Starting phenix.real_space_refine on Wed Mar 4 13:41:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5i_29745/03_2026/8g5i_29745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5i_29745/03_2026/8g5i_29745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g5i_29745/03_2026/8g5i_29745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5i_29745/03_2026/8g5i_29745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5i_29745/03_2026/8g5i_29745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5i_29745/03_2026/8g5i_29745.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 80 5.16 5 C 8859 2.51 5 N 2480 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7430 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 63, 'TRANS': 877} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2986 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2890 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (38 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 2.55, per 1000 atoms: 0.18 Number of scatterers: 14084 At special positions: 0 Unit cell: (94.164, 106.554, 141.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 38 15.00 O 2627 8.00 N 2480 7.00 C 8859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 414.2 milliseconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 41.6% alpha, 11.3% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.277A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Proline residue: A 149 - end of helix removed outlier: 3.503A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.875A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.501A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.000A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.599A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.414A pdb=" N ASP A 487 " --> pdb=" O TRP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 removed outlier: 3.767A pdb=" N GLU A 538 " --> pdb=" O GLU A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 539 through 556 removed outlier: 3.676A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.623A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.656A pdb=" N MET A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.875A pdb=" N ASN A 758 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.715A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.548A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 878 removed outlier: 3.527A pdb=" N LEU A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 944 through 954 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.896A pdb=" N LEU A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 1057 through 1066 removed outlier: 4.133A pdb=" N LEU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.667A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 removed outlier: 3.729A pdb=" N ARG A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 removed outlier: 4.113A pdb=" N ILE A1220 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.552A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.547A pdb=" N LEU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.637A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.570A pdb=" N SER B 424 " --> pdb=" O MET B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.147A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 4.184A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 87 removed outlier: 4.364A pdb=" N SER C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 184 through 191 removed outlier: 4.213A pdb=" N GLY C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.717A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.233A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 393 through 409 removed outlier: 3.643A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 470 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.868A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.785A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AA4, first strand: chain 'A' and resid 1130 through 1133 removed outlier: 3.641A pdb=" N ARG A1138 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1133 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1137 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.127A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.068A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 382 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.269A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.111A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.56 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: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1643 helix: 1.15 (0.22), residues: 595 sheet: 0.04 (0.37), residues: 194 loop : -1.18 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 325 TYR 0.014 0.001 TYR A1108 PHE 0.037 0.001 PHE A 539 TRP 0.016 0.001 TRP A1118 HIS 0.010 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00389 (14516) covalent geometry : angle 0.80024 (19832) hydrogen bonds : bond 0.14606 ( 582) hydrogen bonds : angle 6.03594 ( 1616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 539 PHE cc_start: 0.6585 (p90) cc_final: 0.5405 (p90) REVERT: A 579 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7730 (mmm160) REVERT: A 1195 MET cc_start: 0.7873 (ttm) cc_final: 0.7600 (ptp) REVERT: C 422 GLN cc_start: 0.5878 (tp-100) cc_final: 0.5364 (tp40) outliers start: 19 outliers final: 9 residues processed: 234 average time/residue: 0.5597 time to fit residues: 143.8313 Evaluate side-chains 200 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 134 ASN A 138 HIS A 144 GLN A 226 GLN A 472 GLN A 493 GLN A 618 HIS A 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 A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 305 ASN B 355 GLN C 313 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.155991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122982 restraints weight = 37515.561| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 4.10 r_work: 0.3636 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14516 Z= 0.161 Angle : 0.694 13.256 19832 Z= 0.347 Chirality : 0.044 0.175 2138 Planarity : 0.005 0.051 2416 Dihedral : 14.956 149.892 2221 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 3.93 % Allowed : 24.09 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1643 helix: 1.29 (0.22), residues: 606 sheet: -0.04 (0.35), residues: 206 loop : -1.11 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 579 TYR 0.013 0.001 TYR A 614 PHE 0.014 0.001 PHE A 539 TRP 0.017 0.001 TRP A 607 HIS 0.009 0.001 HIS A1134 Details of bonding type rmsd covalent geometry : bond 0.00364 (14516) covalent geometry : angle 0.69396 (19832) hydrogen bonds : bond 0.04081 ( 582) hydrogen bonds : angle 4.76592 ( 1616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.5895 (ppp) cc_final: 0.5571 (ppp) REVERT: A 363 TYR cc_start: 0.6970 (m-10) cc_final: 0.6733 (m-10) REVERT: A 544 MET cc_start: 0.8709 (ppp) cc_final: 0.8469 (ppp) REVERT: A 647 CYS cc_start: 0.7062 (t) cc_final: 0.6787 (p) REVERT: A 975 GLN cc_start: 0.8641 (pm20) cc_final: 0.8262 (pm20) REVERT: A 1098 ASN cc_start: 0.9093 (m-40) cc_final: 0.8880 (m-40) REVERT: A 1136 GLU cc_start: 0.7976 (tt0) cc_final: 0.7715 (tm-30) REVERT: A 1195 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7002 (ptp) REVERT: A 1208 ARG cc_start: 0.6094 (ptt90) cc_final: 0.5764 (ptt180) REVERT: B 75 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7572 (tpt90) REVERT: B 191 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 445 GLU cc_start: 0.8656 (pm20) cc_final: 0.7610 (pm20) REVERT: B 472 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (tmmm) REVERT: C 310 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: C 396 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7024 (mpp80) outliers start: 56 outliers final: 19 residues processed: 252 average time/residue: 0.5397 time to fit residues: 149.6051 Evaluate side-chains 211 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 948 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 chunk 159 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.9944 ------------------------------------------------------------------------------- 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 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** A1110 HIS A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 272 ASN B 309 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.156869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.125675 restraints weight = 29680.097| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.57 r_work: 0.3650 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14516 Z= 0.144 Angle : 0.672 11.231 19832 Z= 0.333 Chirality : 0.043 0.174 2138 Planarity : 0.005 0.048 2416 Dihedral : 14.953 149.864 2212 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 4.63 % Allowed : 24.58 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1643 helix: 1.30 (0.22), residues: 606 sheet: 0.02 (0.35), residues: 206 loop : -1.08 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.011 0.001 TYR A1108 PHE 0.012 0.001 PHE A 610 TRP 0.015 0.001 TRP A 607 HIS 0.010 0.001 HIS A1134 Details of bonding type rmsd covalent geometry : bond 0.00324 (14516) covalent geometry : angle 0.67182 (19832) hydrogen bonds : bond 0.03626 ( 582) hydrogen bonds : angle 4.56941 ( 1616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6022 (OUTLIER) cc_final: 0.5519 (ppp) REVERT: A 363 TYR cc_start: 0.6981 (m-10) cc_final: 0.6773 (m-10) REVERT: A 544 MET cc_start: 0.8563 (ppp) cc_final: 0.8351 (pp-130) REVERT: A 1098 ASN cc_start: 0.8997 (m-40) cc_final: 0.8660 (m110) REVERT: B 75 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7382 (tpt90) REVERT: B 201 ASN cc_start: 0.7701 (p0) cc_final: 0.7360 (t0) REVERT: B 472 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: C 310 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: C 396 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7062 (mpp80) outliers start: 66 outliers final: 25 residues processed: 240 average time/residue: 0.5203 time to fit residues: 138.1101 Evaluate side-chains 215 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 762 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 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 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 335 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 258 HIS B 318 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.148273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116085 restraints weight = 28563.681| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.50 r_work: 0.3534 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14516 Z= 0.278 Angle : 0.782 11.173 19832 Z= 0.392 Chirality : 0.048 0.178 2138 Planarity : 0.006 0.054 2416 Dihedral : 15.250 151.571 2211 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.03 % Favored : 91.91 % Rotamer: Outliers : 5.83 % Allowed : 24.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1643 helix: 0.86 (0.21), residues: 611 sheet: 0.05 (0.35), residues: 206 loop : -1.34 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 275 TYR 0.016 0.002 TYR A 573 PHE 0.016 0.002 PHE B 266 TRP 0.025 0.002 TRP A 607 HIS 0.007 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00638 (14516) covalent geometry : angle 0.78168 (19832) hydrogen bonds : bond 0.04327 ( 582) hydrogen bonds : angle 4.82378 ( 1616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 184 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.8613 (ppp) cc_final: 0.8388 (pp-130) REVERT: A 853 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7534 (ttm170) REVERT: A 1098 ASN cc_start: 0.9038 (m-40) cc_final: 0.8678 (m110) REVERT: A 1208 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5869 (ptt180) REVERT: B 386 ASP cc_start: 0.8598 (t0) cc_final: 0.8392 (t70) REVERT: C 396 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7884 (ttp-110) outliers start: 83 outliers final: 37 residues processed: 236 average time/residue: 0.5431 time to fit residues: 140.8112 Evaluate side-chains 205 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 741 ASP 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 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1107 ASP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1218 LEU 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 428 LEU Chi-restraints excluded: chain B residue 459 ASP 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 238 SER Chi-restraints excluded: chain C residue 278 CYS 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 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 120 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 298 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN A1134 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.153095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121831 restraints weight = 28560.602| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.46 r_work: 0.3592 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 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 = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2212 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= 0.147 Angle : 0.695 11.858 19832 Z= 0.346 Chirality : 0.043 0.164 2138 Planarity : 0.005 0.069 2416 Dihedral : 15.097 150.799 2209 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 5.41 % Allowed : 24.72 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1643 helix: 0.94 (0.21), residues: 618 sheet: 0.03 (0.37), residues: 181 loop : -1.25 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 75 TYR 0.016 0.001 TYR B 432 PHE 0.010 0.001 PHE A1123 TRP 0.026 0.001 TRP A 607 HIS 0.005 0.001 HIS A1134 Details of bonding type rmsd covalent geometry : bond 0.00333 (14516) covalent geometry : angle 0.69509 (19832) hydrogen bonds : bond 0.03658 ( 582) hydrogen bonds : angle 4.61008 ( 1616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 189 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.8522 (ppp) cc_final: 0.8296 (pp-130) REVERT: A 552 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7754 (mp) REVERT: A 774 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7580 (ptm) REVERT: A 1098 ASN cc_start: 0.8960 (m-40) cc_final: 0.8599 (m110) REVERT: B 123 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: B 386 ASP cc_start: 0.8494 (t0) cc_final: 0.8270 (t70) REVERT: B 465 MET cc_start: 0.7906 (mmm) cc_final: 0.7489 (mmm) REVERT: B 472 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8380 (tmmm) REVERT: C 329 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6925 (pmtt) REVERT: C 386 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.6793 (t0) REVERT: C 396 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7108 (mpp80) outliers start: 77 outliers final: 31 residues processed: 235 average time/residue: 0.5583 time to fit residues: 144.3547 Evaluate side-chains 212 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 540 GLN Chi-restraints excluded: chain A residue 552 LEU 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 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 0.0570 chunk 152 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.152460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120385 restraints weight = 26957.241| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.46 r_work: 0.3598 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2238 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= 0.145 Angle : 0.698 14.549 19832 Z= 0.344 Chirality : 0.043 0.165 2138 Planarity : 0.004 0.053 2416 Dihedral : 15.072 150.699 2209 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 5.20 % Allowed : 25.70 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1643 helix: 1.05 (0.21), residues: 617 sheet: 0.04 (0.36), residues: 197 loop : -1.25 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 325 TYR 0.016 0.001 TYR B 193 PHE 0.012 0.001 PHE A 610 TRP 0.027 0.001 TRP A 607 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00331 (14516) covalent geometry : angle 0.69800 (19832) hydrogen bonds : bond 0.03509 ( 582) hydrogen bonds : angle 4.53878 ( 1616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.8489 (ppp) cc_final: 0.8250 (pp-130) REVERT: A 552 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7790 (mp) REVERT: A 774 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7632 (ptm) REVERT: A 1098 ASN cc_start: 0.8927 (m-40) cc_final: 0.8561 (m110) REVERT: B 75 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7616 (mmm160) REVERT: B 123 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: B 325 ARG cc_start: 0.7811 (ptp-110) cc_final: 0.7379 (ptp-170) REVERT: B 465 MET cc_start: 0.7962 (mmm) cc_final: 0.7616 (mmm) REVERT: B 472 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8330 (tmmm) REVERT: C 329 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6897 (pmtt) REVERT: C 386 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.6834 (t0) REVERT: C 396 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7089 (mpp80) outliers start: 74 outliers final: 40 residues processed: 230 average time/residue: 0.5507 time to fit residues: 139.5686 Evaluate side-chains 220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU 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 540 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 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 1057 MET Chi-restraints excluded: chain A residue 1063 SER 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 79 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 371 VAL 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 113 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.153047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122076 restraints weight = 26599.087| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.30 r_work: 0.3606 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14516 Z= 0.157 Angle : 0.699 14.359 19832 Z= 0.347 Chirality : 0.043 0.166 2138 Planarity : 0.005 0.053 2416 Dihedral : 15.093 150.838 2209 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.61 % Favored : 92.33 % Rotamer: Outliers : 5.13 % Allowed : 25.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1643 helix: 1.02 (0.21), residues: 618 sheet: 0.05 (0.36), residues: 197 loop : -1.26 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 325 TYR 0.016 0.001 TYR B 193 PHE 0.011 0.001 PHE A1123 TRP 0.028 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00361 (14516) covalent geometry : angle 0.69905 (19832) hydrogen bonds : bond 0.03527 ( 582) hydrogen bonds : angle 4.52983 ( 1616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 176 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 228 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5283 (tp) REVERT: A 544 MET cc_start: 0.8465 (ppp) cc_final: 0.8241 (pp-130) REVERT: A 550 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: A 774 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7651 (ptm) REVERT: A 964 ARG cc_start: 0.7513 (tmt-80) cc_final: 0.7207 (tmt-80) REVERT: A 1098 ASN cc_start: 0.8935 (m-40) cc_final: 0.8567 (m110) REVERT: A 1112 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8728 (mtt) REVERT: A 1136 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 69 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8292 (tm) REVERT: B 191 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 325 ARG cc_start: 0.7819 (ptp-110) cc_final: 0.7405 (ptp-170) REVERT: B 465 MET cc_start: 0.7951 (mmm) cc_final: 0.7583 (mmm) REVERT: B 472 LYS cc_start: 0.8651 (tmmt) cc_final: 0.8408 (tmmm) REVERT: C 329 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6874 (pmtt) REVERT: C 386 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.6866 (t0) REVERT: C 396 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7122 (mpp80) outliers start: 73 outliers final: 40 residues processed: 223 average time/residue: 0.5351 time to fit residues: 131.5532 Evaluate side-chains 216 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 125 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 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 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 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 79 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 238 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 B residue 484 ASN 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 238 SER 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 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 chunk 131 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.153834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122152 restraints weight = 26240.669| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.42 r_work: 0.3632 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2348 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= 0.133 Angle : 0.702 13.228 19832 Z= 0.344 Chirality : 0.043 0.218 2138 Planarity : 0.005 0.071 2416 Dihedral : 15.068 150.157 2209 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 4.00 % Allowed : 27.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.21), residues: 1643 helix: 1.05 (0.21), residues: 618 sheet: 0.09 (0.36), residues: 197 loop : -1.20 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 75 TYR 0.017 0.001 TYR B 193 PHE 0.010 0.001 PHE C 403 TRP 0.027 0.001 TRP A 607 HIS 0.007 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00303 (14516) covalent geometry : angle 0.70151 (19832) hydrogen bonds : bond 0.03345 ( 582) hydrogen bonds : angle 4.45320 ( 1616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 228 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5258 (tp) REVERT: A 536 GLU cc_start: 0.8118 (tp30) cc_final: 0.7324 (pt0) REVERT: A 544 MET cc_start: 0.8428 (ppp) cc_final: 0.8205 (pp-130) REVERT: A 550 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 774 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7633 (ptm) REVERT: A 823 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7663 (ptm160) REVERT: A 1098 ASN cc_start: 0.8893 (m-40) cc_final: 0.8555 (m110) REVERT: A 1107 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 1112 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8753 (mtt) REVERT: A 1136 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 191 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 325 ARG cc_start: 0.7811 (ptp-110) cc_final: 0.7437 (ptp-170) REVERT: B 465 MET cc_start: 0.7883 (mmm) cc_final: 0.7502 (mmm) REVERT: C 329 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6849 (pmtt) REVERT: C 396 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7106 (mpp80) outliers start: 57 outliers final: 31 residues processed: 221 average time/residue: 0.5401 time to fit residues: 131.5929 Evaluate side-chains 213 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR 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 1083 LEU Chi-restraints excluded: chain A residue 1107 ASP Chi-restraints excluded: chain A residue 1112 MET 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 79 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP 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 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 113 optimal weight: 0.2980 chunk 159 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- 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 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 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 = 0.4187 r_free = 0.4187 target = 0.155272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.123471 restraints weight = 26896.509| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.49 r_work: 0.3651 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2395 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= 0.129 Angle : 0.697 13.136 19832 Z= 0.342 Chirality : 0.042 0.184 2138 Planarity : 0.004 0.046 2416 Dihedral : 15.037 150.386 2209 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 3.93 % Allowed : 27.74 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1643 helix: 1.15 (0.21), residues: 618 sheet: 0.16 (0.36), residues: 197 loop : -1.17 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1209 TYR 0.019 0.001 TYR B 193 PHE 0.014 0.001 PHE A 610 TRP 0.030 0.001 TRP A 607 HIS 0.011 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00291 (14516) covalent geometry : angle 0.69749 (19832) hydrogen bonds : bond 0.03253 ( 582) hydrogen bonds : angle 4.39692 ( 1616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5158 (tp) REVERT: A 536 GLU cc_start: 0.8128 (tp30) cc_final: 0.7316 (pt0) REVERT: A 544 MET cc_start: 0.8437 (ppp) cc_final: 0.8209 (pp-130) REVERT: A 550 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: A 774 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7640 (ptm) REVERT: A 1098 ASN cc_start: 0.8946 (m-40) cc_final: 0.8492 (m110) REVERT: A 1107 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: A 1112 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8752 (mtt) REVERT: A 1136 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 191 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8062 (mt-10) REVERT: B 325 ARG cc_start: 0.7810 (ptp-110) cc_final: 0.7475 (ptp-170) REVERT: B 465 MET cc_start: 0.7843 (mmm) cc_final: 0.7450 (mmm) REVERT: C 386 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.6843 (t0) REVERT: C 396 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7119 (mpp80) outliers start: 56 outliers final: 30 residues processed: 222 average time/residue: 0.5268 time to fit residues: 129.0865 Evaluate side-chains 211 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 774 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 1074 VAL Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1107 ASP Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 238 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 B residue 429 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 386 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** C 195 ASN ** 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 = 0.4185 r_free = 0.4185 target = 0.154947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.123142 restraints weight = 27310.264| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.52 r_work: 0.3644 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2450 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= 0.137 Angle : 0.712 13.336 19832 Z= 0.351 Chirality : 0.043 0.181 2138 Planarity : 0.005 0.110 2416 Dihedral : 15.028 150.446 2209 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 3.23 % Allowed : 28.51 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1643 helix: 1.14 (0.21), residues: 618 sheet: 0.08 (0.36), residues: 203 loop : -1.13 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 75 TYR 0.018 0.001 TYR B 193 PHE 0.027 0.001 PHE A 539 TRP 0.026 0.001 TRP A 607 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00317 (14516) covalent geometry : angle 0.71157 (19832) hydrogen bonds : bond 0.03279 ( 582) hydrogen bonds : angle 4.38070 ( 1616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.375 Fit side-chains REVERT: A 228 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5134 (tp) REVERT: A 536 GLU cc_start: 0.8056 (tp30) cc_final: 0.7307 (pt0) REVERT: A 540 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7741 (mp10) REVERT: A 544 MET cc_start: 0.8433 (ppp) cc_final: 0.8199 (pp-130) REVERT: A 549 LEU cc_start: 0.8874 (mm) cc_final: 0.8513 (mm) REVERT: A 550 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: A 774 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7613 (ptm) REVERT: A 1098 ASN cc_start: 0.8955 (m-40) cc_final: 0.8519 (m110) REVERT: A 1107 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: A 1136 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 191 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 325 ARG cc_start: 0.7806 (ptp-110) cc_final: 0.7464 (ptp-170) REVERT: B 465 MET cc_start: 0.7850 (mmm) cc_final: 0.7449 (mmm) REVERT: C 329 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6734 (pmtt) REVERT: C 386 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.6856 (t0) REVERT: C 396 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7122 (mpp80) outliers start: 46 outliers final: 31 residues processed: 211 average time/residue: 0.5243 time to fit residues: 122.1838 Evaluate side-chains 214 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 774 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 1074 VAL Chi-restraints excluded: chain A residue 1079 ILE 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 1163 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 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 811 GLN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.154183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121759 restraints weight = 30361.229| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.70 r_work: 0.3621 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14516 Z= 0.144 Angle : 0.720 13.832 19832 Z= 0.355 Chirality : 0.043 0.180 2138 Planarity : 0.004 0.050 2416 Dihedral : 15.048 150.673 2209 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 3.72 % Allowed : 28.02 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1643 helix: 1.12 (0.21), residues: 618 sheet: 0.08 (0.36), residues: 203 loop : -1.13 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1209 TYR 0.016 0.001 TYR B 193 PHE 0.029 0.001 PHE A 539 TRP 0.026 0.001 TRP A 607 HIS 0.008 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00333 (14516) covalent geometry : angle 0.71964 (19832) hydrogen bonds : bond 0.03329 ( 582) hydrogen bonds : angle 4.39423 ( 1616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5992.16 seconds wall clock time: 102 minutes 23.04 seconds (6143.04 seconds total)