Starting phenix.real_space_refine on Sat Sep 12 08:00:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5p_29752/09_2026/8g5p_29752_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5p_29752/09_2026/8g5p_29752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g5p_29752/09_2026/8g5p_29752_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5p_29752/09_2026/8g5p_29752_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5p_29752/09_2026/8g5p_29752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5p_29752/09_2026/8g5p_29752.map" } resolution = 2.78 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 9110 2.51 5 N 2542 2.21 5 O 2731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14500 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7214 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 61, 'TRANS': 857} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3259 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3230 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P DT T 5 " occ=0.50 ... (18 atoms not shown) pdb=" C6 DT T 5 " occ=0.50 residue: pdb=" P DA T 6 " occ=0.50 ... (19 atoms not shown) pdb=" C4 DA T 6 " occ=0.50 residue: pdb=" P DG T 7 " occ=0.50 ... (20 atoms not shown) pdb=" C4 DG T 7 " occ=0.50 Time building chain proxies: 3.28, per 1000 atoms: 0.23 Number of scatterers: 14500 At special positions: 0 Unit cell: (106.502, 104.851, 142.829, 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 2731 8.00 N 2542 7.00 C 9110 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: 1.30 Conformation dependent library (CDL) restraints added in 641.0 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: 55 helices and 10 sheets defined 37.0% alpha, 11.5% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.999A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 160 removed outlier: 3.573A pdb=" N HIS A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.932A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.718A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.912A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (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 421 through 431 Processing helix chain 'A' and resid 440 through 470 Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.548A pdb=" N LEU A 474 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.524A pdb=" N GLN A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 788 through 809 removed outlier: 3.532A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 5.145A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 915 through 923 removed outlier: 4.040A pdb=" N MET A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 940 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.752A pdb=" N TYR A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.670A pdb=" N ASN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 977 Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.523A pdb=" N GLU A1062 " --> pdb=" O PHE A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.577A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.733A pdb=" N PHE A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 removed outlier: 3.571A pdb=" N LEU A1153 " --> pdb=" O ALA A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1179 removed outlier: 3.759A pdb=" N PHE A1179 " --> pdb=" O SER A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'A' and resid 1226 through 1230 removed outlier: 4.000A pdb=" N GLY A1229 " --> pdb=" O LEU A1226 " (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 185 through 193 Processing helix chain 'B' and resid 194 through 201 removed outlier: 3.749A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 199 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.520A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.703A pdb=" N GLN B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.927A pdb=" N LEU B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.764A 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: 3.811A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.624A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.662A pdb=" N ILE C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 201 removed outlier: 3.730A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.071A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 308 through 314 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 395 through 409 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.841A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.690A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA A 212 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 195 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.567A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.826A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.062A 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: 6.660A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA6, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.051A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.196A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.106A pdb=" N TRP C 414 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS C 382 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL C 441 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2285 1.28 - 1.42: 4054 1.42 - 1.55: 8385 1.55 - 1.69: 91 1.69 - 1.82: 125 Bond restraints: 14940 Sorted by residual: bond pdb=" C CYS B 399 " pdb=" O CYS B 399 " ideal model delta sigma weight residual 1.236 1.151 0.086 1.15e-02 7.56e+03 5.55e+01 bond pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta sigma weight residual 1.452 1.495 -0.042 1.18e-02 7.18e+03 1.29e+01 bond pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.14e+01 bond pdb=" P G R 19 " pdb=" O5' G R 19 " ideal model delta sigma weight residual 1.593 1.626 -0.033 1.00e-02 1.00e+04 1.12e+01 bond pdb=" N GLY C 307 " pdb=" CA GLY C 307 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.00e-03 1.23e+04 1.06e+01 ... (remaining 14935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 19737 2.69 - 5.38: 566 5.38 - 8.07: 125 8.07 - 10.75: 5 10.75 - 13.44: 3 Bond angle restraints: 20436 Sorted by residual: angle pdb=" CA PRO C 137 " pdb=" N PRO C 137 " pdb=" CD PRO C 137 " ideal model delta sigma weight residual 112.00 101.15 10.85 1.40e+00 5.10e-01 6.00e+01 angle pdb=" C3' DT T 5 " pdb=" O3' DT T 5 " pdb=" P DA T 6 " ideal model delta sigma weight residual 119.70 110.67 9.03 1.20e+00 6.94e-01 5.66e+01 angle pdb=" C3' C R 8 " pdb=" O3' C R 8 " pdb=" P U R 9 " ideal model delta sigma weight residual 119.70 128.67 -8.97 1.20e+00 6.94e-01 5.58e+01 angle pdb=" N GLN A 281 " pdb=" CA GLN A 281 " pdb=" C GLN A 281 " ideal model delta sigma weight residual 113.50 104.99 8.51 1.23e+00 6.61e-01 4.79e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.38 110.50 -7.12 1.05e+00 9.07e-01 4.59e+01 ... (remaining 20431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 8479 34.96 - 69.92: 394 69.92 - 104.87: 16 104.87 - 139.83: 0 139.83 - 174.79: 2 Dihedral angle restraints: 8891 sinusoidal: 3891 harmonic: 5000 Sorted by residual: dihedral pdb=" CD ARG B 76 " pdb=" NE ARG B 76 " pdb=" CZ ARG B 76 " pdb=" NH1 ARG B 76 " ideal model delta sinusoidal sigma weight residual 0.00 -76.58 76.58 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CD ARG A 227 " pdb=" NE ARG A 227 " pdb=" CZ ARG A 227 " pdb=" NH1 ARG A 227 " ideal model delta sinusoidal sigma weight residual 0.00 -63.97 63.97 1 1.00e+01 1.00e-02 5.39e+01 dihedral pdb=" CD ARG A 279 " pdb=" NE ARG A 279 " pdb=" CZ ARG A 279 " pdb=" NH1 ARG A 279 " ideal model delta sinusoidal sigma weight residual 0.00 -46.90 46.90 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 8888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2132 0.131 - 0.261: 64 0.261 - 0.392: 1 0.392 - 0.523: 22 0.523 - 0.654: 16 Chirality restraints: 2235 Sorted by residual: chirality pdb=" P DA T 8 " pdb=" OP1 DA T 8 " pdb=" OP2 DA T 8 " pdb=" O5' DA T 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 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 2.34 2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DC T 21 " pdb=" OP1 DC T 21 " pdb=" OP2 DC T 21 " pdb=" O5' DC T 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.83e+00 ... (remaining 2232 not shown) Planarity restraints: 2488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 76 " 1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG B 76 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 76 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 76 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 76 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 227 " -0.990 9.50e-02 1.11e+02 4.44e-01 1.19e+02 pdb=" NE ARG A 227 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 227 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 227 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 227 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 279 " 0.791 9.50e-02 1.11e+02 3.54e-01 7.64e+01 pdb=" NE ARG A 279 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 279 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 279 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 279 " 0.023 2.00e-02 2.50e+03 ... (remaining 2485 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 157 2.59 - 3.17: 12613 3.17 - 3.75: 22851 3.75 - 4.32: 30516 4.32 - 4.90: 49614 Nonbonded interactions: 115751 Sorted by model distance: nonbonded pdb=" O THR C 444 " pdb=" OG1 THR C 447 " model vdw 2.013 3.040 nonbonded pdb=" OH TYR C 193 " pdb=" O LEU C 322 " model vdw 2.041 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.053 3.040 nonbonded pdb=" OG SER B 87 " pdb=" OD1 ASP B 89 " model vdw 2.072 3.040 nonbonded pdb=" OG SER A 302 " pdb=" OH TYR A 363 " model vdw 2.091 3.040 ... (remaining 115746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 66 through 146 or (resid 147 and (name N or name CA or nam \ e C or name O or name CB )) or resid 148 through 170 or (resid 171 through 176 a \ nd (name N or name CA or name C or name O or name CB )) or resid 177 through 222 \ or (resid 223 and (name N or name CA or name C or name O or name CB )) or resid \ 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) or r \ esid 226 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 355 or resid 368 through 485)) selection = (chain 'C' and (resid 66 or (resid 67 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 160 or resid 170 t \ hrough 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=0.50 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.950 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 0.118 14940 Z= 0.388 Angle : 1.040 13.443 20436 Z= 0.628 Chirality : 0.085 0.654 2235 Planarity : 0.019 0.475 2488 Dihedral : 17.668 174.789 5665 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.17 % Rotamer: Outliers : 2.33 % Allowed : 22.33 % Favored : 75.34 % 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: -0.71 (0.21), residues: 1712 helix: 1.23 (0.23), residues: 577 sheet: 0.23 (0.34), residues: 226 loop : -1.89 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 325 TYR 0.036 0.002 TYR C 291 PHE 0.015 0.001 PHE A 139 TRP 0.029 0.001 TRP A1099 HIS 0.023 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.39 (14940) covalent geometry : angle 1.03991 / 0.63 (20436) hydrogen bonds : bond 0.15509 / 10.11 ( 558) hydrogen bonds : angle 6.97908 / 4.98 ( 1532) *********************** 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 247 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 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: A 544 MET cc_start: 0.7498 (tpt) cc_final: 0.7224 (tpp) REVERT: A 553 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7531 (mppt) REVERT: C 325 ARG cc_start: 0.6931 (mtp-110) cc_final: 0.6336 (ptp-170) REVERT: C 349 TYR cc_start: 0.8233 (m-10) cc_final: 0.8012 (m-10) outliers start: 34 outliers final: 11 residues processed: 239 average time/residue: 0.4910 time to fit residues: 130.8786 Evaluate side-chains 183 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 393 LEU 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: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0050 chunk 149 optimal weight: 0.6980 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 281 GLN A 398 GLN A 493 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A1089 GLN A1098 ASN A1214 GLN B 158 GLN B 195 ASN C 77 HIS C 84 GLN C 85 GLN C 292 ASN C 339 ASN C 355 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.166083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.121660 restraints weight = 27850.995| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.08 r_work: 0.3645 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14940 Z= 0.148 Angle : 0.727 11.366 20436 Z= 0.369 Chirality : 0.048 0.415 2235 Planarity : 0.005 0.079 2488 Dihedral : 16.057 168.885 2396 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 3.90 % Allowed : 20.41 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.21), residues: 1712 helix: 1.35 (0.22), residues: 578 sheet: 0.45 (0.34), residues: 236 loop : -1.94 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 325 TYR 0.014 0.002 TYR B 193 PHE 0.019 0.001 PHE A 389 TRP 0.017 0.001 TRP A 918 HIS 0.011 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (14940) covalent geometry : angle 0.72709 / 0.37 (20436) hydrogen bonds : bond 0.04531 / 2.92 ( 558) hydrogen bonds : angle 4.81198 / 3.42 ( 1532) *********************** 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 258 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 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: A 295 MET cc_start: 0.8230 (mtp) cc_final: 0.8002 (mtp) REVERT: A 541 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: A 557 GLU cc_start: 0.8685 (tp30) cc_final: 0.8215 (mm-30) REVERT: A 580 LEU cc_start: 0.7023 (mp) cc_final: 0.6775 (tm) REVERT: A 616 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7179 (pp20) REVERT: A 793 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 873 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7967 (pp20) REVERT: A 910 MET cc_start: 0.5209 (mtt) cc_final: 0.4738 (mmm) REVERT: A 968 GLN cc_start: 0.8204 (mt0) cc_final: 0.7862 (tm-30) REVERT: A 975 GLN cc_start: 0.9243 (mp10) cc_final: 0.8983 (mp10) REVERT: A 976 GLN cc_start: 0.8313 (pt0) cc_final: 0.8057 (pm20) REVERT: B 405 GLU cc_start: 0.8531 (tt0) cc_final: 0.8191 (pt0) REVERT: C 92 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7899 (mm) REVERT: C 325 ARG cc_start: 0.6875 (mtp-110) cc_final: 0.6292 (ptm-80) REVERT: C 349 TYR cc_start: 0.8505 (m-10) cc_final: 0.8239 (m-10) REVERT: C 477 LYS cc_start: 0.8989 (mptt) cc_final: 0.8771 (mptt) outliers start: 57 outliers final: 19 residues processed: 239 average time/residue: 0.4656 time to fit residues: 124.6086 Evaluate side-chains 203 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 932 HIS Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 77 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 264 GLN A 277 HIS A 281 GLN A 971 HIS A1102 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.160963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114992 restraints weight = 28325.908| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.09 r_work: 0.3539 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14940 Z= 0.220 Angle : 0.739 13.188 20436 Z= 0.373 Chirality : 0.047 0.377 2235 Planarity : 0.005 0.064 2488 Dihedral : 16.009 169.477 2389 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.76 % Rotamer: Outliers : 4.73 % Allowed : 22.12 % Favored : 73.15 % 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: -0.79 (0.21), residues: 1712 helix: 1.18 (0.22), residues: 583 sheet: 0.15 (0.34), residues: 239 loop : -2.00 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 225 TYR 0.036 0.002 TYR C 291 PHE 0.022 0.002 PHE B 266 TRP 0.024 0.002 TRP A 490 HIS 0.010 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (14940) covalent geometry : angle 0.73934 / 0.37 (20436) hydrogen bonds : bond 0.04373 / 2.85 ( 558) hydrogen bonds : angle 4.75131 / 3.40 ( 1532) *********************** 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 264 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.6989 (ttp-170) cc_final: 0.5907 (ttp-170) REVERT: A 288 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7308 (mtm110) REVERT: A 580 LEU cc_start: 0.7187 (mp) cc_final: 0.6849 (tm) REVERT: A 612 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5231 (tp) REVERT: A 616 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7471 (pp20) REVERT: A 793 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 873 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7838 (pp20) REVERT: A 910 MET cc_start: 0.5120 (mtt) cc_final: 0.4707 (mmm) REVERT: A 968 GLN cc_start: 0.8265 (mt0) cc_final: 0.7930 (tm-30) REVERT: A 976 GLN cc_start: 0.8242 (pt0) cc_final: 0.7990 (pm20) REVERT: A 1083 LEU cc_start: 0.7890 (tp) cc_final: 0.7559 (tm) REVERT: B 219 PHE cc_start: 0.7953 (p90) cc_final: 0.7697 (p90) REVERT: B 325 ARG cc_start: 0.6778 (mmt90) cc_final: 0.6523 (mmt90) REVERT: B 405 GLU cc_start: 0.8654 (tt0) cc_final: 0.8337 (pt0) REVERT: C 92 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7890 (mm) REVERT: C 322 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8327 (pp) REVERT: C 466 MET cc_start: 0.8319 (tmm) cc_final: 0.8025 (tmm) REVERT: C 477 LYS cc_start: 0.9005 (mptt) cc_final: 0.8736 (mptt) outliers start: 69 outliers final: 30 residues processed: 235 average time/residue: 0.4537 time to fit residues: 120.1512 Evaluate side-chains 214 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 117 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 172 optimal weight: 40.0000 chunk 157 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 906 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 305 ASN B 397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.160536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114612 restraints weight = 28233.253| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 4.10 r_work: 0.3528 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14940 Z= 0.191 Angle : 0.717 11.394 20436 Z= 0.361 Chirality : 0.047 0.393 2235 Planarity : 0.005 0.063 2488 Dihedral : 15.901 169.180 2387 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.59 % Favored : 91.36 % Rotamer: Outliers : 4.25 % Allowed : 22.95 % Favored : 72.81 % 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: -0.84 (0.20), residues: 1712 helix: 1.13 (0.22), residues: 584 sheet: 0.06 (0.33), residues: 239 loop : -2.01 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 458 TYR 0.031 0.002 TYR C 291 PHE 0.018 0.001 PHE C 403 TRP 0.021 0.001 TRP A 345 HIS 0.012 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (14940) covalent geometry : angle 0.71730 / 0.36 (20436) hydrogen bonds : bond 0.04003 / 2.59 ( 558) hydrogen bonds : angle 4.64534 / 3.33 ( 1532) *********************** 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 240 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7354 (mt) REVERT: A 279 ARG cc_start: 0.6942 (ttp-170) cc_final: 0.6614 (ttp-170) REVERT: A 557 GLU cc_start: 0.8758 (tp30) cc_final: 0.8257 (mm-30) REVERT: A 580 LEU cc_start: 0.7205 (mp) cc_final: 0.6874 (tm) REVERT: A 612 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5478 (tp) REVERT: A 616 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6865 (pp20) REVERT: A 793 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 797 MET cc_start: 0.8771 (mtt) cc_final: 0.8519 (mtt) REVERT: A 873 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: A 968 GLN cc_start: 0.8225 (mt0) cc_final: 0.7980 (tm-30) REVERT: A 976 GLN cc_start: 0.8312 (pt0) cc_final: 0.8061 (pm20) REVERT: A 1083 LEU cc_start: 0.7982 (tp) cc_final: 0.7635 (tm) REVERT: B 405 GLU cc_start: 0.8672 (tt0) cc_final: 0.8400 (pt0) REVERT: C 92 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7859 (mm) REVERT: C 322 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8316 (pp) REVERT: C 419 GLU cc_start: 0.8139 (tp30) cc_final: 0.7918 (tp30) REVERT: C 421 MET cc_start: 0.8781 (tmm) cc_final: 0.8443 (ppp) outliers start: 62 outliers final: 28 residues processed: 218 average time/residue: 0.4309 time to fit residues: 106.2855 Evaluate side-chains 208 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 34 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 172 optimal weight: 40.0000 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 HIS A 740 ASN ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.159523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.113467 restraints weight = 28089.880| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 4.08 r_work: 0.3515 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14940 Z= 0.199 Angle : 0.717 12.064 20436 Z= 0.362 Chirality : 0.047 0.371 2235 Planarity : 0.005 0.063 2488 Dihedral : 15.840 169.367 2387 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.17 % Favored : 90.77 % Rotamer: Outliers : 5.14 % Allowed : 22.74 % Favored : 72.12 % 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: -0.93 (0.20), residues: 1712 helix: 1.08 (0.22), residues: 583 sheet: -0.02 (0.33), residues: 239 loop : -2.06 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 225 TYR 0.035 0.002 TYR C 291 PHE 0.018 0.001 PHE B 266 TRP 0.022 0.002 TRP A 345 HIS 0.010 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (14940) covalent geometry : angle 0.71720 / 0.36 (20436) hydrogen bonds : bond 0.03887 / 2.54 ( 558) hydrogen bonds : angle 4.60994 / 3.30 ( 1532) *********************** 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 256 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 181 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7391 (mt) REVERT: A 279 ARG cc_start: 0.6866 (ttp-170) cc_final: 0.6510 (ttp-170) REVERT: A 557 GLU cc_start: 0.8760 (tp30) cc_final: 0.8312 (mm-30) REVERT: A 616 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6974 (pp20) REVERT: A 793 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 796 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8035 (tttm) REVERT: A 797 MET cc_start: 0.8791 (mtt) cc_final: 0.8538 (mtt) REVERT: A 873 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7702 (pp20) REVERT: A 902 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6688 (tm) REVERT: A 910 MET cc_start: 0.5217 (mtt) cc_final: 0.4929 (mmt) REVERT: A 968 GLN cc_start: 0.8220 (mt0) cc_final: 0.8006 (tm-30) REVERT: A 1083 LEU cc_start: 0.8057 (tp) cc_final: 0.7712 (tm) REVERT: B 219 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7498 (p90) REVERT: B 405 GLU cc_start: 0.8699 (tt0) cc_final: 0.8434 (pt0) REVERT: B 407 LEU cc_start: 0.9004 (mp) cc_final: 0.8791 (mp) REVERT: B 470 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8580 (pttt) REVERT: C 92 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7923 (mm) REVERT: C 134 LYS cc_start: 0.8548 (tptt) cc_final: 0.8278 (tppt) REVERT: C 322 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8350 (pp) REVERT: C 462 MET cc_start: 0.8091 (ppp) cc_final: 0.7752 (mmm) REVERT: C 466 MET cc_start: 0.8341 (tmm) cc_final: 0.8033 (tmm) REVERT: C 477 LYS cc_start: 0.8999 (mptt) cc_final: 0.8731 (mptt) outliers start: 75 outliers final: 33 residues processed: 230 average time/residue: 0.4371 time to fit residues: 113.7087 Evaluate side-chains 207 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.159922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113950 restraints weight = 28153.295| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.08 r_work: 0.3521 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14940 Z= 0.172 Angle : 0.722 11.905 20436 Z= 0.360 Chirality : 0.047 0.399 2235 Planarity : 0.005 0.063 2488 Dihedral : 15.784 169.574 2387 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.00 % Favored : 90.95 % Rotamer: Outliers : 4.45 % Allowed : 24.93 % Favored : 70.62 % 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: -0.92 (0.20), residues: 1712 helix: 1.12 (0.22), residues: 589 sheet: 0.01 (0.33), residues: 239 loop : -2.11 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 325 TYR 0.030 0.002 TYR C 291 PHE 0.017 0.001 PHE C 403 TRP 0.022 0.001 TRP A 345 HIS 0.009 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (14940) covalent geometry : angle 0.72154 / 0.36 (20436) hydrogen bonds : bond 0.03785 / 2.47 ( 558) hydrogen bonds : angle 4.61206 / 3.31 ( 1532) *********************** 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 242 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7351 (mt) REVERT: A 279 ARG cc_start: 0.6832 (ttp-170) cc_final: 0.6482 (ttp-170) REVERT: A 557 GLU cc_start: 0.8765 (tp30) cc_final: 0.8276 (mm-30) REVERT: A 616 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: A 793 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 796 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8113 (tttm) REVERT: A 797 MET cc_start: 0.8789 (mtt) cc_final: 0.8426 (mtp) REVERT: A 812 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7417 (ttp) REVERT: A 873 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7552 (pp20) REVERT: A 902 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6734 (tm) REVERT: A 910 MET cc_start: 0.5202 (mtt) cc_final: 0.4841 (mmm) REVERT: A 968 GLN cc_start: 0.8226 (mt0) cc_final: 0.8015 (tm-30) REVERT: A 973 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7692 (pp) REVERT: A 976 GLN cc_start: 0.8481 (pt0) cc_final: 0.8253 (pm20) REVERT: A 1083 LEU cc_start: 0.8075 (tp) cc_final: 0.7814 (tm) REVERT: B 405 GLU cc_start: 0.8703 (tt0) cc_final: 0.8458 (pt0) REVERT: B 407 LEU cc_start: 0.9009 (mp) cc_final: 0.8733 (mp) REVERT: B 470 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8569 (pttt) REVERT: C 92 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7868 (mm) REVERT: C 134 LYS cc_start: 0.8545 (tptt) cc_final: 0.8275 (tppt) REVERT: C 322 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 325 ARG cc_start: 0.7170 (mtm110) cc_final: 0.6065 (mmm160) REVERT: C 462 MET cc_start: 0.8122 (ppp) cc_final: 0.7634 (mmt) REVERT: C 466 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8025 (tmm) REVERT: C 477 LYS cc_start: 0.9003 (mptt) cc_final: 0.8732 (mptt) outliers start: 65 outliers final: 34 residues processed: 221 average time/residue: 0.4195 time to fit residues: 105.1029 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 104 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 440 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 879 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.160317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.114543 restraints weight = 27970.299| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 4.05 r_work: 0.3530 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14940 Z= 0.156 Angle : 0.704 12.027 20436 Z= 0.350 Chirality : 0.046 0.376 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.712 169.922 2387 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.35 % Favored : 90.60 % Rotamer: Outliers : 4.86 % Allowed : 24.59 % Favored : 70.55 % 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: -0.83 (0.20), residues: 1712 helix: 1.25 (0.22), residues: 582 sheet: 0.07 (0.33), residues: 237 loop : -2.07 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 396 TYR 0.031 0.002 TYR C 291 PHE 0.016 0.001 PHE C 403 TRP 0.026 0.001 TRP A 345 HIS 0.010 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (14940) covalent geometry : angle 0.70390 / 0.35 (20436) hydrogen bonds : bond 0.03598 / 2.35 ( 558) hydrogen bonds : angle 4.52027 / 3.23 ( 1532) *********************** 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 253 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 182 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7321 (mt) REVERT: A 279 ARG cc_start: 0.6882 (ttp-170) cc_final: 0.6531 (ttp-170) REVERT: A 472 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: A 557 GLU cc_start: 0.8811 (tp30) cc_final: 0.8326 (mm-30) REVERT: A 580 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6862 (tm) REVERT: A 612 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5585 (tp) REVERT: A 616 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: A 793 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 812 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7381 (ttp) REVERT: A 873 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: A 910 MET cc_start: 0.5340 (mtt) cc_final: 0.5003 (mmt) REVERT: A 968 GLN cc_start: 0.8263 (mt0) cc_final: 0.8059 (tm-30) REVERT: A 973 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7632 (pp) REVERT: A 975 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8944 (mp10) REVERT: A 976 GLN cc_start: 0.8489 (pt0) cc_final: 0.8261 (pm20) REVERT: A 1083 LEU cc_start: 0.8147 (tp) cc_final: 0.7821 (tm) REVERT: B 219 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7362 (p90) REVERT: B 405 GLU cc_start: 0.8699 (tt0) cc_final: 0.8475 (pt0) REVERT: B 407 LEU cc_start: 0.8986 (mp) cc_final: 0.8707 (mp) REVERT: C 92 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7847 (mm) REVERT: C 134 LYS cc_start: 0.8543 (tptt) cc_final: 0.8283 (tppt) REVERT: C 321 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8163 (pmtt) REVERT: C 322 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 466 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8024 (tmm) REVERT: C 477 LYS cc_start: 0.8997 (mptt) cc_final: 0.8720 (mptt) outliers start: 71 outliers final: 34 residues processed: 228 average time/residue: 0.4206 time to fit residues: 108.4075 Evaluate side-chains 220 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.159700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113859 restraints weight = 27874.798| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.05 r_work: 0.3523 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14940 Z= 0.170 Angle : 0.731 11.813 20436 Z= 0.362 Chirality : 0.046 0.377 2235 Planarity : 0.005 0.073 2488 Dihedral : 15.686 170.246 2386 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.40 % Favored : 90.54 % Rotamer: Outliers : 4.52 % Allowed : 25.62 % Favored : 69.86 % 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: -0.90 (0.20), residues: 1712 helix: 1.16 (0.22), residues: 589 sheet: -0.02 (0.33), residues: 239 loop : -2.11 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 325 TYR 0.035 0.002 TYR C 291 PHE 0.016 0.001 PHE C 403 TRP 0.027 0.001 TRP A 345 HIS 0.010 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (14940) covalent geometry : angle 0.73131 / 0.36 (20436) hydrogen bonds : bond 0.03656 / 2.39 ( 558) hydrogen bonds : angle 4.53181 / 3.25 ( 1532) *********************** 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 240 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7304 (mt) REVERT: A 279 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6462 (ttp-170) REVERT: A 472 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: A 553 LYS cc_start: 0.8448 (mmmt) cc_final: 0.7619 (mmtm) REVERT: A 557 GLU cc_start: 0.8842 (tp30) cc_final: 0.8355 (mm-30) REVERT: A 580 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6865 (tm) REVERT: A 616 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7072 (pp20) REVERT: A 793 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 812 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7349 (ttp) REVERT: A 873 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7683 (pp20) REVERT: A 910 MET cc_start: 0.5416 (mtt) cc_final: 0.4967 (mmm) REVERT: A 968 GLN cc_start: 0.8244 (mt0) cc_final: 0.8011 (tm-30) REVERT: A 973 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7582 (pp) REVERT: A 975 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8918 (mp10) REVERT: A 976 GLN cc_start: 0.8487 (pt0) cc_final: 0.8234 (pm20) REVERT: A 1083 LEU cc_start: 0.8154 (tp) cc_final: 0.7835 (tm) REVERT: B 75 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7695 (ptp-170) REVERT: B 219 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7370 (p90) REVERT: B 405 GLU cc_start: 0.8696 (tt0) cc_final: 0.8476 (pt0) REVERT: C 92 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7838 (mm) REVERT: C 134 LYS cc_start: 0.8555 (tptt) cc_final: 0.8295 (tppt) REVERT: C 321 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8182 (pmtt) REVERT: C 322 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 466 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: C 477 LYS cc_start: 0.9002 (mptt) cc_final: 0.8730 (mptt) outliers start: 66 outliers final: 35 residues processed: 220 average time/residue: 0.4338 time to fit residues: 108.2552 Evaluate side-chains 223 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 5 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS ** B 74 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 = 0.4369 r_free = 0.4369 target = 0.160972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.115520 restraints weight = 28034.167| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 4.09 r_work: 0.3545 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14940 Z= 0.138 Angle : 0.736 13.173 20436 Z= 0.359 Chirality : 0.046 0.381 2235 Planarity : 0.005 0.070 2488 Dihedral : 15.650 170.398 2386 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.94 % Favored : 91.00 % Rotamer: Outliers : 3.63 % Allowed : 26.37 % Favored : 70.00 % 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: -0.70 (0.21), residues: 1712 helix: 1.34 (0.22), residues: 583 sheet: 0.19 (0.34), residues: 240 loop : -2.00 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 325 TYR 0.030 0.002 TYR C 291 PHE 0.016 0.001 PHE C 403 TRP 0.034 0.001 TRP A1099 HIS 0.010 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14940) covalent geometry : angle 0.73554 / 0.36 (20436) hydrogen bonds : bond 0.03453 / 2.24 ( 558) hydrogen bonds : angle 4.49092 / 3.21 ( 1532) *********************** 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 234 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7368 (mt) REVERT: A 279 ARG cc_start: 0.6924 (ttp-170) cc_final: 0.6573 (ttp-170) REVERT: A 472 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: A 538 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: A 557 GLU cc_start: 0.8819 (tp30) cc_final: 0.8348 (mm-30) REVERT: A 580 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6848 (tm) REVERT: A 616 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: A 793 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 797 MET cc_start: 0.8693 (mtt) cc_final: 0.8465 (mtp) REVERT: A 873 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: A 910 MET cc_start: 0.5432 (mtt) cc_final: 0.5077 (mmt) REVERT: A 968 GLN cc_start: 0.8274 (mt0) cc_final: 0.8039 (tm-30) REVERT: A 973 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7632 (pp) REVERT: A 976 GLN cc_start: 0.8503 (pt0) cc_final: 0.8292 (pm20) REVERT: A 1083 LEU cc_start: 0.8137 (tp) cc_final: 0.7818 (tm) REVERT: B 75 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7718 (ptp-170) REVERT: B 219 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7413 (p90) REVERT: C 92 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7836 (mm) REVERT: C 134 LYS cc_start: 0.8535 (tptt) cc_final: 0.8285 (tppt) REVERT: C 325 ARG cc_start: 0.7233 (mtm110) cc_final: 0.6151 (mmm160) REVERT: C 349 TYR cc_start: 0.8525 (m-10) cc_final: 0.8301 (m-10) REVERT: C 436 SER cc_start: 0.8145 (m) cc_final: 0.7836 (t) REVERT: C 466 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8023 (tmm) REVERT: C 477 LYS cc_start: 0.9008 (mptt) cc_final: 0.8725 (mptt) outliers start: 53 outliers final: 30 residues processed: 214 average time/residue: 0.4190 time to fit residues: 101.4958 Evaluate side-chains 213 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 70 optimal weight: 0.0010 chunk 3 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 52 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 overall best weight: 0.8324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.161568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.116158 restraints weight = 27921.739| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.08 r_work: 0.3560 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14940 Z= 0.138 Angle : 0.750 12.743 20436 Z= 0.364 Chirality : 0.046 0.381 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.625 170.404 2386 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.17 % Favored : 90.77 % Rotamer: Outliers : 3.22 % Allowed : 27.05 % Favored : 69.73 % 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: -0.76 (0.21), residues: 1712 helix: 1.23 (0.22), residues: 590 sheet: 0.20 (0.34), residues: 245 loop : -2.04 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 325 TYR 0.030 0.002 TYR C 291 PHE 0.023 0.001 PHE B 145 TRP 0.038 0.001 TRP A1099 HIS 0.011 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14940) covalent geometry : angle 0.75014 / 0.36 (20436) hydrogen bonds : bond 0.03508 / 2.26 ( 558) hydrogen bonds : angle 4.47821 / 3.21 ( 1532) ********************** 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 226 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7163 (mt) REVERT: A 279 ARG cc_start: 0.6705 (ttp-170) cc_final: 0.6362 (ttp-170) REVERT: A 472 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: A 553 LYS cc_start: 0.8418 (mmmt) cc_final: 0.7566 (mmtm) REVERT: A 557 GLU cc_start: 0.8808 (tp30) cc_final: 0.8345 (mm-30) REVERT: A 580 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6785 (tm) REVERT: A 616 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: A 793 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 873 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7638 (pp20) REVERT: A 910 MET cc_start: 0.5411 (mtt) cc_final: 0.5064 (mmt) REVERT: A 968 GLN cc_start: 0.8303 (mt0) cc_final: 0.8079 (tm-30) REVERT: A 973 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7631 (pp) REVERT: A 976 GLN cc_start: 0.8495 (pt0) cc_final: 0.8291 (pm20) REVERT: A 985 MET cc_start: 0.4837 (ptp) cc_final: 0.4624 (pmt) REVERT: A 1083 LEU cc_start: 0.8041 (tp) cc_final: 0.7729 (tm) REVERT: B 75 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7738 (ptp-170) REVERT: B 219 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7340 (p90) REVERT: C 92 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7828 (mm) REVERT: C 134 LYS cc_start: 0.8513 (tptt) cc_final: 0.8267 (tppt) REVERT: C 321 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8178 (pmtt) REVERT: C 325 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6062 (mmm160) REVERT: C 349 TYR cc_start: 0.8490 (m-10) cc_final: 0.8268 (m-10) REVERT: C 436 SER cc_start: 0.8130 (m) cc_final: 0.7816 (t) REVERT: C 466 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8007 (tmm) REVERT: C 477 LYS cc_start: 0.9002 (mptt) cc_final: 0.8703 (mptt) outliers start: 47 outliers final: 29 residues processed: 208 average time/residue: 0.4093 time to fit residues: 96.8177 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 4 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.161610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116153 restraints weight = 27980.634| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.08 r_work: 0.3556 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14940 Z= 0.137 Angle : 0.739 12.649 20436 Z= 0.359 Chirality : 0.046 0.382 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.618 170.385 2386 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.05 % Favored : 90.89 % Rotamer: Outliers : 3.22 % Allowed : 27.26 % Favored : 69.52 % 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: -0.77 (0.21), residues: 1712 helix: 1.18 (0.22), residues: 594 sheet: 0.29 (0.34), residues: 238 loop : -2.05 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 325 TYR 0.028 0.002 TYR C 291 PHE 0.013 0.001 PHE C 403 TRP 0.048 0.001 TRP A1099 HIS 0.010 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14940) covalent geometry : angle 0.73943 / 0.36 (20436) hydrogen bonds : bond 0.03417 / 2.21 ( 558) hydrogen bonds : angle 4.44884 / 3.18 ( 1532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6539.42 seconds wall clock time: 111 minutes 55.41 seconds (6715.41 seconds total)