Starting phenix.real_space_refine on Fri May 16 16:16:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5p_29752/05_2025/8g5p_29752_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5p_29752/05_2025/8g5p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5p_29752/05_2025/8g5p_29752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5p_29752/05_2025/8g5p_29752.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5p_29752/05_2025/8g5p_29752_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5p_29752/05_2025/8g5p_29752_neut.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 7, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 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: 8.31, per 1000 atoms: 0.57 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: 3.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.49 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: 4.66 Time building geometry restraints manager: 4.24 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=" 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 bond pdb=" C PRO C 244 " pdb=" O PRO C 244 " ideal model delta sigma weight residual 1.246 1.218 0.028 8.50e-03 1.38e+04 1.05e+01 ... (remaining 14935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 19523 2.35 - 4.70: 730 4.70 - 7.06: 154 7.06 - 9.41: 25 9.41 - 11.76: 4 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' U R 9 " pdb=" C2' U R 9 " pdb=" O2' U R 9 " ideal model delta sigma weight residual 110.70 99.86 10.84 1.50e+00 4.44e-01 5.23e+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 angle pdb=" N PRO A 340 " pdb=" CA PRO A 340 " pdb=" CB PRO A 340 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+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 - 0.129: 2119 0.129 - 0.257: 77 0.257 - 0.386: 1 0.386 - 0.515: 22 0.515 - 0.643: 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 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+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 2.35 2.97 -0.63 2.00e-01 2.50e+01 9.80e+00 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 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.51e+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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 35.200 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 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= 0.360 Angle : 1.046 11.759 20436 Z= 0.609 Chirality : 0.085 0.643 2235 Planarity : 0.019 0.475 2488 Dihedral : 17.668 174.789 5665 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (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 TRP 0.029 0.001 TRP A1099 HIS 0.023 0.001 HIS B 309 PHE 0.015 0.001 PHE A 139 TYR 0.036 0.002 TYR C 291 ARG 0.020 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.15509 ( 558) hydrogen bonds : angle 6.97908 ( 1532) covalent geometry : bond 0.00625 (14940) covalent geometry : angle 1.04609 (20436) *********************** 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 : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.6337 (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: 1.0434 time to fit residues: 279.1820 Evaluate side-chains 184 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 146 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 136 optimal weight: 0.0010 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 108 GLN A 398 GLN A 493 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS A1089 GLN A1098 ASN A1102 GLN A1214 GLN B 132 HIS B 158 GLN B 195 ASN B 258 HIS 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.163768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.118789 restraints weight = 27865.752| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 4.07 r_work: 0.3595 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14940 Z= 0.165 Angle : 0.697 11.968 20436 Z= 0.355 Chirality : 0.046 0.350 2235 Planarity : 0.005 0.068 2488 Dihedral : 16.017 169.167 2396 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 3.90 % Allowed : 20.89 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1712 helix: 1.44 (0.22), residues: 583 sheet: 0.35 (0.34), residues: 238 loop : -1.94 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 918 HIS 0.010 0.001 HIS C 258 PHE 0.018 0.001 PHE A 389 TYR 0.016 0.002 TYR B 193 ARG 0.010 0.001 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 558) hydrogen bonds : angle 4.69161 ( 1532) covalent geometry : bond 0.00358 (14940) covalent geometry : angle 0.69698 (20436) *********************** 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 262 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.8392 (mt) cc_final: 0.8190 (mt) REVERT: A 295 MET cc_start: 0.8275 (mtp) cc_final: 0.7994 (mtp) REVERT: A 472 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.6630 (mp10) REVERT: A 541 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: A 580 LEU cc_start: 0.7114 (mp) cc_final: 0.6820 (tm) REVERT: A 612 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5102 (tp) REVERT: A 616 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6792 (pp20) REVERT: A 793 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 873 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8002 (pp20) REVERT: A 910 MET cc_start: 0.5242 (mtt) cc_final: 0.4842 (mmm) REVERT: A 968 GLN cc_start: 0.8245 (mt0) cc_final: 0.7878 (tm-30) REVERT: A 975 GLN cc_start: 0.9230 (mp10) cc_final: 0.8966 (mp10) REVERT: A 976 GLN cc_start: 0.8281 (pt0) cc_final: 0.8026 (pm20) REVERT: B 405 GLU cc_start: 0.8546 (tt0) cc_final: 0.8230 (pt0) REVERT: C 92 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7912 (mm) REVERT: C 325 ARG cc_start: 0.6907 (mtp-110) cc_final: 0.6304 (ptm-80) REVERT: C 349 TYR cc_start: 0.8574 (m-10) cc_final: 0.8232 (m-10) REVERT: C 477 LYS cc_start: 0.8990 (mptt) cc_final: 0.8707 (mptt) outliers start: 57 outliers final: 18 residues processed: 239 average time/residue: 0.9997 time to fit residues: 269.5598 Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 350 ILE Chi-restraints excluded: chain A residue 472 GLN 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 1226 LEU 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 323 HIS 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 392 THR Chi-restraints excluded: chain C residue 92 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 147 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 277 HIS ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.161201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.115203 restraints weight = 27978.516| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 4.09 r_work: 0.3547 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2067 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= 0.184 Angle : 0.708 13.045 20436 Z= 0.354 Chirality : 0.045 0.318 2235 Planarity : 0.005 0.064 2488 Dihedral : 15.921 168.884 2387 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.12 % Favored : 91.82 % Rotamer: Outliers : 4.73 % Allowed : 21.92 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1712 helix: 1.26 (0.22), residues: 586 sheet: 0.32 (0.34), residues: 232 loop : -1.99 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 345 HIS 0.011 0.001 HIS A 298 PHE 0.017 0.001 PHE B 266 TYR 0.031 0.002 TYR C 291 ARG 0.007 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 558) hydrogen bonds : angle 4.59599 ( 1532) covalent geometry : bond 0.00418 (14940) covalent geometry : angle 0.70763 (20436) *********************** 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 258 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7282 (mt) REVERT: A 279 ARG cc_start: 0.6963 (ttp-170) cc_final: 0.5933 (ttp-170) REVERT: A 295 MET cc_start: 0.8256 (mtp) cc_final: 0.8039 (mtp) REVERT: A 557 GLU cc_start: 0.8741 (tp30) cc_final: 0.8258 (mm-30) REVERT: A 580 LEU cc_start: 0.7143 (mp) cc_final: 0.6832 (tm) REVERT: A 612 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5355 (tp) REVERT: A 793 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 873 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7953 (pp20) REVERT: A 910 MET cc_start: 0.5300 (mtt) cc_final: 0.4868 (mmm) REVERT: A 968 GLN cc_start: 0.8284 (mt0) cc_final: 0.7981 (tm-30) REVERT: A 976 GLN cc_start: 0.8303 (pt0) cc_final: 0.8071 (pm20) REVERT: A 1083 LEU cc_start: 0.7929 (tp) cc_final: 0.7583 (tm) REVERT: B 325 ARG cc_start: 0.6980 (mmt90) cc_final: 0.6713 (mmt90) REVERT: B 405 GLU cc_start: 0.8627 (tt0) cc_final: 0.8340 (pt0) REVERT: C 92 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7829 (mm) REVERT: C 134 LYS cc_start: 0.8508 (tptt) cc_final: 0.8250 (tppt) REVERT: C 322 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8314 (pp) REVERT: C 466 MET cc_start: 0.8345 (tmm) cc_final: 0.8065 (tmm) REVERT: C 477 LYS cc_start: 0.9005 (mptt) cc_final: 0.8745 (mptt) outliers start: 69 outliers final: 26 residues processed: 228 average time/residue: 0.9545 time to fit residues: 246.0001 Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 278 ILE 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 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 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 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 278 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 277 HIS A 540 GLN A 740 ASN ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.156903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.110637 restraints weight = 27927.260| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 4.04 r_work: 0.3470 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14940 Z= 0.282 Angle : 0.777 11.380 20436 Z= 0.394 Chirality : 0.048 0.266 2235 Planarity : 0.006 0.066 2488 Dihedral : 15.954 168.513 2387 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.17 % Favored : 90.77 % Rotamer: Outliers : 5.89 % Allowed : 22.19 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1712 helix: 0.81 (0.21), residues: 585 sheet: -0.08 (0.33), residues: 239 loop : -2.11 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 607 HIS 0.013 0.002 HIS A 298 PHE 0.026 0.002 PHE B 266 TYR 0.044 0.002 TYR C 291 ARG 0.006 0.001 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 558) hydrogen bonds : angle 4.82695 ( 1532) covalent geometry : bond 0.00639 (14940) covalent geometry : angle 0.77727 (20436) *********************** 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 259 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 173 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.7068 (ttp-170) cc_final: 0.6187 (ttp-170) REVERT: A 295 MET cc_start: 0.8283 (mtp) cc_final: 0.8058 (mtp) REVERT: A 557 GLU cc_start: 0.8761 (tp30) cc_final: 0.8340 (mm-30) REVERT: A 580 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6982 (tm) REVERT: A 616 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7131 (pp20) REVERT: A 793 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 968 GLN cc_start: 0.8299 (mt0) cc_final: 0.8066 (tm-30) REVERT: A 1083 LEU cc_start: 0.8140 (tp) cc_final: 0.7788 (tm) REVERT: B 75 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7965 (ptp-170) REVERT: B 405 GLU cc_start: 0.8721 (tt0) cc_final: 0.8435 (pt0) REVERT: C 134 LYS cc_start: 0.8567 (tptt) cc_final: 0.8292 (tppt) REVERT: C 321 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8163 (pmtt) REVERT: C 322 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8422 (pp) REVERT: C 325 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6048 (mmm160) REVERT: C 466 MET cc_start: 0.8412 (tmm) cc_final: 0.8124 (tmm) outliers start: 86 outliers final: 35 residues processed: 233 average time/residue: 0.9271 time to fit residues: 244.9904 Evaluate side-chains 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 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 580 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 851 THR 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 954 ILE Chi-restraints excluded: chain A residue 1054 GLU 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 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 326 ASP 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 C residue 92 LEU Chi-restraints excluded: chain C residue 243 THR 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 413 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 420 THR 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 8 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.158611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.112240 restraints weight = 28042.498| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.10 r_work: 0.3497 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2774 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= 0.183 Angle : 0.714 12.316 20436 Z= 0.357 Chirality : 0.046 0.218 2235 Planarity : 0.005 0.063 2488 Dihedral : 15.820 168.012 2387 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.11 % Favored : 90.83 % Rotamer: Outliers : 4.38 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1712 helix: 0.99 (0.22), residues: 583 sheet: -0.05 (0.33), residues: 242 loop : -2.08 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 347 HIS 0.009 0.001 HIS B 309 PHE 0.017 0.001 PHE C 403 TYR 0.030 0.002 TYR C 291 ARG 0.004 0.000 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 558) hydrogen bonds : angle 4.68824 ( 1532) covalent geometry : bond 0.00416 (14940) covalent geometry : angle 0.71357 (20436) *********************** 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 240 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.6989 (ttp-170) cc_final: 0.6605 (ttp-170) REVERT: A 295 MET cc_start: 0.8263 (mtp) cc_final: 0.8039 (mtp) REVERT: A 347 TRP cc_start: 0.7823 (p90) cc_final: 0.7505 (p90) REVERT: A 553 LYS cc_start: 0.8598 (mmmt) cc_final: 0.7839 (mmtm) REVERT: A 557 GLU cc_start: 0.8782 (tp30) cc_final: 0.8348 (mm-30) REVERT: A 793 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 873 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7370 (pp20) REVERT: A 910 MET cc_start: 0.5259 (mtt) cc_final: 0.4988 (mmt) REVERT: A 968 GLN cc_start: 0.8308 (mt0) cc_final: 0.8072 (tm-30) REVERT: A 1083 LEU cc_start: 0.8106 (tp) cc_final: 0.7823 (tm) REVERT: B 75 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8039 (ptp-170) REVERT: B 219 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7226 (p90) REVERT: B 405 GLU cc_start: 0.8700 (tt0) cc_final: 0.8446 (pt0) REVERT: C 92 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7918 (mm) REVERT: C 134 LYS cc_start: 0.8567 (tptt) cc_final: 0.8303 (tppt) REVERT: C 322 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8339 (pp) REVERT: C 462 MET cc_start: 0.8127 (ppp) cc_final: 0.7706 (mmm) REVERT: C 466 MET cc_start: 0.8418 (tmm) cc_final: 0.8107 (tmm) REVERT: C 477 LYS cc_start: 0.9017 (mptt) cc_final: 0.8711 (mptt) outliers start: 64 outliers final: 29 residues processed: 220 average time/residue: 0.9520 time to fit residues: 237.6597 Evaluate side-chains 199 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 740 ASN 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 1054 GLU 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 219 PHE Chi-restraints excluded: chain B residue 312 LEU 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 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 322 LEU 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 149 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 171 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** 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 = 0.4353 r_free = 0.4353 target = 0.159582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113549 restraints weight = 28132.808| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 4.08 r_work: 0.3516 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14940 Z= 0.158 Angle : 0.709 11.797 20436 Z= 0.351 Chirality : 0.045 0.269 2235 Planarity : 0.005 0.064 2488 Dihedral : 15.733 168.002 2386 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.71 % Rotamer: Outliers : 4.18 % Allowed : 25.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1712 helix: 1.09 (0.22), residues: 582 sheet: 0.03 (0.33), residues: 243 loop : -2.05 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 347 HIS 0.009 0.001 HIS B 309 PHE 0.017 0.001 PHE C 403 TYR 0.029 0.002 TYR C 291 ARG 0.011 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 558) hydrogen bonds : angle 4.61259 ( 1532) covalent geometry : bond 0.00360 (14940) covalent geometry : angle 0.70930 (20436) *********************** 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 239 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.6788 (ttp-170) cc_final: 0.6487 (ttp-170) REVERT: A 347 TRP cc_start: 0.7905 (p90) cc_final: 0.7107 (p90) REVERT: A 382 MET cc_start: 0.7381 (tmm) cc_final: 0.7065 (tmm) REVERT: A 472 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.6988 (mp10) REVERT: A 580 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6889 (tm) REVERT: A 616 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: A 793 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 812 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7177 (ttp) REVERT: A 873 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: A 910 MET cc_start: 0.5386 (mtt) cc_final: 0.5024 (mmt) REVERT: A 968 GLN cc_start: 0.8321 (mt0) cc_final: 0.8102 (tm-30) REVERT: A 976 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8595 (pt0) REVERT: A 1083 LEU cc_start: 0.8121 (tp) cc_final: 0.7756 (tm) REVERT: B 75 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8073 (ptp-170) REVERT: B 219 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7298 (p90) REVERT: B 405 GLU cc_start: 0.8713 (tt0) cc_final: 0.8473 (pt0) REVERT: B 407 LEU cc_start: 0.9018 (mp) cc_final: 0.8786 (mp) REVERT: C 92 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7846 (mm) REVERT: C 134 LYS cc_start: 0.8551 (tptt) cc_final: 0.8284 (tppt) REVERT: C 321 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8191 (pmtt) REVERT: C 349 TYR cc_start: 0.8527 (m-10) cc_final: 0.8224 (m-10) REVERT: C 466 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8108 (tmm) REVERT: C 477 LYS cc_start: 0.9014 (mptt) cc_final: 0.8695 (mptt) outliers start: 61 outliers final: 28 residues processed: 216 average time/residue: 0.9214 time to fit residues: 226.8167 Evaluate side-chains 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 287 SER 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 812 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1054 GLU 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 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 312 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 C residue 92 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 321 LYS 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 165 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** 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** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.159082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.113026 restraints weight = 28016.530| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 4.06 r_work: 0.3506 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14940 Z= 0.173 Angle : 0.713 11.472 20436 Z= 0.354 Chirality : 0.045 0.216 2235 Planarity : 0.005 0.064 2488 Dihedral : 15.693 168.138 2386 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.40 % Favored : 90.54 % Rotamer: Outliers : 4.93 % Allowed : 25.14 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1712 helix: 1.08 (0.22), residues: 584 sheet: -0.11 (0.33), residues: 244 loop : -2.02 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 347 HIS 0.009 0.001 HIS B 309 PHE 0.016 0.001 PHE C 403 TYR 0.034 0.002 TYR C 291 ARG 0.012 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 558) hydrogen bonds : angle 4.62536 ( 1532) covalent geometry : bond 0.00396 (14940) covalent geometry : angle 0.71258 (20436) *********************** 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 250 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.6796 (ttp-170) cc_final: 0.6505 (ttp-170) REVERT: A 347 TRP cc_start: 0.7972 (p90) cc_final: 0.7130 (p90) REVERT: A 382 MET cc_start: 0.7485 (tmm) cc_final: 0.7248 (tmm) REVERT: A 472 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: A 557 GLU cc_start: 0.8807 (tp30) cc_final: 0.8375 (mm-30) REVERT: A 580 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6892 (tm) REVERT: A 616 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: A 793 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 873 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: A 910 MET cc_start: 0.5443 (mtt) cc_final: 0.5065 (mmt) REVERT: A 968 GLN cc_start: 0.8302 (mt0) cc_final: 0.8053 (tm-30) REVERT: A 976 GLN cc_start: 0.8907 (mm110) cc_final: 0.8611 (pt0) REVERT: A 1083 LEU cc_start: 0.8121 (tp) cc_final: 0.7749 (tm) REVERT: A 1163 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.7482 (tpt) REVERT: B 219 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7317 (p90) REVERT: B 405 GLU cc_start: 0.8714 (tt0) cc_final: 0.8479 (pt0) REVERT: C 92 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7862 (mm) REVERT: C 134 LYS cc_start: 0.8556 (tptt) cc_final: 0.8296 (tppt) REVERT: C 321 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8143 (pmtt) REVERT: C 325 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6089 (mmm160) REVERT: C 466 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8085 (tmm) REVERT: C 477 LYS cc_start: 0.9020 (mptt) cc_final: 0.8706 (mptt) outliers start: 72 outliers final: 34 residues processed: 224 average time/residue: 0.8991 time to fit residues: 229.2667 Evaluate side-chains 209 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 580 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 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1163 MET 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 218 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 319 VAL 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 C residue 92 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 228 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 106 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN ** A 906 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 = 0.4367 r_free = 0.4367 target = 0.160642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.114734 restraints weight = 27830.873| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 4.05 r_work: 0.3541 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14940 Z= 0.142 Angle : 0.718 12.777 20436 Z= 0.353 Chirality : 0.044 0.204 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.635 168.108 2386 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.88 % Favored : 91.06 % Rotamer: Outliers : 3.90 % Allowed : 26.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1712 helix: 1.21 (0.22), residues: 584 sheet: 0.14 (0.33), residues: 243 loop : -1.97 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1099 HIS 0.009 0.001 HIS B 309 PHE 0.015 0.001 PHE C 403 TYR 0.030 0.002 TYR C 291 ARG 0.009 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 558) hydrogen bonds : angle 4.54221 ( 1532) covalent geometry : bond 0.00319 (14940) covalent geometry : angle 0.71826 (20436) *********************** 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 229 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.6673 (ttp-170) cc_final: 0.6416 (ttp-170) REVERT: A 347 TRP cc_start: 0.7931 (p90) cc_final: 0.7100 (p90) REVERT: A 382 MET cc_start: 0.7540 (tmm) cc_final: 0.7272 (tmm) REVERT: A 472 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: A 553 LYS cc_start: 0.8488 (mmmt) cc_final: 0.7682 (mmtm) REVERT: A 557 GLU cc_start: 0.8800 (tp30) cc_final: 0.8348 (mm-30) REVERT: A 616 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7157 (pp20) REVERT: A 793 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7768 (tm-30) REVERT: A 873 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: A 910 MET cc_start: 0.5421 (mtt) cc_final: 0.5096 (mmt) REVERT: A 968 GLN cc_start: 0.8319 (mt0) cc_final: 0.8096 (tm-30) REVERT: A 976 GLN cc_start: 0.8968 (mm110) cc_final: 0.8661 (pt0) REVERT: A 1083 LEU cc_start: 0.8075 (tp) cc_final: 0.7706 (tm) REVERT: A 1206 MET cc_start: 0.5111 (mmt) cc_final: 0.4775 (mmm) REVERT: B 219 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7381 (p90) REVERT: B 405 GLU cc_start: 0.8685 (tt0) cc_final: 0.8479 (pt0) REVERT: C 92 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7849 (mm) REVERT: C 134 LYS cc_start: 0.8528 (tptt) cc_final: 0.8277 (tppt) REVERT: C 321 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8173 (pmtt) REVERT: C 349 TYR cc_start: 0.8500 (m-10) cc_final: 0.8195 (m-10) REVERT: C 436 SER cc_start: 0.8188 (m) cc_final: 0.7816 (t) REVERT: C 466 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8034 (tmm) REVERT: C 477 LYS cc_start: 0.9016 (mptt) cc_final: 0.8686 (mptt) outliers start: 57 outliers final: 35 residues processed: 207 average time/residue: 0.9344 time to fit residues: 219.1765 Evaluate side-chains 209 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE 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 902 LEU Chi-restraints excluded: chain A residue 1054 GLU 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 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 319 VAL 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 228 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 44 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.0070 chunk 172 optimal weight: 10.0000 overall best weight: 1.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4352 r_free = 0.4352 target = 0.159413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113341 restraints weight = 27914.894| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.05 r_work: 0.3518 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14940 Z= 0.169 Angle : 0.728 12.084 20436 Z= 0.360 Chirality : 0.045 0.204 2235 Planarity : 0.005 0.075 2488 Dihedral : 15.639 168.774 2386 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.29 % Favored : 90.65 % Rotamer: Outliers : 3.63 % Allowed : 26.58 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1712 helix: 1.15 (0.22), residues: 584 sheet: 0.01 (0.33), residues: 237 loop : -2.02 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1099 HIS 0.010 0.001 HIS B 309 PHE 0.023 0.001 PHE B 145 TYR 0.034 0.002 TYR C 291 ARG 0.014 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 558) hydrogen bonds : angle 4.55720 ( 1532) covalent geometry : bond 0.00387 (14940) covalent geometry : angle 0.72824 (20436) *********************** 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 225 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.6746 (ttp-170) cc_final: 0.6488 (ttp-170) REVERT: A 347 TRP cc_start: 0.8031 (p90) cc_final: 0.7225 (p90) REVERT: A 382 MET cc_start: 0.7665 (tmm) cc_final: 0.7412 (tmm) REVERT: A 472 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: A 557 GLU cc_start: 0.8751 (tp30) cc_final: 0.8337 (mm-30) REVERT: A 580 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6840 (tm) REVERT: A 616 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: A 793 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 873 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: A 910 MET cc_start: 0.5384 (mtt) cc_final: 0.5052 (mmt) REVERT: A 968 GLN cc_start: 0.8318 (mt0) cc_final: 0.8050 (tm-30) REVERT: A 976 GLN cc_start: 0.8970 (mm110) cc_final: 0.8594 (pt0) REVERT: A 1083 LEU cc_start: 0.8080 (tp) cc_final: 0.7708 (tm) REVERT: B 219 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7314 (p90) REVERT: B 405 GLU cc_start: 0.8724 (tt0) cc_final: 0.8517 (pt0) REVERT: C 92 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7795 (mm) REVERT: C 134 LYS cc_start: 0.8542 (tptt) cc_final: 0.8292 (tppt) REVERT: C 321 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8194 (pmtt) REVERT: C 466 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8066 (tmm) REVERT: C 477 LYS cc_start: 0.9020 (mptt) cc_final: 0.8691 (mptt) outliers start: 53 outliers final: 34 residues processed: 205 average time/residue: 0.9534 time to fit residues: 222.9592 Evaluate side-chains 210 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 393 MET 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 740 ASN 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 902 LEU Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1093 MET 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 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 319 VAL 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 243 THR 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 157 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 142 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 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 = 0.4367 r_free = 0.4367 target = 0.160713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114944 restraints weight = 27963.104| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 4.03 r_work: 0.3540 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14940 Z= 0.141 Angle : 0.732 12.824 20436 Z= 0.360 Chirality : 0.044 0.205 2235 Planarity : 0.005 0.064 2488 Dihedral : 15.613 168.872 2386 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.71 % Rotamer: Outliers : 2.88 % Allowed : 27.53 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1712 helix: 1.29 (0.22), residues: 578 sheet: 0.16 (0.33), residues: 241 loop : -2.00 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1099 HIS 0.010 0.001 HIS B 309 PHE 0.015 0.001 PHE C 403 TYR 0.032 0.002 TYR C 291 ARG 0.014 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 558) hydrogen bonds : angle 4.53208 ( 1532) covalent geometry : bond 0.00321 (14940) covalent geometry : angle 0.73208 (20436) ********************** 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 216 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.6708 (ttp-170) cc_final: 0.6450 (ttp-170) REVERT: A 347 TRP cc_start: 0.7998 (p90) cc_final: 0.7194 (p90) REVERT: A 382 MET cc_start: 0.7657 (tmm) cc_final: 0.7404 (tmm) REVERT: A 472 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: A 553 LYS cc_start: 0.8462 (mmmt) cc_final: 0.7654 (mmtm) REVERT: A 557 GLU cc_start: 0.8752 (tp30) cc_final: 0.8367 (mm-30) REVERT: A 616 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7273 (pp20) REVERT: A 793 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 873 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7664 (pp20) REVERT: A 910 MET cc_start: 0.5386 (mtt) cc_final: 0.5065 (mmt) REVERT: A 968 GLN cc_start: 0.8353 (mt0) cc_final: 0.8087 (tm-30) REVERT: A 976 GLN cc_start: 0.8973 (mm110) cc_final: 0.8577 (pt0) REVERT: A 1083 LEU cc_start: 0.8023 (tp) cc_final: 0.7649 (tm) REVERT: B 219 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7370 (p90) REVERT: C 92 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7830 (mm) REVERT: C 134 LYS cc_start: 0.8521 (tptt) cc_final: 0.8272 (tppt) REVERT: C 321 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8203 (pmtt) REVERT: C 325 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6154 (mmm160) REVERT: C 349 TYR cc_start: 0.8507 (m-10) cc_final: 0.8211 (m-10) REVERT: C 466 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8021 (tmm) REVERT: C 477 LYS cc_start: 0.9020 (mptt) cc_final: 0.8690 (mptt) outliers start: 42 outliers final: 31 residues processed: 201 average time/residue: 0.9058 time to fit residues: 206.9110 Evaluate side-chains 209 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 539 PHE 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 902 LEU Chi-restraints excluded: chain A residue 1054 GLU 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 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 319 VAL 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 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 167 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 613 HIS A 740 ASN A 754 HIS ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4377 r_free = 0.4377 target = 0.161566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115909 restraints weight = 27895.537| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 4.06 r_work: 0.3555 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14940 Z= 0.134 Angle : 0.716 13.093 20436 Z= 0.350 Chirality : 0.044 0.204 2235 Planarity : 0.004 0.064 2488 Dihedral : 15.550 169.459 2386 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.71 % Rotamer: Outliers : 3.08 % Allowed : 27.60 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1712 helix: 1.27 (0.23), residues: 582 sheet: 0.17 (0.33), residues: 241 loop : -1.97 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1099 HIS 0.010 0.001 HIS B 309 PHE 0.032 0.001 PHE B 145 TYR 0.029 0.002 TYR C 291 ARG 0.013 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 558) hydrogen bonds : angle 4.48368 ( 1532) covalent geometry : bond 0.00302 (14940) covalent geometry : angle 0.71602 (20436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14749.20 seconds wall clock time: 253 minutes 15.73 seconds (15195.73 seconds total)