Starting phenix.real_space_refine on Thu Aug 6 06:41:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5i_29745/08_2026/8g5i_29745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5i_29745/08_2026/8g5i_29745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g5i_29745/08_2026/8g5i_29745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5i_29745/08_2026/8g5i_29745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5i_29745/08_2026/8g5i_29745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5i_29745/08_2026/8g5i_29745.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 80 5.16 5 C 8859 2.51 5 N 2480 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7430 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 63, 'TRANS': 877} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2986 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2890 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (38 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 3.25, per 1000 atoms: 0.23 Number of scatterers: 14084 At special positions: 0 Unit cell: (94.164, 106.554, 141.246, 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 80 16.00 P 38 15.00 O 2627 8.00 N 2480 7.00 C 8859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 543.7 milliseconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 41.6% alpha, 11.3% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.277A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Proline residue: A 149 - end of helix removed outlier: 3.503A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.875A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.501A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.000A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.599A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.414A pdb=" N ASP A 487 " --> pdb=" O TRP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 removed outlier: 3.767A pdb=" N GLU A 538 " --> pdb=" O GLU A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 539 through 556 removed outlier: 3.676A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.623A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.656A pdb=" N MET A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.875A pdb=" N ASN A 758 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.715A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.548A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 878 removed outlier: 3.527A pdb=" N LEU A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 944 through 954 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.896A pdb=" N LEU A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 1057 through 1066 removed outlier: 4.133A pdb=" N LEU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.667A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 removed outlier: 3.729A pdb=" N ARG A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 removed outlier: 4.113A pdb=" N ILE A1220 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 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 200 removed outlier: 3.552A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 199 " --> pdb=" O ASN B 195 " (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: 3.547A pdb=" N LEU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.637A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.570A pdb=" N SER B 424 " --> pdb=" O MET B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.147A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 4.184A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 87 removed outlier: 4.364A pdb=" N SER C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 184 through 191 removed outlier: 4.213A pdb=" N GLY C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.717A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.233A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 393 through 409 removed outlier: 3.643A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 470 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.868A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.785A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AA4, first strand: chain 'A' and resid 1130 through 1133 removed outlier: 3.641A pdb=" N ARG A1138 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1133 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1137 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.127A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.068A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 382 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.269A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.111A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4439 1.34 - 1.46: 2856 1.46 - 1.58: 7023 1.58 - 1.70: 73 1.70 - 1.82: 125 Bond restraints: 14516 Sorted by residual: bond pdb=" O3' DG P 26 " pdb=" P A DA P 27 " ideal model delta sigma weight residual 1.607 1.524 0.083 1.20e-02 6.94e+03 4.80e+01 bond pdb=" C1' DT P 18 " pdb=" N1 DT P 18 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.52e+01 bond pdb=" C3' DC P 25 " pdb=" C2' DC P 25 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C1' DC T 10 " pdb=" N1 DC T 10 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.69e+00 bond pdb=" C1' DC T 12 " pdb=" N1 DC T 12 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.44e+00 ... (remaining 14511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19425 2.79 - 5.57: 382 5.57 - 8.36: 22 8.36 - 11.14: 2 11.14 - 13.93: 1 Bond angle restraints: 19832 Sorted by residual: angle pdb=" N PRO A 560 " pdb=" CA PRO A 560 " pdb=" CB PRO A 560 " ideal model delta sigma weight residual 103.25 111.48 -8.23 1.05e+00 9.07e-01 6.15e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.33 110.42 -7.09 9.30e-01 1.16e+00 5.81e+01 angle pdb=" N PRO A 250 " pdb=" CA PRO A 250 " pdb=" CB PRO A 250 " ideal model delta sigma weight residual 103.25 111.10 -7.85 1.05e+00 9.07e-01 5.59e+01 angle pdb=" C3' DG P 26 " pdb=" O3' DG P 26 " pdb=" P B DA P 27 " ideal model delta sigma weight residual 119.70 111.04 8.66 1.20e+00 6.94e-01 5.21e+01 angle pdb=" N ILE A 954 " pdb=" CA ILE A 954 " pdb=" C ILE A 954 " ideal model delta sigma weight residual 110.21 104.84 5.37 1.13e+00 7.83e-01 2.26e+01 ... (remaining 19827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 8015 30.68 - 61.36: 487 61.36 - 92.04: 27 92.04 - 122.72: 0 122.72 - 153.41: 2 Dihedral angle restraints: 8531 sinusoidal: 3718 harmonic: 4813 Sorted by residual: dihedral pdb=" CA PRO A1070 " pdb=" C PRO A1070 " pdb=" N ARG A1071 " pdb=" CA ARG A1071 " ideal model delta harmonic sigma weight residual -180.00 -154.51 -25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CD ARG B 75 " pdb=" NE ARG B 75 " pdb=" CZ ARG B 75 " pdb=" NH1 ARG B 75 " ideal model delta sinusoidal sigma weight residual 0.00 -37.38 37.38 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA LEU B 393 " pdb=" C LEU B 393 " pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2062 0.113 - 0.226: 75 0.226 - 0.339: 0 0.339 - 0.453: 0 0.453 - 0.566: 1 Chirality restraints: 2138 Sorted by residual: chirality pdb=" P DG P 26 " pdb=" OP1 DG P 26 " pdb=" OP2 DG P 26 " pdb=" O5' DG P 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA PRO A 625 " pdb=" N PRO A 625 " pdb=" C PRO A 625 " pdb=" CB PRO A 625 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA LEU A 605 " pdb=" N LEU A 605 " pdb=" C LEU A 605 " pdb=" CB LEU A 605 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 2135 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 75 " 0.665 9.50e-02 1.11e+02 2.98e-01 5.43e+01 pdb=" NE ARG B 75 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 75 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 75 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 75 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 363 " 0.546 9.50e-02 1.11e+02 2.45e-01 3.66e+01 pdb=" NE ARG B 363 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 363 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 363 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 363 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 852 " -0.406 9.50e-02 1.11e+02 1.82e-01 2.03e+01 pdb=" NE ARG A 852 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 852 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 852 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 852 " -0.013 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 261 2.65 - 3.21: 13315 3.21 - 3.77: 22571 3.77 - 4.34: 30448 4.34 - 4.90: 49068 Nonbonded interactions: 115663 Sorted by model distance: nonbonded pdb=" OG SER C 90 " pdb=" O CYS C 95 " model vdw 2.085 3.040 nonbonded pdb=" O PRO A 857 " pdb=" OG1 THR A 861 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.121 3.040 nonbonded pdb=" O LYS A 553 " pdb=" NZ LYS A 553 " model vdw 2.122 3.120 nonbonded pdb=" N GLU A 280 " pdb=" OE1 GLU A 280 " model vdw 2.153 3.120 ... (remaining 115658 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 68 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or re \ sid 180 through 219 or resid 227 through 355 or resid 368 through 420 or (resid \ 421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ h 485)) selection = (chain 'C' and (resid 68 through 136 or resid 180 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 through 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.260 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 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 : 0.004 0.083 14516 Z= 0.258 Angle : 0.818 13.928 19832 Z= 0.474 Chirality : 0.047 0.566 2138 Planarity : 0.010 0.298 2416 Dihedral : 17.633 153.406 5427 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.12 % Rotamer: Outliers : 1.33 % Allowed : 26.97 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1643 helix: 1.15 (0.22), residues: 595 sheet: 0.04 (0.37), residues: 194 loop : -1.18 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 325 TYR 0.014 0.001 TYR A1108 PHE 0.037 0.001 PHE A 539 TRP 0.016 0.001 TRP A1118 HIS 0.010 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.26 (14516) covalent geometry : angle 0.81762 / 0.47 (19832) hydrogen bonds : bond 0.14606 / 9.21 ( 582) hydrogen bonds : angle 6.03594 / 4.12 ( 1616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 539 PHE cc_start: 0.6585 (p90) cc_final: 0.5405 (p90) REVERT: A 579 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7730 (mmm160) REVERT: A 1195 MET cc_start: 0.7873 (ttm) cc_final: 0.7600 (ptp) REVERT: C 422 GLN cc_start: 0.5878 (tp-100) cc_final: 0.5364 (tp40) outliers start: 19 outliers final: 9 residues processed: 234 average time/residue: 0.5567 time to fit residues: 143.6619 Evaluate side-chains 200 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 134 ASN A 138 HIS A 144 GLN A 226 GLN A 472 GLN A 493 GLN A 618 HIS A 811 GLN A 843 GLN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN A1110 HIS A1134 HIS A1157 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 355 GLN C 313 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.156298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123212 restraints weight = 37410.987| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.10 r_work: 0.3641 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14516 Z= 0.164 Angle : 0.712 13.645 19832 Z= 0.360 Chirality : 0.045 0.274 2138 Planarity : 0.005 0.053 2416 Dihedral : 14.925 149.231 2221 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 4.35 % Allowed : 23.38 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1643 helix: 1.25 (0.22), residues: 605 sheet: -0.04 (0.35), residues: 206 loop : -1.10 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 81 TYR 0.012 0.001 TYR A 614 PHE 0.016 0.001 PHE A 539 TRP 0.016 0.001 TRP A 607 HIS 0.010 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (14516) covalent geometry : angle 0.71226 / 0.36 (19832) hydrogen bonds : bond 0.04409 / 2.80 ( 582) hydrogen bonds : angle 4.84185 / 3.32 ( 1616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.5762 (ppp) cc_final: 0.5404 (ppp) REVERT: A 363 TYR cc_start: 0.6984 (m-10) cc_final: 0.6730 (m-10) REVERT: A 544 MET cc_start: 0.8721 (ppp) cc_final: 0.8505 (pp-130) REVERT: A 975 GLN cc_start: 0.8658 (pm20) cc_final: 0.8277 (pm20) REVERT: A 985 MET cc_start: 0.7629 (mmt) cc_final: 0.7402 (mmt) REVERT: A 1098 ASN cc_start: 0.9104 (m-40) cc_final: 0.8879 (m-40) REVERT: A 1136 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: A 1195 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7026 (ptp) REVERT: A 1208 ARG cc_start: 0.6044 (ptt90) cc_final: 0.5801 (ptt180) REVERT: B 75 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7534 (tpt90) REVERT: B 191 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 445 GLU cc_start: 0.8658 (pm20) cc_final: 0.7626 (pm20) REVERT: B 472 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8053 (tmmm) REVERT: C 310 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: C 396 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7016 (mpp80) outliers start: 62 outliers final: 21 residues processed: 254 average time/residue: 0.5371 time to fit residues: 150.9562 Evaluate side-chains 213 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 159 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 272 ASN B 305 ASN B 309 HIS B 318 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.156530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.125434 restraints weight = 29369.433| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.52 r_work: 0.3645 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14516 Z= 0.156 Angle : 0.681 11.623 19832 Z= 0.344 Chirality : 0.044 0.256 2138 Planarity : 0.005 0.050 2416 Dihedral : 14.908 148.697 2212 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.24 % Rotamer: Outliers : 4.49 % Allowed : 24.65 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1643 helix: 1.25 (0.22), residues: 605 sheet: -0.00 (0.35), residues: 206 loop : -1.11 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 325 TYR 0.010 0.001 TYR A1108 PHE 0.016 0.001 PHE A 610 TRP 0.015 0.001 TRP A 607 HIS 0.010 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (14516) covalent geometry : angle 0.68131 / 0.34 (19832) hydrogen bonds : bond 0.03932 / 2.50 ( 582) hydrogen bonds : angle 4.65273 / 3.20 ( 1616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5554 (ppp) REVERT: A 363 TYR cc_start: 0.6996 (m-10) cc_final: 0.6760 (m-10) REVERT: A 544 MET cc_start: 0.8594 (ppp) cc_final: 0.8385 (pp-130) REVERT: A 647 CYS cc_start: 0.7018 (t) cc_final: 0.6775 (p) REVERT: A 985 MET cc_start: 0.7507 (mmt) cc_final: 0.7233 (mmt) REVERT: A 1098 ASN cc_start: 0.9036 (m-40) cc_final: 0.8715 (m110) REVERT: A 1144 GLU cc_start: 0.8403 (pt0) cc_final: 0.8118 (pm20) REVERT: B 75 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7398 (tpt90) REVERT: B 201 ASN cc_start: 0.7658 (p0) cc_final: 0.7330 (t0) REVERT: B 325 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7711 (mtm180) REVERT: B 472 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8217 (ttpp) REVERT: C 310 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: C 396 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7054 (mpp80) outliers start: 64 outliers final: 25 residues processed: 244 average time/residue: 0.5076 time to fit residues: 137.9282 Evaluate side-chains 221 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN A1134 HIS B 133 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.153680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122214 restraints weight = 30582.985| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.57 r_work: 0.3599 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14516 Z= 0.194 Angle : 0.715 11.587 19832 Z= 0.358 Chirality : 0.045 0.241 2138 Planarity : 0.005 0.052 2416 Dihedral : 14.996 149.178 2211 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 5.34 % Allowed : 24.16 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1643 helix: 1.06 (0.21), residues: 611 sheet: 0.06 (0.34), residues: 208 loop : -1.19 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.013 0.001 TYR A 573 PHE 0.012 0.001 PHE A 389 TRP 0.023 0.001 TRP A 607 HIS 0.005 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (14516) covalent geometry : angle 0.71517 / 0.36 (19832) hydrogen bonds : bond 0.03975 / 2.55 ( 582) hydrogen bonds : angle 4.64576 / 3.19 ( 1616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 196 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5695 (ppp) REVERT: A 544 MET cc_start: 0.8556 (ppp) cc_final: 0.8326 (pp-130) REVERT: A 552 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7581 (mp) REVERT: A 647 CYS cc_start: 0.7097 (t) cc_final: 0.6830 (p) REVERT: A 985 MET cc_start: 0.7483 (mmt) cc_final: 0.7189 (mmt) REVERT: A 1098 ASN cc_start: 0.8992 (m-40) cc_final: 0.8627 (m110) REVERT: A 1144 GLU cc_start: 0.8444 (pt0) cc_final: 0.8123 (pm20) REVERT: B 75 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7402 (tpt90) REVERT: B 325 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7812 (mtm180) REVERT: B 472 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8358 (ttpp) REVERT: C 310 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: C 396 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7117 (mpp80) outliers start: 76 outliers final: 33 residues processed: 239 average time/residue: 0.5414 time to fit residues: 143.3392 Evaluate side-chains 223 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1134 HIS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 93 optimal weight: 5.9990 chunk 130 optimal weight: 0.0370 chunk 28 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS C 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.156299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124080 restraints weight = 27754.456| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.54 r_work: 0.3642 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14516 Z= 0.131 Angle : 0.674 11.023 19832 Z= 0.338 Chirality : 0.043 0.243 2138 Planarity : 0.004 0.049 2416 Dihedral : 14.962 148.579 2211 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.82 % Rotamer: Outliers : 4.42 % Allowed : 25.21 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1643 helix: 1.17 (0.21), residues: 610 sheet: 0.09 (0.35), residues: 211 loop : -1.13 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 853 TYR 0.011 0.001 TYR B 193 PHE 0.009 0.001 PHE C 403 TRP 0.026 0.001 TRP A 607 HIS 0.006 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14516) covalent geometry : angle 0.67427 / 0.34 (19832) hydrogen bonds : bond 0.03568 / 2.26 ( 582) hydrogen bonds : angle 4.50699 / 3.10 ( 1616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5530 (ppp) REVERT: A 544 MET cc_start: 0.8496 (ppp) cc_final: 0.8267 (pp-130) REVERT: A 550 GLN cc_start: 0.8463 (tp40) cc_final: 0.8239 (mm110) REVERT: A 552 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7473 (mp) REVERT: A 774 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7502 (ptm) REVERT: A 850 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8507 (pt) REVERT: A 985 MET cc_start: 0.7409 (mmt) cc_final: 0.7066 (mmt) REVERT: A 1098 ASN cc_start: 0.8928 (m-40) cc_final: 0.8571 (m110) REVERT: A 1144 GLU cc_start: 0.8470 (pt0) cc_final: 0.8100 (pm20) REVERT: B 465 MET cc_start: 0.7945 (mmm) cc_final: 0.7643 (mmm) REVERT: B 472 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8306 (ttpp) REVERT: C 310 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: C 396 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7102 (mpp80) outliers start: 63 outliers final: 33 residues processed: 236 average time/residue: 0.4841 time to fit residues: 127.2879 Evaluate side-chains 224 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 152 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.155458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.124731 restraints weight = 26157.704| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.30 r_work: 0.3641 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14516 Z= 0.150 Angle : 0.692 15.291 19832 Z= 0.344 Chirality : 0.044 0.234 2138 Planarity : 0.005 0.087 2416 Dihedral : 14.998 148.888 2211 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 4.92 % Allowed : 25.28 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1643 helix: 1.14 (0.21), residues: 618 sheet: 0.08 (0.36), residues: 197 loop : -1.17 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 75 TYR 0.012 0.001 TYR A 573 PHE 0.013 0.001 PHE A 610 TRP 0.028 0.001 TRP A 607 HIS 0.009 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (14516) covalent geometry : angle 0.69155 / 0.34 (19832) hydrogen bonds : bond 0.03629 / 2.31 ( 582) hydrogen bonds : angle 4.48615 / 3.08 ( 1616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5605 (ppp) REVERT: A 544 MET cc_start: 0.8462 (ppp) cc_final: 0.8230 (pp-130) REVERT: A 552 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7566 (mp) REVERT: A 594 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7125 (mm) REVERT: A 774 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7559 (ptm) REVERT: A 985 MET cc_start: 0.7396 (mmt) cc_final: 0.7028 (mmt) REVERT: A 1098 ASN cc_start: 0.8912 (m-40) cc_final: 0.8549 (m110) REVERT: A 1112 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8694 (mtt) REVERT: A 1144 GLU cc_start: 0.8472 (pt0) cc_final: 0.8094 (pm20) REVERT: B 386 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8253 (t70) REVERT: B 472 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8341 (ttpp) REVERT: C 310 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: C 396 ARG cc_start: 0.8049 (tpp-160) cc_final: 0.7096 (mpp80) outliers start: 70 outliers final: 36 residues processed: 234 average time/residue: 0.5221 time to fit residues: 135.0699 Evaluate side-chains 226 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 164 optimal weight: 0.7980 chunk 150 optimal weight: 0.0970 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 = 0.4200 r_free = 0.4200 target = 0.156363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124283 restraints weight = 28789.867| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.59 r_work: 0.3637 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14516 Z= 0.130 Angle : 0.694 13.749 19832 Z= 0.344 Chirality : 0.043 0.234 2138 Planarity : 0.004 0.048 2416 Dihedral : 14.954 148.647 2209 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 4.28 % Allowed : 26.47 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1643 helix: 1.20 (0.21), residues: 617 sheet: 0.06 (0.36), residues: 197 loop : -1.15 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.012 0.001 TYR B 193 PHE 0.009 0.001 PHE C 403 TRP 0.027 0.001 TRP A 607 HIS 0.006 0.001 HIS A1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14516) covalent geometry : angle 0.69418 / 0.34 (19832) hydrogen bonds : bond 0.03450 / 2.20 ( 582) hydrogen bonds : angle 4.42002 / 3.04 ( 1616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5498 (ppp) REVERT: A 544 MET cc_start: 0.8458 (ppp) cc_final: 0.8231 (pp-130) REVERT: A 774 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7549 (ptm) REVERT: A 985 MET cc_start: 0.7368 (mmt) cc_final: 0.6999 (mmt) REVERT: A 1098 ASN cc_start: 0.8924 (m-40) cc_final: 0.8577 (m110) REVERT: A 1112 MET cc_start: 0.8988 (mtt) cc_final: 0.8713 (mtt) REVERT: A 1144 GLU cc_start: 0.8465 (pt0) cc_final: 0.8109 (pm20) REVERT: B 191 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 472 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8316 (ttpp) REVERT: C 310 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: C 386 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6719 (t0) REVERT: C 396 ARG cc_start: 0.8066 (tpp-160) cc_final: 0.7092 (mpp80) outliers start: 61 outliers final: 38 residues processed: 231 average time/residue: 0.5289 time to fit residues: 135.6729 Evaluate side-chains 222 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1077 CYS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 = 0.4186 r_free = 0.4186 target = 0.155072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123547 restraints weight = 25860.698| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.40 r_work: 0.3654 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14516 Z= 0.139 Angle : 0.710 13.814 19832 Z= 0.348 Chirality : 0.043 0.231 2138 Planarity : 0.004 0.065 2416 Dihedral : 14.978 148.875 2209 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 4.42 % Allowed : 27.32 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1643 helix: 1.23 (0.22), residues: 613 sheet: 0.10 (0.36), residues: 197 loop : -1.14 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 75 TYR 0.016 0.001 TYR B 193 PHE 0.014 0.001 PHE A 610 TRP 0.028 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14516) covalent geometry : angle 0.70984 / 0.35 (19832) hydrogen bonds : bond 0.03472 / 2.23 ( 582) hydrogen bonds : angle 4.39070 / 3.03 ( 1616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5648 (ppp) REVERT: A 81 ARG cc_start: 0.4794 (mmt180) cc_final: 0.3610 (mpp-170) REVERT: A 465 ASP cc_start: 0.8774 (t70) cc_final: 0.8501 (t70) REVERT: A 544 MET cc_start: 0.8386 (ppp) cc_final: 0.8132 (ppp) REVERT: A 774 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7597 (ptm) REVERT: A 985 MET cc_start: 0.7380 (mmt) cc_final: 0.7032 (mmt) REVERT: A 1098 ASN cc_start: 0.8962 (m-40) cc_final: 0.8543 (m110) REVERT: A 1144 GLU cc_start: 0.8434 (pt0) cc_final: 0.8085 (pm20) REVERT: B 75 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.7179 (mmm160) REVERT: B 191 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8159 (mt-10) REVERT: B 386 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8245 (t70) REVERT: B 472 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8321 (tmmm) REVERT: C 310 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: C 386 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6722 (t0) REVERT: C 396 ARG cc_start: 0.8048 (tpp-160) cc_final: 0.7039 (mpp80) outliers start: 63 outliers final: 40 residues processed: 226 average time/residue: 0.4812 time to fit residues: 121.2258 Evaluate side-chains 227 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1077 CYS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 159 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 = 0.4198 r_free = 0.4198 target = 0.156410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124168 restraints weight = 29653.511| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.66 r_work: 0.3660 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14516 Z= 0.131 Angle : 0.703 15.430 19832 Z= 0.347 Chirality : 0.043 0.231 2138 Planarity : 0.004 0.046 2416 Dihedral : 14.975 148.858 2209 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 4.07 % Allowed : 27.32 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1643 helix: 1.21 (0.21), residues: 617 sheet: 0.12 (0.36), residues: 197 loop : -1.14 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 75 TYR 0.017 0.001 TYR B 193 PHE 0.009 0.001 PHE C 403 TRP 0.029 0.001 TRP A 607 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14516) covalent geometry : angle 0.70259 / 0.35 (19832) hydrogen bonds : bond 0.03432 / 2.20 ( 582) hydrogen bonds : angle 4.37433 / 3.02 ( 1616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.503 Fit side-chains REVERT: A 78 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5670 (ppp) REVERT: A 81 ARG cc_start: 0.4865 (mmt180) cc_final: 0.3751 (mpp-170) REVERT: A 465 ASP cc_start: 0.8768 (t70) cc_final: 0.8496 (t70) REVERT: A 544 MET cc_start: 0.8381 (ppp) cc_final: 0.8129 (ppp) REVERT: A 552 LEU cc_start: 0.7882 (mt) cc_final: 0.7628 (mp) REVERT: A 774 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7606 (ptm) REVERT: A 985 MET cc_start: 0.7362 (mmt) cc_final: 0.7018 (mmt) REVERT: A 1098 ASN cc_start: 0.8936 (m-40) cc_final: 0.8536 (m110) REVERT: A 1144 GLU cc_start: 0.8396 (pt0) cc_final: 0.8006 (pm20) REVERT: B 75 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.7048 (mmm160) REVERT: B 191 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 472 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8288 (tmmm) REVERT: C 310 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: C 386 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6690 (t0) REVERT: C 396 ARG cc_start: 0.8115 (tpp-160) cc_final: 0.7083 (mpp80) outliers start: 58 outliers final: 34 residues processed: 226 average time/residue: 0.4895 time to fit residues: 122.9922 Evaluate side-chains 220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1077 CYS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 55 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 = 0.4200 r_free = 0.4200 target = 0.156496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124202 restraints weight = 30067.150| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.69 r_work: 0.3651 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14516 Z= 0.133 Angle : 0.719 14.506 19832 Z= 0.352 Chirality : 0.043 0.230 2138 Planarity : 0.004 0.048 2416 Dihedral : 14.983 148.971 2209 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 3.51 % Allowed : 27.81 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1643 helix: 1.22 (0.21), residues: 617 sheet: 0.08 (0.35), residues: 203 loop : -1.14 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 75 TYR 0.016 0.001 TYR B 193 PHE 0.010 0.001 PHE C 403 TRP 0.031 0.001 TRP A 607 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14516) covalent geometry : angle 0.71893 / 0.35 (19832) hydrogen bonds : bond 0.03392 / 2.17 ( 582) hydrogen bonds : angle 4.35708 / 3.00 ( 1616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5532 (ppp) REVERT: A 465 ASP cc_start: 0.8771 (t70) cc_final: 0.8493 (t70) REVERT: A 536 GLU cc_start: 0.8036 (tp30) cc_final: 0.7155 (pt0) REVERT: A 544 MET cc_start: 0.8377 (ppp) cc_final: 0.8122 (ppp) REVERT: A 550 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: A 552 LEU cc_start: 0.7828 (mt) cc_final: 0.7578 (mp) REVERT: A 774 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7623 (ptm) REVERT: A 985 MET cc_start: 0.7342 (mmt) cc_final: 0.6976 (mmt) REVERT: A 1098 ASN cc_start: 0.8930 (m-40) cc_final: 0.8551 (m110) REVERT: A 1144 GLU cc_start: 0.8379 (pt0) cc_final: 0.7992 (pm20) REVERT: B 75 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.7015 (mmm160) REVERT: B 191 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 386 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8265 (t70) REVERT: B 472 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8320 (ttpp) REVERT: C 310 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: C 332 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 386 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.6794 (t0) REVERT: C 396 ARG cc_start: 0.8084 (tpp-160) cc_final: 0.7069 (mpp80) outliers start: 50 outliers final: 34 residues processed: 214 average time/residue: 0.4729 time to fit residues: 112.3499 Evaluate side-chains 220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1077 CYS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 165 optimal weight: 0.0570 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.122260 restraints weight = 27452.398| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.50 r_work: 0.3637 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14516 Z= 0.155 Angle : 0.724 13.849 19832 Z= 0.358 Chirality : 0.044 0.226 2138 Planarity : 0.004 0.050 2416 Dihedral : 15.033 149.497 2209 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 3.65 % Allowed : 27.88 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1643 helix: 1.18 (0.21), residues: 617 sheet: 0.05 (0.35), residues: 203 loop : -1.16 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 75 TYR 0.017 0.001 TYR B 193 PHE 0.010 0.001 PHE A 389 TRP 0.028 0.001 TRP A 607 HIS 0.009 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (14516) covalent geometry : angle 0.72395 / 0.36 (19832) hydrogen bonds : bond 0.03539 / 2.27 ( 582) hydrogen bonds : angle 4.39007 / 3.02 ( 1616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6032.39 seconds wall clock time: 103 minutes 18.80 seconds (6198.80 seconds total)