Starting phenix.real_space_refine on Fri May 16 04:53:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5i_29745/05_2025/8g5i_29745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5i_29745/05_2025/8g5i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5i_29745/05_2025/8g5i_29745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5i_29745/05_2025/8g5i_29745.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5i_29745/05_2025/8g5i_29745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5i_29745/05_2025/8g5i_29745.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: 8.50, per 1000 atoms: 0.60 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: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 4.66 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: 4.70 Time building geometry restraints manager: 4.12 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 1.50e-02 4.44e+03 3.07e+01 bond pdb=" N ARG A 852 " pdb=" CA ARG A 852 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.15e-02 7.56e+03 7.68e+00 bond pdb=" N LEU A 605 " pdb=" CA LEU A 605 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.20e+00 bond pdb=" N ARG A 853 " pdb=" CA ARG A 853 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.14e+00 bond pdb=" N VAL A1101 " pdb=" CA VAL A1101 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.94e+00 ... (remaining 14511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19454 2.79 - 5.57: 353 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 120.20 111.04 9.16 1.50e+00 4.44e-01 3.73e+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 - 0.111: 2088 0.111 - 0.222: 49 0.222 - 0.333: 0 0.333 - 0.444: 0 0.444 - 0.555: 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 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.71e+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: 0.010 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.150 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:9.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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= 0.192 Angle : 0.800 13.928 19832 Z= 0.433 Chirality : 0.044 0.555 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (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 TRP 0.016 0.001 TRP A1118 HIS 0.010 0.001 HIS C 313 PHE 0.037 0.001 PHE A 539 TYR 0.014 0.001 TYR A1108 ARG 0.013 0.001 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.14606 ( 582) hydrogen bonds : angle 6.03594 ( 1616) covalent geometry : bond 0.00389 (14516) covalent geometry : angle 0.80024 (19832) *********************** 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 : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 PHE cc_start: 0.6585 (p90) cc_final: 0.5406 (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: 1.1507 time to fit residues: 298.0730 Evaluate side-chains 201 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 141 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 134 ASN A 138 HIS A 144 GLN A 226 GLN A 394 GLN A 472 GLN A 493 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 305 ASN B 355 GLN ** B 397 GLN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.152407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118921 restraints weight = 38154.417| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 4.13 r_work: 0.3572 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14516 Z= 0.216 Angle : 0.733 12.535 19832 Z= 0.369 Chirality : 0.046 0.189 2138 Planarity : 0.005 0.051 2416 Dihedral : 15.095 150.917 2221 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 4.78 % Allowed : 23.31 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1643 helix: 1.14 (0.21), residues: 607 sheet: -0.02 (0.35), residues: 208 loop : -1.19 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 607 HIS 0.009 0.001 HIS A1134 PHE 0.014 0.002 PHE B 266 TYR 0.014 0.002 TYR A1108 ARG 0.008 0.001 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 582) hydrogen bonds : angle 4.77173 ( 1616) covalent geometry : bond 0.00493 (14516) covalent geometry : angle 0.73316 (19832) *********************** 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 277 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 1.666 Fit side-chains REVERT: A 78 MET cc_start: 0.5999 (ppp) cc_final: 0.5636 (ppp) REVERT: A 544 MET cc_start: 0.8725 (ppp) cc_final: 0.8483 (ppp) REVERT: A 647 CYS cc_start: 0.7010 (t) cc_final: 0.6679 (p) REVERT: A 762 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7607 (t) REVERT: A 975 GLN cc_start: 0.8615 (pm20) cc_final: 0.8234 (pm20) REVERT: A 1098 ASN cc_start: 0.9128 (m-40) cc_final: 0.8922 (m-40) REVERT: A 1144 GLU cc_start: 0.8446 (pt0) cc_final: 0.8078 (pm20) REVERT: B 74 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8048 (mm-40) REVERT: B 75 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7615 (tpt90) REVERT: B 445 GLU cc_start: 0.8693 (pm20) cc_final: 0.7662 (pm20) REVERT: B 465 MET cc_start: 0.8089 (mmm) cc_final: 0.7840 (mmm) REVERT: B 472 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (tmmm) REVERT: C 310 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: C 396 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7051 (mpp80) outliers start: 68 outliers final: 26 residues processed: 251 average time/residue: 1.1418 time to fit residues: 317.0161 Evaluate side-chains 214 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1083 LEU 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 72 ILE Chi-restraints excluded: chain B residue 238 SER 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 HIS A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 258 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.153448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122149 restraints weight = 28770.346| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.47 r_work: 0.3596 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 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 = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14516 Z= 0.175 Angle : 0.686 11.674 19832 Z= 0.344 Chirality : 0.044 0.166 2138 Planarity : 0.005 0.048 2416 Dihedral : 15.107 150.567 2214 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.00 % Favored : 92.94 % Rotamer: Outliers : 5.41 % Allowed : 24.16 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1643 helix: 1.09 (0.21), residues: 612 sheet: 0.07 (0.35), residues: 206 loop : -1.22 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 607 HIS 0.009 0.001 HIS A1134 PHE 0.017 0.001 PHE A 610 TYR 0.011 0.001 TYR B 206 ARG 0.005 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 582) hydrogen bonds : angle 4.65238 ( 1616) covalent geometry : bond 0.00397 (14516) covalent geometry : angle 0.68641 (19832) *********************** 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 275 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5683 (ppp) REVERT: A 544 MET cc_start: 0.8533 (ppp) cc_final: 0.8319 (pp-130) REVERT: A 552 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 647 CYS cc_start: 0.6982 (t) cc_final: 0.6677 (p) REVERT: A 975 GLN cc_start: 0.8658 (pm20) cc_final: 0.8291 (pm20) REVERT: A 1098 ASN cc_start: 0.9071 (m-40) cc_final: 0.8734 (m110) REVERT: A 1144 GLU cc_start: 0.8428 (pt0) cc_final: 0.8044 (pm20) REVERT: B 74 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7896 (mm-40) REVERT: B 325 ARG cc_start: 0.7783 (ptp-110) cc_final: 0.7469 (mtm180) REVERT: B 465 MET cc_start: 0.8095 (mmm) cc_final: 0.7680 (mmm) REVERT: B 472 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8358 (tmmm) REVERT: C 310 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: C 396 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7097 (mpp80) outliers start: 77 outliers final: 33 residues processed: 239 average time/residue: 1.1597 time to fit residues: 306.3180 Evaluate side-chains 220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 552 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 910 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL 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 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 B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** 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 261 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** C 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.154047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.123237 restraints weight = 26667.597| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.33 r_work: 0.3611 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 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 = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14516 Z= 0.155 Angle : 0.688 13.290 19832 Z= 0.340 Chirality : 0.043 0.179 2138 Planarity : 0.005 0.049 2416 Dihedral : 15.092 150.601 2212 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 5.62 % Allowed : 24.30 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1643 helix: 1.08 (0.21), residues: 617 sheet: 0.02 (0.35), residues: 194 loop : -1.24 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 607 HIS 0.005 0.001 HIS A1134 PHE 0.009 0.001 PHE B 266 TYR 0.011 0.001 TYR B 206 ARG 0.008 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 582) hydrogen bonds : angle 4.57979 ( 1616) covalent geometry : bond 0.00353 (14516) covalent geometry : angle 0.68791 (19832) *********************** 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 271 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5670 (ppp) REVERT: A 544 MET cc_start: 0.8523 (ppp) cc_final: 0.8286 (pp-130) REVERT: A 550 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: A 552 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7561 (mp) REVERT: A 647 CYS cc_start: 0.6901 (t) cc_final: 0.6696 (p) REVERT: A 1098 ASN cc_start: 0.9044 (m-40) cc_final: 0.8667 (m110) REVERT: A 1136 GLU cc_start: 0.7939 (tt0) cc_final: 0.7609 (tm-30) REVERT: A 1144 GLU cc_start: 0.8426 (pt0) cc_final: 0.8018 (pm20) REVERT: B 74 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7814 (mm-40) REVERT: B 325 ARG cc_start: 0.7760 (ptp-110) cc_final: 0.7501 (mtm180) REVERT: B 445 GLU cc_start: 0.8645 (pm20) cc_final: 0.8412 (pm20) REVERT: B 465 MET cc_start: 0.8020 (mmm) cc_final: 0.7758 (mmt) REVERT: B 472 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8372 (tmmm) REVERT: C 396 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7062 (mpp80) outliers start: 80 outliers final: 35 residues processed: 237 average time/residue: 1.1454 time to fit residues: 300.4308 Evaluate side-chains 220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 435 LEU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 550 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 910 MET Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL 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 123 GLU 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 B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU 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 Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN A 805 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.146321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114226 restraints weight = 27991.342| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.44 r_work: 0.3505 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 14516 Z= 0.318 Angle : 0.817 11.807 19832 Z= 0.411 Chirality : 0.049 0.192 2138 Planarity : 0.006 0.059 2416 Dihedral : 15.362 152.446 2210 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.54 % Rotamer: Outliers : 6.88 % Allowed : 23.10 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1643 helix: 0.55 (0.21), residues: 623 sheet: 0.03 (0.35), residues: 196 loop : -1.53 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 607 HIS 0.008 0.001 HIS A 613 PHE 0.017 0.002 PHE B 266 TYR 0.020 0.002 TYR A 573 ARG 0.006 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 582) hydrogen bonds : angle 4.94553 ( 1616) covalent geometry : bond 0.00728 (14516) covalent geometry : angle 0.81694 (19832) *********************** 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 279 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 181 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 ASP cc_start: 0.8824 (m-30) cc_final: 0.8604 (m-30) REVERT: A 544 MET cc_start: 0.8627 (ppp) cc_final: 0.8399 (pp-130) REVERT: A 594 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7294 (mm) REVERT: A 774 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7798 (ptm) REVERT: A 977 GLU cc_start: 0.7372 (tp30) cc_final: 0.7040 (tp30) REVERT: A 1098 ASN cc_start: 0.9112 (m-40) cc_final: 0.8704 (m110) REVERT: A 1144 GLU cc_start: 0.8513 (pt0) cc_final: 0.8305 (pt0) REVERT: B 69 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8379 (tm) REVERT: B 74 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8006 (mm-40) REVERT: B 325 ARG cc_start: 0.7839 (ptp-110) cc_final: 0.7510 (mtm180) REVERT: B 386 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8418 (t70) REVERT: B 465 MET cc_start: 0.8200 (mmm) cc_final: 0.7933 (mmt) REVERT: C 329 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7134 (pmtt) REVERT: C 396 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7833 (ttp-110) REVERT: C 465 MET cc_start: 0.8418 (mmm) cc_final: 0.8197 (mmm) outliers start: 98 outliers final: 41 residues processed: 244 average time/residue: 1.1576 time to fit residues: 313.1418 Evaluate side-chains 212 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 234 SER 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 594 LEU 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 948 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1107 ASP Chi-restraints excluded: chain A residue 1141 VAL 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 69 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 261 GLN 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 413 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP 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 329 LYS 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 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 0.0060 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 911 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 261 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.152286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.119903 restraints weight = 28719.060| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.59 r_work: 0.3601 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 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 = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2430 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= 0.137 Angle : 0.702 14.446 19832 Z= 0.348 Chirality : 0.043 0.166 2138 Planarity : 0.005 0.052 2416 Dihedral : 15.176 150.781 2210 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 4.49 % Allowed : 25.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1643 helix: 0.88 (0.21), residues: 623 sheet: -0.04 (0.36), residues: 197 loop : -1.35 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 607 HIS 0.004 0.001 HIS B 77 PHE 0.010 0.001 PHE B 254 TYR 0.015 0.001 TYR B 432 ARG 0.004 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 582) hydrogen bonds : angle 4.62204 ( 1616) covalent geometry : bond 0.00306 (14516) covalent geometry : angle 0.70159 (19832) *********************** 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 255 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 228 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5496 (tp) REVERT: A 544 MET cc_start: 0.8496 (ppp) cc_final: 0.8278 (pp-130) REVERT: A 550 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: A 552 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7763 (mp) REVERT: A 647 CYS cc_start: 0.6949 (t) cc_final: 0.6737 (p) REVERT: A 762 VAL cc_start: 0.7754 (OUTLIER) cc_final: 0.7473 (t) REVERT: A 774 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7657 (ptm) REVERT: A 1098 ASN cc_start: 0.9020 (m-40) cc_final: 0.8599 (m110) REVERT: A 1136 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 1144 GLU cc_start: 0.8483 (pt0) cc_final: 0.8104 (pm20) REVERT: B 69 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8317 (tm) REVERT: B 74 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7896 (mm-40) REVERT: B 123 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: B 325 ARG cc_start: 0.7765 (ptp-110) cc_final: 0.7478 (mtm180) REVERT: B 445 GLU cc_start: 0.8604 (pm20) cc_final: 0.8400 (pm20) REVERT: B 465 MET cc_start: 0.7994 (mmm) cc_final: 0.7527 (mmm) REVERT: B 472 LYS cc_start: 0.8900 (tmmm) cc_final: 0.8682 (tmmm) REVERT: C 329 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6925 (pmtt) outliers start: 64 outliers final: 33 residues processed: 230 average time/residue: 1.1480 time to fit residues: 291.5137 Evaluate side-chains 214 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 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 550 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 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR 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 69 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 123 GLU 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 428 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 329 LYS 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 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 157 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 740 ASN ** 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** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN ** 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 = 0.4140 r_free = 0.4140 target = 0.151665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.119570 restraints weight = 27875.173| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.51 r_work: 0.3595 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 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 = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14516 Z= 0.152 Angle : 0.703 14.301 19832 Z= 0.347 Chirality : 0.043 0.168 2138 Planarity : 0.004 0.049 2416 Dihedral : 15.167 150.981 2210 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.85 % Favored : 92.09 % Rotamer: Outliers : 4.71 % Allowed : 25.91 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1643 helix: 0.96 (0.21), residues: 624 sheet: 0.02 (0.36), residues: 197 loop : -1.32 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 607 HIS 0.009 0.001 HIS A 84 PHE 0.011 0.001 PHE C 403 TYR 0.014 0.001 TYR B 193 ARG 0.004 0.000 ARG A1148 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 582) hydrogen bonds : angle 4.56448 ( 1616) covalent geometry : bond 0.00348 (14516) covalent geometry : angle 0.70274 (19832) *********************** 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 247 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 180 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5467 (tp) REVERT: A 536 GLU cc_start: 0.8166 (tp30) cc_final: 0.7353 (pt0) REVERT: A 544 MET cc_start: 0.8467 (ppp) cc_final: 0.8255 (pp-130) REVERT: A 550 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: A 552 LEU cc_start: 0.8115 (mt) cc_final: 0.7841 (mp) REVERT: A 647 CYS cc_start: 0.6749 (t) cc_final: 0.6528 (p) REVERT: A 762 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7499 (t) REVERT: A 774 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7685 (ptm) REVERT: A 1098 ASN cc_start: 0.9020 (m-40) cc_final: 0.8595 (m110) REVERT: A 1136 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7650 (tm-30) REVERT: A 1144 GLU cc_start: 0.8465 (pt0) cc_final: 0.8106 (pm20) REVERT: B 69 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8326 (tm) REVERT: B 74 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7885 (mm-40) REVERT: B 191 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 325 ARG cc_start: 0.7760 (ptp-110) cc_final: 0.7482 (mtm180) REVERT: B 445 GLU cc_start: 0.8614 (pm20) cc_final: 0.8349 (pm20) REVERT: B 465 MET cc_start: 0.8022 (mmm) cc_final: 0.7749 (mmt) REVERT: C 329 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6897 (pmtt) outliers start: 67 outliers final: 39 residues processed: 225 average time/residue: 1.1404 time to fit residues: 284.4181 Evaluate side-chains 213 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 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 751 LYS Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR 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 69 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 80 SER 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 C residue 70 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 329 LYS 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 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 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0370 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.154088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122987 restraints weight = 27834.677| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.42 r_work: 0.3621 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 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 = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14516 Z= 0.139 Angle : 0.708 13.236 19832 Z= 0.348 Chirality : 0.043 0.170 2138 Planarity : 0.004 0.052 2416 Dihedral : 15.141 150.736 2210 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 3.93 % Allowed : 27.11 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1643 helix: 1.02 (0.21), residues: 623 sheet: 0.04 (0.36), residues: 198 loop : -1.27 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 607 HIS 0.011 0.001 HIS A 84 PHE 0.010 0.001 PHE C 403 TYR 0.019 0.001 TYR B 193 ARG 0.005 0.000 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 582) hydrogen bonds : angle 4.50221 ( 1616) covalent geometry : bond 0.00315 (14516) covalent geometry : angle 0.70751 (19832) *********************** 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 235 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5382 (tp) REVERT: A 536 GLU cc_start: 0.8085 (tp30) cc_final: 0.7405 (pt0) REVERT: A 540 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7757 (mp10) REVERT: A 544 MET cc_start: 0.8450 (ppp) cc_final: 0.8233 (pp-130) REVERT: A 552 LEU cc_start: 0.8095 (mt) cc_final: 0.7813 (mp) REVERT: A 762 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7491 (t) REVERT: A 934 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8638 (ttmm) REVERT: A 1098 ASN cc_start: 0.9001 (m-40) cc_final: 0.8564 (m110) REVERT: A 1136 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 1144 GLU cc_start: 0.8429 (pt0) cc_final: 0.8081 (pm20) REVERT: B 74 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7865 (mm-40) REVERT: B 191 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 325 ARG cc_start: 0.7730 (ptp-110) cc_final: 0.7455 (mtm180) REVERT: B 445 GLU cc_start: 0.8565 (pm20) cc_final: 0.8332 (pm20) REVERT: B 465 MET cc_start: 0.7957 (mmm) cc_final: 0.7519 (mmm) REVERT: C 309 HIS cc_start: 0.8015 (t-90) cc_final: 0.7727 (t-90) REVERT: C 310 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: C 329 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6839 (pmtt) REVERT: C 396 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7068 (mpp80) outliers start: 56 outliers final: 38 residues processed: 219 average time/residue: 1.1239 time to fit residues: 273.2334 Evaluate side-chains 215 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 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 751 LYS Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR 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 1195 MET 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 80 SER 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 C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 329 LYS 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 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 69 optimal weight: 0.0040 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 264 GLN A 740 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 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 = 0.4171 r_free = 0.4171 target = 0.154868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122802 restraints weight = 27139.232| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.48 r_work: 0.3630 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14516 Z= 0.134 Angle : 0.699 13.155 19832 Z= 0.345 Chirality : 0.043 0.165 2138 Planarity : 0.004 0.048 2416 Dihedral : 15.103 150.561 2210 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Rotamer: Outliers : 3.58 % Allowed : 27.60 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1643 helix: 1.08 (0.21), residues: 623 sheet: 0.09 (0.36), residues: 198 loop : -1.23 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 748 HIS 0.011 0.001 HIS A 84 PHE 0.010 0.001 PHE C 403 TYR 0.020 0.001 TYR B 193 ARG 0.005 0.000 ARG A 853 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 582) hydrogen bonds : angle 4.43136 ( 1616) covalent geometry : bond 0.00304 (14516) covalent geometry : angle 0.69874 (19832) *********************** 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 232 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: A 228 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5261 (tp) REVERT: A 536 GLU cc_start: 0.8047 (tp30) cc_final: 0.7407 (pt0) REVERT: A 540 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7698 (mp10) REVERT: A 544 MET cc_start: 0.8409 (ppp) cc_final: 0.8151 (pp-130) REVERT: A 552 LEU cc_start: 0.8032 (mt) cc_final: 0.7751 (mp) REVERT: A 762 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7476 (t) REVERT: A 1098 ASN cc_start: 0.8978 (m-40) cc_final: 0.8461 (m-40) REVERT: A 1136 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 1144 GLU cc_start: 0.8427 (pt0) cc_final: 0.8076 (pm20) REVERT: B 74 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7845 (mm-40) REVERT: B 191 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8131 (mt-10) REVERT: B 325 ARG cc_start: 0.7732 (ptp-110) cc_final: 0.7517 (ptp-170) REVERT: B 445 GLU cc_start: 0.8581 (pm20) cc_final: 0.8333 (pm20) REVERT: B 465 MET cc_start: 0.7893 (mmm) cc_final: 0.7424 (mmm) REVERT: C 310 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7689 (pm20) outliers start: 51 outliers final: 37 residues processed: 217 average time/residue: 1.0765 time to fit residues: 260.1938 Evaluate side-chains 210 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 615 SER 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 948 ILE Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR 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 80 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 352 ASP 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 C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 329 LYS 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 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 155 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.154683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122515 restraints weight = 28865.546| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.54 r_work: 0.3624 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14516 Z= 0.138 Angle : 0.713 13.697 19832 Z= 0.351 Chirality : 0.043 0.178 2138 Planarity : 0.004 0.051 2416 Dihedral : 15.102 150.565 2210 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 3.16 % Allowed : 27.81 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1643 helix: 1.08 (0.21), residues: 623 sheet: 0.09 (0.36), residues: 198 loop : -1.22 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 607 HIS 0.013 0.001 HIS A 84 PHE 0.011 0.001 PHE B 78 TYR 0.020 0.001 TYR A 614 ARG 0.006 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 582) hydrogen bonds : angle 4.41646 ( 1616) covalent geometry : bond 0.00317 (14516) covalent geometry : angle 0.71257 (19832) ********************** 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 220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 228 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5225 (tp) REVERT: A 536 GLU cc_start: 0.8064 (tp30) cc_final: 0.7396 (pt0) REVERT: A 540 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7715 (mp10) REVERT: A 544 MET cc_start: 0.8405 (ppp) cc_final: 0.8143 (pp-130) REVERT: A 762 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7506 (t) REVERT: A 1098 ASN cc_start: 0.8934 (m-40) cc_final: 0.8413 (m-40) REVERT: A 1144 GLU cc_start: 0.8441 (pt0) cc_final: 0.8079 (pm20) REVERT: B 74 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7835 (mm-40) REVERT: B 191 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 325 ARG cc_start: 0.7725 (ptp-110) cc_final: 0.7522 (ptp-170) REVERT: B 445 GLU cc_start: 0.8572 (pm20) cc_final: 0.8316 (pm20) REVERT: B 465 MET cc_start: 0.7911 (mmm) cc_final: 0.7416 (mmm) REVERT: C 310 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: C 329 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6768 (pmtt) outliers start: 45 outliers final: 33 residues processed: 208 average time/residue: 1.0387 time to fit residues: 241.8713 Evaluate side-chains 208 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 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 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR 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 80 SER 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 C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 329 LYS 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 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 99 optimal weight: 0.0870 chunk 121 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 49 optimal weight: 0.0370 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 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 = 0.4197 r_free = 0.4197 target = 0.156141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124199 restraints weight = 28428.225| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.61 r_work: 0.3652 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14516 Z= 0.129 Angle : 0.704 12.892 19832 Z= 0.346 Chirality : 0.042 0.164 2138 Planarity : 0.004 0.045 2416 Dihedral : 15.076 150.350 2210 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 2.81 % Allowed : 28.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1643 helix: 1.18 (0.21), residues: 616 sheet: 0.17 (0.37), residues: 198 loop : -1.15 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 607 HIS 0.012 0.001 HIS A 84 PHE 0.012 0.001 PHE C 403 TYR 0.020 0.001 TYR A 614 ARG 0.006 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 582) hydrogen bonds : angle 4.33490 ( 1616) covalent geometry : bond 0.00291 (14516) covalent geometry : angle 0.70423 (19832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12498.32 seconds wall clock time: 215 minutes 15.25 seconds (12915.25 seconds total)