 - 3.69: 22516 3.69 - 4.29: 31284 4.29 - 4.90: 51146 Nonbonded interactions: 115427 Sorted by model distance: nonbonded pdb=" OG SER A 237 " pdb=" OG SER A 240 " model vdw 1.871 3.040 nonbonded pdb=" O TYR A 282 " pdb=" OH TYR A 434 " model vdw 2.055 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.113 3.040 nonbonded pdb=" O THR A 210 " pdb=" OG SER A 225 " model vdw 2.119 3.040 nonbonded pdb=" O CYS A 224 " pdb=" OG SER A 225 " model vdw 2.123 3.040 ... (remaining 115422 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 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 146 or (resid 147 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 through 170 or (resid 1 \ 71 through 176 and (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 nam \ e CB )) or resid 224 or (resid 225 and (name N or name CA or name C or name O or \ name CB )) or resid 226 through 283 or (resid 284 and (name N or name CA or nam \ e 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 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 145 o \ r (resid 146 through 147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 148 through 160 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 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 0.129 14924 Z= 0.347 Angle : 1.004 16.720 20417 Z= 0.601 Chirality : 0.079 0.637 2235 Planarity : 0.016 0.443 2486 Dihedral : 17.819 89.437 5655 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.85 % Allowed : 24.35 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1712 helix: 1.43 (0.23), residues: 588 sheet: 1.07 (0.36), residues: 215 loop : -1.54 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 866 TYR 0.010 0.001 TYR C 315 PHE 0.025 0.001 PHE A 539 TRP 0.016 0.001 TRP B 255 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00594 (14924) covalent geometry : angle 1.00447 (20417) hydrogen bonds : bond 0.14517 ( 560) hydrogen bonds : angle 6.88705 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.581 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: symmetry clash REVERT: A 299 MET cc_start: 0.7260 (mmm) cc_final: 0.6974 (mmm) REVERT: B 465 MET cc_start: 0.7255 (mmm) cc_final: 0.7000 (mmm) outliers start: 27 outliers final: 12 residues processed: 236 average time/residue: 0.4654 time to fit residues: 123.0991 Evaluate side-chains 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN A 843 GLN A 879 GLN A 976 GLN A1214 GLN B 158 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS C 85 GLN C 305 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.187175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.139301 restraints weight = 26892.466| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 4.41 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14924 Z= 0.178 Angle : 0.710 10.997 20417 Z= 0.355 Chirality : 0.045 0.277 2235 Planarity : 0.006 0.069 2486 Dihedral : 15.379 88.223 2397 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.05 % Allowed : 22.63 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1712 helix: 1.30 (0.22), residues: 606 sheet: 1.07 (0.37), residues: 209 loop : -1.68 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 325 TYR 0.012 0.002 TYR A1108 PHE 0.019 0.002 PHE A 610 TRP 0.023 0.001 TRP A 607 HIS 0.004 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00402 (14924) covalent geometry : angle 0.70959 (20417) hydrogen bonds : bond 0.04063 ( 560) hydrogen bonds : angle 4.42612 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.569 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 544 MET cc_start: 0.6784 (mpp) cc_final: 0.6544 (mpp) REVERT: A 594 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6217 (mt) REVERT: A 597 ARG cc_start: 0.8066 (tmm160) cc_final: 0.7749 (tmm160) REVERT: A 821 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5423 (mm) REVERT: A 1167 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8552 (mptp) REVERT: A 1206 MET cc_start: 0.2390 (OUTLIER) cc_final: 0.2029 (mmt) REVERT: B 180 LYS cc_start: 0.6641 (tttt) cc_final: 0.6373 (tmtt) REVERT: B 206 TYR cc_start: 0.6532 (p90) cc_final: 0.6274 (p90) REVERT: B 241 TRP cc_start: 0.7015 (t-100) cc_final: 0.6704 (t-100) REVERT: B 405 GLU cc_start: 0.8144 (tp30) cc_final: 0.7857 (tp30) REVERT: B 427 GLN cc_start: 0.9054 (tt0) cc_final: 0.8697 (pt0) REVERT: B 465 MET cc_start: 0.6782 (mmm) cc_final: 0.6372 (mmm) outliers start: 59 outliers final: 24 residues processed: 242 average time/residue: 0.4591 time to fit residues: 124.8502 Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 161 optimal weight: 20.0000 chunk 43 optimal weight: 0.0030 chunk 135 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 740 ASN B 96 HIS ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 133 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.187902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.140009 restraints weight = 26808.448| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 4.39 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14924 Z= 0.149 Angle : 0.671 10.384 20417 Z= 0.333 Chirality : 0.043 0.204 2235 Planarity : 0.005 0.064 2486 Dihedral : 15.036 86.411 2384 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.18 % Allowed : 23.94 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1712 helix: 1.15 (0.22), residues: 614 sheet: 1.01 (0.36), residues: 212 loop : -1.71 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 325 TYR 0.016 0.001 TYR B 315 PHE 0.026 0.001 PHE A 610 TRP 0.020 0.001 TRP A 607 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00339 (14924) covalent geometry : angle 0.67086 (20417) hydrogen bonds : bond 0.03530 ( 560) hydrogen bonds : angle 4.23721 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 194 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.6963 (mpp) cc_final: 0.6533 (mpt) REVERT: A 585 TRP cc_start: 0.6703 (t-100) cc_final: 0.6231 (t-100) REVERT: A 596 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7885 (mtp) REVERT: A 597 ARG cc_start: 0.8125 (tmm160) cc_final: 0.7662 (tmm-80) REVERT: A 967 MET cc_start: 0.6049 (mmt) cc_final: 0.5807 (mmt) REVERT: A 1093 MET cc_start: 0.7245 (pmt) cc_final: 0.7005 (pmm) REVERT: A 1167 LYS cc_start: 0.8767 (mmtp) cc_final: 0.8504 (mptp) REVERT: A 1206 MET cc_start: 0.1996 (OUTLIER) cc_final: 0.1605 (mmt) REVERT: B 84 GLN cc_start: 0.8066 (tp40) cc_final: 0.7788 (tp-100) REVERT: B 405 GLU cc_start: 0.8157 (tp30) cc_final: 0.7691 (tp30) REVERT: B 427 GLN cc_start: 0.9077 (tt0) cc_final: 0.8722 (pt0) REVERT: B 465 MET cc_start: 0.6945 (mmm) cc_final: 0.6520 (mmm) REVERT: C 301 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7790 (tp30) REVERT: C 326 ASP cc_start: 0.5368 (OUTLIER) cc_final: 0.5157 (p0) outliers start: 61 outliers final: 26 residues processed: 239 average time/residue: 0.4630 time to fit residues: 124.3748 Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 33 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.185601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.137256 restraints weight = 27061.663| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.40 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14924 Z= 0.166 Angle : 0.683 9.699 20417 Z= 0.338 Chirality : 0.044 0.197 2235 Planarity : 0.005 0.064 2486 Dihedral : 14.968 86.568 2384 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.08 % Allowed : 24.07 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1712 helix: 0.99 (0.21), residues: 619 sheet: 1.06 (0.37), residues: 209 loop : -1.70 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 866 TYR 0.026 0.002 TYR B 206 PHE 0.040 0.002 PHE A 610 TRP 0.025 0.001 TRP A 607 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00379 (14924) covalent geometry : angle 0.68259 (20417) hydrogen bonds : bond 0.03575 ( 560) hydrogen bonds : angle 4.24476 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7196 (mpp) cc_final: 0.6876 (mpt) REVERT: A 585 TRP cc_start: 0.6666 (t-100) cc_final: 0.6110 (t-100) REVERT: A 594 LEU cc_start: 0.6278 (mt) cc_final: 0.5909 (mp) REVERT: A 597 ARG cc_start: 0.8327 (tmm160) cc_final: 0.7864 (ttp80) REVERT: A 821 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5353 (mm) REVERT: A 910 MET cc_start: 0.6833 (mpt) cc_final: 0.6143 (mpt) REVERT: A 967 MET cc_start: 0.5822 (mmt) cc_final: 0.5520 (mmt) REVERT: A 972 ARG cc_start: 0.8220 (mtm110) cc_final: 0.8005 (mtm110) REVERT: A 1093 MET cc_start: 0.7249 (pmt) cc_final: 0.7010 (pmm) REVERT: A 1138 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7541 (mpt180) REVERT: A 1163 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.6910 (tpt) REVERT: A 1167 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8557 (mptt) REVERT: B 84 GLN cc_start: 0.8084 (tp40) cc_final: 0.7786 (tp-100) REVERT: B 134 LYS cc_start: 0.8203 (mppt) cc_final: 0.7834 (mmtm) REVERT: B 257 ARG cc_start: 0.8951 (ttm-80) cc_final: 0.8314 (ttm110) REVERT: B 405 GLU cc_start: 0.8228 (tp30) cc_final: 0.7705 (tp30) REVERT: B 427 GLN cc_start: 0.9080 (tt0) cc_final: 0.8743 (pt0) REVERT: B 465 MET cc_start: 0.6763 (mmm) cc_final: 0.6341 (mmm) REVERT: C 301 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7861 (tp30) REVERT: C 406 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8659 (tt) outliers start: 74 outliers final: 37 residues processed: 238 average time/residue: 0.4347 time to fit residues: 116.5856 Evaluate side-chains 217 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 157 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.187048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.138628 restraints weight = 26849.899| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 4.44 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14924 Z= 0.135 Angle : 0.678 12.552 20417 Z= 0.332 Chirality : 0.043 0.220 2235 Planarity : 0.005 0.059 2486 Dihedral : 14.861 86.410 2384 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.46 % Allowed : 24.90 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1712 helix: 1.08 (0.22), residues: 613 sheet: 1.00 (0.36), residues: 212 loop : -1.72 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 866 TYR 0.017 0.001 TYR A 178 PHE 0.040 0.001 PHE A 610 TRP 0.019 0.001 TRP A 607 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00307 (14924) covalent geometry : angle 0.67769 (20417) hydrogen bonds : bond 0.03290 ( 560) hydrogen bonds : angle 4.19275 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.6848 (mpt) REVERT: A 544 MET cc_start: 0.7240 (mpp) cc_final: 0.7000 (mpt) REVERT: A 585 TRP cc_start: 0.6625 (t-100) cc_final: 0.6063 (t-100) REVERT: A 597 ARG cc_start: 0.8327 (tmm160) cc_final: 0.7893 (tmm-80) REVERT: A 821 LEU cc_start: 0.5564 (OUTLIER) cc_final: 0.5303 (mm) REVERT: A 910 MET cc_start: 0.6848 (mpt) cc_final: 0.6303 (mpt) REVERT: A 967 MET cc_start: 0.5776 (mmt) cc_final: 0.5470 (mmt) REVERT: A 1093 MET cc_start: 0.7203 (pmt) cc_final: 0.6957 (pmm) REVERT: A 1206 MET cc_start: 0.2015 (OUTLIER) cc_final: 0.1674 (mmt) REVERT: B 84 GLN cc_start: 0.8059 (tp40) cc_final: 0.7774 (tp-100) REVERT: B 206 TYR cc_start: 0.6400 (p90) cc_final: 0.6193 (p90) REVERT: B 257 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8318 (ttm110) REVERT: B 308 ASP cc_start: 0.9185 (t0) cc_final: 0.8392 (m-30) REVERT: B 405 GLU cc_start: 0.8222 (tp30) cc_final: 0.7810 (tp30) REVERT: B 427 GLN cc_start: 0.9089 (tt0) cc_final: 0.8748 (pt0) REVERT: B 465 MET cc_start: 0.6803 (mmm) cc_final: 0.6354 (mmm) outliers start: 65 outliers final: 30 residues processed: 231 average time/residue: 0.4870 time to fit residues: 126.0100 Evaluate side-chains 203 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 77 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 119 optimal weight: 0.0020 chunk 91 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 overall best weight: 0.7908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.187432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.139530 restraints weight = 26919.273| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 4.43 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14924 Z= 0.134 Angle : 0.687 12.098 20417 Z= 0.334 Chirality : 0.043 0.237 2235 Planarity : 0.005 0.058 2486 Dihedral : 14.785 86.065 2384 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.39 % Allowed : 25.10 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1712 helix: 1.08 (0.22), residues: 612 sheet: 1.18 (0.36), residues: 205 loop : -1.75 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 101 TYR 0.016 0.001 TYR A 178 PHE 0.034 0.001 PHE A 610 TRP 0.019 0.001 TRP A 607 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00300 (14924) covalent geometry : angle 0.68674 (20417) hydrogen bonds : bond 0.03200 ( 560) hydrogen bonds : angle 4.17535 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8565 (ttp80) cc_final: 0.8288 (ttp80) REVERT: A 297 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.6852 (mpt) REVERT: A 585 TRP cc_start: 0.6599 (t-100) cc_final: 0.6050 (t-100) REVERT: A 597 ARG cc_start: 0.8284 (tmm160) cc_final: 0.7869 (tmm-80) REVERT: A 821 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5268 (mm) REVERT: A 910 MET cc_start: 0.6781 (mpt) cc_final: 0.6364 (mpt) REVERT: A 937 THR cc_start: 0.8392 (p) cc_final: 0.8175 (p) REVERT: A 967 MET cc_start: 0.5819 (mmt) cc_final: 0.5491 (mmt) REVERT: A 1093 MET cc_start: 0.7178 (pmt) cc_final: 0.6915 (pmm) REVERT: A 1206 MET cc_start: 0.1889 (OUTLIER) cc_final: 0.1551 (mmt) REVERT: B 206 TYR cc_start: 0.6440 (p90) cc_final: 0.6216 (p90) REVERT: B 257 ARG cc_start: 0.8945 (ttm-80) cc_final: 0.8293 (ttm110) REVERT: B 347 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8688 (mm) REVERT: B 405 GLU cc_start: 0.8271 (tp30) cc_final: 0.7853 (tp30) REVERT: B 427 GLN cc_start: 0.9089 (tt0) cc_final: 0.8768 (pt0) REVERT: B 465 MET cc_start: 0.6923 (mmm) cc_final: 0.6483 (mmm) REVERT: C 298 GLU cc_start: 0.7018 (pm20) cc_final: 0.6775 (pm20) REVERT: C 301 GLU cc_start: 0.7798 (tp30) cc_final: 0.7381 (tm-30) outliers start: 64 outliers final: 31 residues processed: 226 average time/residue: 0.4578 time to fit residues: 116.2907 Evaluate side-chains 208 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 435 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 91 optimal weight: 0.0670 chunk 161 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 108 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 144 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.188728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.141101 restraints weight = 26727.387| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 4.41 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14924 Z= 0.128 Angle : 0.693 12.122 20417 Z= 0.335 Chirality : 0.042 0.224 2235 Planarity : 0.004 0.055 2486 Dihedral : 14.619 85.707 2384 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.91 % Allowed : 26.95 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1712 helix: 1.11 (0.22), residues: 612 sheet: 1.23 (0.37), residues: 205 loop : -1.75 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 101 TYR 0.020 0.001 TYR A1108 PHE 0.028 0.001 PHE A 610 TRP 0.019 0.001 TRP A 607 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00284 (14924) covalent geometry : angle 0.69344 (20417) hydrogen bonds : bond 0.03053 ( 560) hydrogen bonds : angle 4.14442 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 GLU cc_start: 0.8605 (mp0) cc_final: 0.8243 (mp0) REVERT: A 544 MET cc_start: 0.6599 (mpt) cc_final: 0.6245 (mpp) REVERT: A 585 TRP cc_start: 0.6539 (t-100) cc_final: 0.5944 (t-100) REVERT: A 597 ARG cc_start: 0.8245 (tmm160) cc_final: 0.7848 (tmm-80) REVERT: A 821 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.5281 (mm) REVERT: A 910 MET cc_start: 0.6736 (mpt) cc_final: 0.6389 (mpt) REVERT: A 967 MET cc_start: 0.5913 (mmt) cc_final: 0.5574 (mmt) REVERT: A 1093 MET cc_start: 0.7224 (pmt) cc_final: 0.6941 (pmm) REVERT: A 1206 MET cc_start: 0.1980 (OUTLIER) cc_final: 0.1655 (mmt) REVERT: B 206 TYR cc_start: 0.6379 (p90) cc_final: 0.6021 (OUTLIER) REVERT: B 257 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8287 (ttm110) REVERT: B 308 ASP cc_start: 0.9097 (t0) cc_final: 0.8211 (m-30) REVERT: B 347 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8680 (mm) REVERT: B 405 GLU cc_start: 0.8246 (tp30) cc_final: 0.7828 (tp30) REVERT: B 427 GLN cc_start: 0.9070 (tt0) cc_final: 0.8796 (pt0) REVERT: B 465 MET cc_start: 0.7053 (mmm) cc_final: 0.6605 (mmm) REVERT: C 301 GLU cc_start: 0.7764 (tp30) cc_final: 0.7376 (tm-30) outliers start: 57 outliers final: 38 residues processed: 225 average time/residue: 0.4883 time to fit residues: 123.0549 Evaluate side-chains 214 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 116 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 261 GLN ** 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 = 0.4643 r_free = 0.4643 target = 0.188136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.140024 restraints weight = 26874.338| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 4.46 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14924 Z= 0.132 Angle : 0.705 12.057 20417 Z= 0.342 Chirality : 0.043 0.235 2235 Planarity : 0.005 0.055 2486 Dihedral : 14.576 85.397 2384 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 3.70 % Allowed : 27.57 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1712 helix: 1.07 (0.22), residues: 613 sheet: 1.23 (0.37), residues: 206 loop : -1.77 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 101 TYR 0.015 0.001 TYR A 178 PHE 0.030 0.001 PHE A 389 TRP 0.020 0.001 TRP A 607 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00299 (14924) covalent geometry : angle 0.70490 (20417) hydrogen bonds : bond 0.03140 ( 560) hydrogen bonds : angle 4.18049 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.6627 (mpt) cc_final: 0.6378 (mpp) REVERT: A 585 TRP cc_start: 0.6529 (t-100) cc_final: 0.5994 (t-100) REVERT: A 597 ARG cc_start: 0.8246 (tmm160) cc_final: 0.7842 (tmm-80) REVERT: A 796 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6748 (mmtt) REVERT: A 821 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5264 (mm) REVERT: A 910 MET cc_start: 0.6623 (mpt) cc_final: 0.6378 (mpt) REVERT: A 937 THR cc_start: 0.8275 (t) cc_final: 0.7859 (p) REVERT: A 967 MET cc_start: 0.5867 (mmt) cc_final: 0.5518 (mmt) REVERT: A 972 ARG cc_start: 0.8226 (mtm110) cc_final: 0.6797 (ptt-90) REVERT: A 1093 MET cc_start: 0.7245 (pmt) cc_final: 0.6949 (pmm) REVERT: A 1163 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.6937 (tpt) REVERT: A 1206 MET cc_start: 0.2081 (OUTLIER) cc_final: 0.1706 (mmt) REVERT: B 73 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 206 TYR cc_start: 0.6359 (p90) cc_final: 0.6026 (OUTLIER) REVERT: B 257 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8282 (ttm110) REVERT: B 308 ASP cc_start: 0.9101 (t0) cc_final: 0.8228 (m-30) REVERT: B 347 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8715 (mm) REVERT: B 405 GLU cc_start: 0.8251 (tp30) cc_final: 0.7830 (tp30) REVERT: B 419 GLU cc_start: 0.8484 (tp30) cc_final: 0.8153 (tm-30) REVERT: B 427 GLN cc_start: 0.9076 (tt0) cc_final: 0.8776 (pt0) REVERT: B 465 MET cc_start: 0.7028 (mmm) cc_final: 0.6586 (mmm) REVERT: C 301 GLU cc_start: 0.7814 (tp30) cc_final: 0.7421 (tm-30) outliers start: 54 outliers final: 30 residues processed: 219 average time/residue: 0.4735 time to fit residues: 116.4215 Evaluate side-chains 209 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 59 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 226 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.186907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.138853 restraints weight = 26777.942| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 4.42 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14924 Z= 0.144 Angle : 0.723 11.631 20417 Z= 0.352 Chirality : 0.043 0.231 2235 Planarity : 0.005 0.056 2486 Dihedral : 14.533 84.975 2383 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 3.84 % Allowed : 27.78 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.21), residues: 1712 helix: 1.10 (0.22), residues: 607 sheet: 1.17 (0.36), residues: 208 loop : -1.81 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 101 TYR 0.016 0.001 TYR A 178 PHE 0.033 0.002 PHE B 219 TRP 0.025 0.001 TRP A 607 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00331 (14924) covalent geometry : angle 0.72261 (20417) hydrogen bonds : bond 0.03182 ( 560) hydrogen bonds : angle 4.24387 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.6707 (mpt) cc_final: 0.6470 (mpp) REVERT: A 585 TRP cc_start: 0.6554 (t-100) cc_final: 0.6078 (t-100) REVERT: A 597 ARG cc_start: 0.8305 (tmm160) cc_final: 0.7803 (ttp80) REVERT: A 821 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5260 (mm) REVERT: A 910 MET cc_start: 0.6664 (mpt) cc_final: 0.6435 (mpt) REVERT: A 967 MET cc_start: 0.5817 (mmt) cc_final: 0.5460 (mmt) REVERT: A 972 ARG cc_start: 0.8203 (mtm110) cc_final: 0.6932 (ptt-90) REVERT: A 1093 MET cc_start: 0.7252 (pmt) cc_final: 0.6955 (pmm) REVERT: A 1163 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6937 (tpt) REVERT: B 73 CYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8054 (p) REVERT: B 84 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7594 (tp-100) REVERT: B 206 TYR cc_start: 0.6355 (p90) cc_final: 0.5954 (OUTLIER) REVERT: B 241 TRP cc_start: 0.7038 (t-100) cc_final: 0.6680 (t-100) REVERT: B 257 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8270 (ttm110) REVERT: B 347 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8764 (mm) REVERT: B 405 GLU cc_start: 0.8271 (tp30) cc_final: 0.7730 (tp30) REVERT: B 419 GLU cc_start: 0.8326 (tp30) cc_final: 0.7958 (tm-30) REVERT: B 427 GLN cc_start: 0.9069 (tt0) cc_final: 0.8748 (pt0) REVERT: B 465 MET cc_start: 0.7012 (mmm) cc_final: 0.6566 (mmm) REVERT: C 301 GLU cc_start: 0.7774 (tp30) cc_final: 0.7408 (tm-30) outliers start: 56 outliers final: 35 residues processed: 211 average time/residue: 0.4626 time to fit residues: 109.5428 Evaluate side-chains 216 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 123 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 261 GLN ** 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 = 0.4625 r_free = 0.4625 target = 0.186590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.138503 restraints weight = 26868.990| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 4.43 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14924 Z= 0.147 Angle : 0.731 11.649 20417 Z= 0.358 Chirality : 0.044 0.203 2235 Planarity : 0.005 0.057 2486 Dihedral : 14.532 84.674 2383 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.76 % Rotamer: Outliers : 3.29 % Allowed : 28.53 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1712 helix: 1.04 (0.22), residues: 613 sheet: 1.14 (0.36), residues: 208 loop : -1.82 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 344 TYR 0.018 0.001 TYR A 178 PHE 0.032 0.001 PHE A 389 TRP 0.026 0.001 TRP A 345 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00337 (14924) covalent geometry : angle 0.73147 (20417) hydrogen bonds : bond 0.03225 ( 560) hydrogen bonds : angle 4.26698 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.6809 (mpt) cc_final: 0.6583 (mpp) REVERT: A 585 TRP cc_start: 0.6532 (t-100) cc_final: 0.6060 (t-100) REVERT: A 597 ARG cc_start: 0.8337 (tmm160) cc_final: 0.7836 (ttp80) REVERT: A 796 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7032 (mmmm) REVERT: A 821 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.5309 (mm) REVERT: A 910 MET cc_start: 0.6625 (mpt) cc_final: 0.6402 (mpt) REVERT: A 967 MET cc_start: 0.5880 (mmt) cc_final: 0.5497 (mmt) REVERT: A 972 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7127 (ptt-90) REVERT: A 1093 MET cc_start: 0.7254 (pmt) cc_final: 0.6956 (pmm) REVERT: A 1163 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.6963 (tpt) REVERT: B 73 CYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 84 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7548 (tp-100) REVERT: B 206 TYR cc_start: 0.6340 (p90) cc_final: 0.6116 (p90) REVERT: B 257 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8269 (ttm110) REVERT: B 347 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8742 (mm) REVERT: B 405 GLU cc_start: 0.8239 (tp30) cc_final: 0.7700 (tp30) REVERT: B 419 GLU cc_start: 0.8050 (tp30) cc_final: 0.7648 (pp20) REVERT: B 421 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7797 (pmm) REVERT: B 427 GLN cc_start: 0.9055 (tt0) cc_final: 0.8747 (pt0) REVERT: B 465 MET cc_start: 0.6973 (mmm) cc_final: 0.6528 (mmm) REVERT: C 72 ILE cc_start: 0.6343 (pp) cc_final: 0.6115 (pp) REVERT: C 301 GLU cc_start: 0.7766 (tp30) cc_final: 0.7468 (tm-30) outliers start: 48 outliers final: 36 residues processed: 213 average time/residue: 0.4704 time to fit residues: 112.7790 Evaluate side-chains 216 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 86 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.186688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.138774 restraints weight = 26721.091| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 4.40 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14924 Z= 0.144 Angle : 0.740 11.690 20417 Z= 0.362 Chirality : 0.044 0.223 2235 Planarity : 0.005 0.058 2486 Dihedral : 14.517 84.409 2383 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 3.36 % Allowed : 28.53 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1712 helix: 1.03 (0.22), residues: 612 sheet: 0.96 (0.36), residues: 215 loop : -1.81 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 344 TYR 0.018 0.001 TYR A 178 PHE 0.038 0.002 PHE B 219 TRP 0.029 0.001 TRP A 345 HIS 0.009 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00328 (14924) covalent geometry : angle 0.73989 (20417) hydrogen bonds : bond 0.03266 ( 560) hydrogen bonds : angle 4.30714 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.39 seconds wall clock time: 86 minutes 49.64 seconds (5209.64 seconds total)