Starting phenix.real_space_refine on Sat Aug 23 23:45:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f56_28861/08_2025/8f56_28861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f56_28861/08_2025/8f56_28861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f56_28861/08_2025/8f56_28861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f56_28861/08_2025/8f56_28861.map" model { file = "/net/cci-nas-00/data/ceres_data/8f56_28861/08_2025/8f56_28861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f56_28861/08_2025/8f56_28861.cif" } resolution = 2.98 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= 0.072 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 9992 2.51 5 N 2634 2.21 5 O 2917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15631 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7730 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 966} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7901 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 990} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.88, per 1000 atoms: 0.25 Number of scatterers: 15631 At special positions: 0 Unit cell: (79.18, 123.05, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 2917 8.00 N 2634 7.00 C 9992 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: 1.66 Conformation dependent library (CDL) restraints added in 957.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 15 sheets defined 61.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 3.593A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.828A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 99 through 118 removed outlier: 3.766A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.765A pdb=" N ASN A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.668A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 387 Proline residue: A 368 - end of helix removed outlier: 3.724A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 423 removed outlier: 3.785A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 5.589A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 458 removed outlier: 4.419A pdb=" N MET A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 458' Processing helix chain 'A' and resid 460 through 486 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.820A pdb=" N ALA A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.974A pdb=" N LYS A 501 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.019A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 708 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 834 through 848 removed outlier: 3.720A pdb=" N GLN A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 891 removed outlier: 3.521A pdb=" N GLN A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.517A pdb=" N LEU A 901 " --> pdb=" O PHE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.550A pdb=" N GLY A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 954 removed outlier: 4.417A pdb=" N PHE A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 988 removed outlier: 4.975A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.332A pdb=" N GLY A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.586A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.584A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.620A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.513A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.624A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 315 Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 Proline residue: B 368 - end of helix removed outlier: 3.874A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.380A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.716A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.572A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'B' and resid 460 through 486 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.941A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 536 Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.976A pdb=" N TRP B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 657 removed outlier: 3.527A pdb=" N ALA B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 782 through 786 removed outlier: 4.058A pdb=" N ASN B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 834 through 849 Processing helix chain 'B' and resid 858 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.514A pdb=" N LEU B 901 " --> pdb=" O PHE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.685A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 4.435A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 988 removed outlier: 5.111A pdb=" N ARG B 970 " --> pdb=" O ARG B 966 " (cutoff:3.500A) Proline residue: B 971 - end of helix Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 993 through 1030 removed outlier: 4.285A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Proline residue: B1020 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.035A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A 828 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG A 713 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.035A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER A 821 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.821A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.993A pdb=" N TYR A 182 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.744A pdb=" N ARG A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 803 through 810 removed outlier: 3.829A pdb=" N THR B 233 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.044A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 612 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.970A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA B 773 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER B 754 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 716 removed outlier: 4.872A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 722 through 729 removed outlier: 3.639A pdb=" N ARG B 806 " --> pdb=" O GLN B 726 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 788 through 790 1088 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.09 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: 5118 1.34 - 1.46: 2193 1.46 - 1.57: 8455 1.57 - 1.69: 0 1.69 - 1.80: 168 Bond restraints: 15934 Sorted by residual: bond pdb=" CA VAL B 306 " pdb=" C VAL B 306 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.22e-02 6.72e+03 2.60e+00 bond pdb=" CA GLU B 66 " pdb=" C GLU B 66 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.27e-02 6.20e+03 2.16e+00 bond pdb=" CA LEU A 737 " pdb=" C LEU A 737 " ideal model delta sigma weight residual 1.523 1.502 0.020 1.41e-02 5.03e+03 2.08e+00 bond pdb=" CA ASP B 922 " pdb=" C ASP B 922 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.45e-02 4.76e+03 2.06e+00 bond pdb=" N LEU B 307 " pdb=" CA LEU B 307 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.21e-02 6.83e+03 1.99e+00 ... (remaining 15929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21289 1.82 - 3.64: 298 3.64 - 5.46: 41 5.46 - 7.28: 9 7.28 - 9.10: 2 Bond angle restraints: 21639 Sorted by residual: angle pdb=" C ALA B 859 " pdb=" CA ALA B 859 " pdb=" CB ALA B 859 " ideal model delta sigma weight residual 116.63 110.03 6.60 1.16e+00 7.43e-01 3.23e+01 angle pdb=" C VAL B 61 " pdb=" CA VAL B 61 " pdb=" CB VAL B 61 " ideal model delta sigma weight residual 111.71 107.76 3.95 8.50e-01 1.38e+00 2.16e+01 angle pdb=" CA ALA B 859 " pdb=" C ALA B 859 " pdb=" N MET B 860 " ideal model delta sigma weight residual 119.63 116.20 3.43 8.10e-01 1.52e+00 1.80e+01 angle pdb=" N VAL B 61 " pdb=" CA VAL B 61 " pdb=" C VAL B 61 " ideal model delta sigma weight residual 111.48 115.35 -3.87 9.40e-01 1.13e+00 1.70e+01 angle pdb=" N THR B 462 " pdb=" CA THR B 462 " pdb=" C THR B 462 " ideal model delta sigma weight residual 111.28 107.16 4.12 1.09e+00 8.42e-01 1.43e+01 ... (remaining 21634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.59: 8842 13.59 - 27.17: 498 27.17 - 40.76: 132 40.76 - 54.34: 36 54.34 - 67.93: 9 Dihedral angle restraints: 9517 sinusoidal: 3661 harmonic: 5856 Sorted by residual: dihedral pdb=" CA ILE B 249 " pdb=" C ILE B 249 " pdb=" N THR B 250 " pdb=" CA THR B 250 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP A 311 " pdb=" CB ASP A 311 " pdb=" CG ASP A 311 " pdb=" OD1 ASP A 311 " ideal model delta sinusoidal sigma weight residual -30.00 -87.08 57.08 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB ARG B 661 " pdb=" CG ARG B 661 " pdb=" CD ARG B 661 " pdb=" NE ARG B 661 " ideal model delta sinusoidal sigma weight residual 180.00 120.27 59.73 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1671 0.029 - 0.058: 556 0.058 - 0.087: 167 0.087 - 0.115: 110 0.115 - 0.144: 8 Chirality restraints: 2512 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR A 489 " pdb=" N THR A 489 " pdb=" C THR A 489 " pdb=" CB THR A 489 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CB VAL A 482 " pdb=" CA VAL A 482 " pdb=" CG1 VAL A 482 " pdb=" CG2 VAL A 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2509 not shown) Planarity restraints: 2786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 921 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C ASN A 921 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN A 921 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 922 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 250 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C THR B 250 " -0.026 2.00e-02 2.50e+03 pdb=" O THR B 250 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 251 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 454 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C VAL B 454 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 454 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO B 455 " -0.009 2.00e-02 2.50e+03 ... (remaining 2783 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1621 2.74 - 3.28: 16429 3.28 - 3.82: 27105 3.82 - 4.36: 31663 4.36 - 4.90: 55207 Nonbonded interactions: 132025 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU A 601 " pdb=" ND2 ASN A 604 " model vdw 2.202 3.120 nonbonded pdb=" OG SER B 279 " pdb=" O ALA B 286 " model vdw 2.213 3.040 nonbonded pdb=" OG SER A 279 " pdb=" O ALA A 286 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN A 415 " pdb=" NH1 ARG A 418 " model vdw 2.281 3.120 ... (remaining 132020 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 'A' and (resid 1 through 508 or (resid 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 1032)) selection = (chain 'B' and (resid 1 through 211 or resid 237 through 505 or (resid 506 and ( \ name N or name CA or name C or name O or name CB )) or resid 507 through 1032)) } 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=1.00 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.510 Find NCS groups from input model: 0.300 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:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 0.036 15934 Z= 0.209 Angle : 0.557 9.097 21639 Z= 0.327 Chirality : 0.036 0.144 2512 Planarity : 0.003 0.029 2786 Dihedral : 9.889 67.925 5757 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.64 % Allowed : 4.61 % Favored : 92.75 % 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 aren not related in a simple way. whole: 1.81 (0.19), residues: 2033 helix: 2.22 (0.15), residues: 1165 sheet: -0.18 (0.32), residues: 282 loop : -0.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 636 TYR 0.009 0.001 TYR A 77 PHE 0.011 0.001 PHE B 958 TRP 0.013 0.001 TRP B 540 HIS 0.002 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00406 (15934) covalent geometry : angle 0.55687 (21639) hydrogen bonds : bond 0.16024 ( 1061) hydrogen bonds : angle 6.33225 ( 3186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 495 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.7049 (mt0) cc_final: 0.6792 (mt0) REVERT: B 184 MET cc_start: 0.7433 (tpp) cc_final: 0.7154 (tpp) REVERT: B 395 MET cc_start: 0.8094 (mmm) cc_final: 0.7760 (mmm) REVERT: B 900 MET cc_start: 0.6754 (mmm) cc_final: 0.6390 (mmp) outliers start: 44 outliers final: 8 residues processed: 525 average time/residue: 0.5793 time to fit residues: 337.8893 Evaluate side-chains 269 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 261 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 108 GLN A 152 GLN A 197 GLN A 254 ASN A 308 ASN A 517 GLN A 584 GLN A 655 ASN A 686 HIS A 691 HIS A 716 HIS A 848 GLN A 926 GLN A 955 HIS A 967 GLN B 55 GLN B 63 GLN B 81 GLN B 108 GLN B 112 GLN B 228 GLN B 237 GLN B 254 ASN B 255 GLN B 361 ASN B 437 GLN B 576 GLN B 604 ASN B 699 ASN B 708 ASN B 863 GLN B 926 GLN B 955 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115377 restraints weight = 20412.005| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.50 r_work: 0.3208 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15934 Z= 0.133 Angle : 0.551 8.138 21639 Z= 0.287 Chirality : 0.039 0.160 2512 Planarity : 0.004 0.048 2786 Dihedral : 4.418 58.173 2201 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.61 % Allowed : 15.40 % Favored : 79.99 % 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 aren not related in a simple way. whole: 1.79 (0.19), residues: 2033 helix: 2.22 (0.15), residues: 1170 sheet: -0.18 (0.30), residues: 297 loop : -0.19 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 732 TYR 0.016 0.001 TYR A 384 PHE 0.021 0.001 PHE A 4 TRP 0.010 0.001 TRP A 540 HIS 0.005 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00281 (15934) covalent geometry : angle 0.55118 (21639) hydrogen bonds : bond 0.04559 ( 1061) hydrogen bonds : angle 4.88093 ( 3186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 300 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 27 ILE cc_start: 0.8122 (mt) cc_final: 0.7847 (mt) REVERT: A 28 PHE cc_start: 0.8194 (m-80) cc_final: 0.7923 (m-80) REVERT: A 151 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8161 (ptmm) REVERT: A 184 MET cc_start: 0.8450 (mmt) cc_final: 0.7999 (tpt) REVERT: A 205 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: A 240 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 414 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7913 (tp30) REVERT: A 900 MET cc_start: 0.8454 (mmm) cc_final: 0.8250 (mmm) REVERT: B 108 GLN cc_start: 0.7146 (mt0) cc_final: 0.6714 (mm110) REVERT: B 115 MET cc_start: 0.7790 (ttp) cc_final: 0.7092 (tpp) REVERT: B 151 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8014 (ptpp) REVERT: B 182 TYR cc_start: 0.8323 (m-10) cc_final: 0.8106 (m-80) REVERT: B 346 GLU cc_start: 0.8097 (tt0) cc_final: 0.7834 (mt-10) REVERT: B 398 MET cc_start: 0.8621 (tpp) cc_final: 0.7950 (mmt) REVERT: B 520 ASN cc_start: 0.7326 (m-40) cc_final: 0.7091 (m110) REVERT: B 522 ASN cc_start: 0.7618 (m-40) cc_final: 0.7111 (m110) REVERT: B 632 ASP cc_start: 0.8042 (t0) cc_final: 0.7771 (t0) REVERT: B 639 LYS cc_start: 0.8321 (mptt) cc_final: 0.7666 (mmmm) REVERT: B 743 ASP cc_start: 0.6921 (m-30) cc_final: 0.6689 (m-30) REVERT: B 789 VAL cc_start: 0.7527 (t) cc_final: 0.7134 (p) outliers start: 77 outliers final: 26 residues processed: 349 average time/residue: 0.5595 time to fit residues: 217.6068 Evaluate side-chains 256 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 319 HIS A 437 GLN A 604 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN B 63 GLN B 67 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111168 restraints weight = 20613.232| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.53 r_work: 0.3135 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15934 Z= 0.164 Angle : 0.553 8.039 21639 Z= 0.287 Chirality : 0.040 0.164 2512 Planarity : 0.004 0.042 2786 Dihedral : 4.367 54.909 2194 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.85 % Allowed : 17.56 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.19), residues: 2033 helix: 2.08 (0.15), residues: 1181 sheet: -0.37 (0.29), residues: 306 loop : -0.30 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B1027 TYR 0.012 0.001 TYR B 35 PHE 0.012 0.001 PHE A 760 TRP 0.014 0.001 TRP A 540 HIS 0.006 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00381 (15934) covalent geometry : angle 0.55292 (21639) hydrogen bonds : bond 0.04631 ( 1061) hydrogen bonds : angle 4.68146 ( 3186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 3 ASN cc_start: 0.7580 (m-40) cc_final: 0.7295 (m-40) REVERT: A 28 PHE cc_start: 0.8304 (m-80) cc_final: 0.8062 (m-80) REVERT: A 106 GLN cc_start: 0.8692 (mt0) cc_final: 0.8470 (mt0) REVERT: A 151 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8213 (ptmm) REVERT: A 240 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 370 ILE cc_start: 0.8798 (mt) cc_final: 0.8523 (mm) REVERT: A 414 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 486 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8268 (mmm) REVERT: A 518 MET cc_start: 0.8538 (ppp) cc_final: 0.8188 (ppp) REVERT: A 652 LYS cc_start: 0.8704 (mttm) cc_final: 0.8341 (mtpm) REVERT: A 656 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: A 970 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8056 (ttm-80) REVERT: B 63 GLN cc_start: 0.7817 (mt0) cc_final: 0.7615 (mt0) REVERT: B 81 GLN cc_start: 0.8435 (pt0) cc_final: 0.8075 (pt0) REVERT: B 108 GLN cc_start: 0.7206 (mt0) cc_final: 0.6787 (mm110) REVERT: B 152 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7516 (mm110) REVERT: B 213 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: B 520 ASN cc_start: 0.7376 (m-40) cc_final: 0.7133 (m110) REVERT: B 632 ASP cc_start: 0.8394 (t0) cc_final: 0.8182 (t70) REVERT: B 639 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7595 (mmmm) REVERT: B 744 ILE cc_start: 0.7063 (pt) cc_final: 0.6761 (mt) REVERT: B 890 TYR cc_start: 0.7632 (m-80) cc_final: 0.7345 (m-80) outliers start: 81 outliers final: 39 residues processed: 319 average time/residue: 0.6144 time to fit residues: 217.5025 Evaluate side-chains 270 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 639 LYS Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 152 optimal weight: 5.9990 chunk 73 optimal weight: 0.0870 chunk 169 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 361 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111322 restraints weight = 20507.523| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.51 r_work: 0.3149 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15934 Z= 0.125 Angle : 0.510 8.696 21639 Z= 0.262 Chirality : 0.039 0.179 2512 Planarity : 0.004 0.037 2786 Dihedral : 4.283 56.864 2194 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.37 % Allowed : 19.29 % Favored : 76.33 % 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 aren not related in a simple way. whole: 1.69 (0.19), residues: 2033 helix: 2.19 (0.15), residues: 1178 sheet: -0.29 (0.29), residues: 300 loop : -0.33 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 732 TYR 0.014 0.001 TYR B 77 PHE 0.014 0.001 PHE B 853 TRP 0.015 0.001 TRP A 540 HIS 0.003 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00278 (15934) covalent geometry : angle 0.51041 (21639) hydrogen bonds : bond 0.04062 ( 1061) hydrogen bonds : angle 4.53947 ( 3186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 255 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 3 ASN cc_start: 0.7580 (m-40) cc_final: 0.7331 (m-40) REVERT: A 28 PHE cc_start: 0.8372 (m-80) cc_final: 0.8079 (m-80) REVERT: A 106 GLN cc_start: 0.8602 (mt0) cc_final: 0.8345 (mt0) REVERT: A 151 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8187 (ptmm) REVERT: A 184 MET cc_start: 0.8508 (mmt) cc_final: 0.8179 (tpt) REVERT: A 240 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7874 (mp) REVERT: A 270 MET cc_start: 0.8527 (mmm) cc_final: 0.8284 (tpt) REVERT: A 370 ILE cc_start: 0.8765 (mt) cc_final: 0.8557 (mm) REVERT: A 414 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 518 MET cc_start: 0.8605 (ppp) cc_final: 0.8209 (ppp) REVERT: A 536 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6810 (mtp180) REVERT: A 732 ARG cc_start: 0.7588 (ttm110) cc_final: 0.7305 (ttm110) REVERT: A 974 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8285 (ptp) REVERT: A 1013 ILE cc_start: 0.8668 (mm) cc_final: 0.8467 (mp) REVERT: B 59 ASN cc_start: 0.7290 (m-40) cc_final: 0.7082 (m110) REVERT: B 81 GLN cc_start: 0.8387 (pt0) cc_final: 0.8106 (pt0) REVERT: B 108 GLN cc_start: 0.7185 (mt0) cc_final: 0.6786 (mm110) REVERT: B 447 MET cc_start: 0.8098 (ttm) cc_final: 0.7580 (mtt) REVERT: B 520 ASN cc_start: 0.7344 (m-40) cc_final: 0.7091 (m110) REVERT: B 632 ASP cc_start: 0.8357 (t0) cc_final: 0.8144 (t70) REVERT: B 639 LYS cc_start: 0.8261 (mptt) cc_final: 0.7590 (mmmm) REVERT: B 856 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: B 897 PHE cc_start: 0.8199 (t80) cc_final: 0.7988 (t80) outliers start: 73 outliers final: 27 residues processed: 305 average time/residue: 0.6354 time to fit residues: 214.7103 Evaluate side-chains 263 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 14 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN B 123 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107502 restraints weight = 20502.072| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.54 r_work: 0.3088 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15934 Z= 0.177 Angle : 0.559 8.608 21639 Z= 0.287 Chirality : 0.041 0.201 2512 Planarity : 0.004 0.040 2786 Dihedral : 4.417 57.559 2194 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.21 % Allowed : 19.53 % Favored : 75.25 % 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 aren not related in a simple way. whole: 1.54 (0.19), residues: 2033 helix: 2.07 (0.15), residues: 1176 sheet: -0.44 (0.29), residues: 315 loop : -0.30 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 521 TYR 0.013 0.001 TYR B 77 PHE 0.018 0.002 PHE B 853 TRP 0.023 0.001 TRP A 540 HIS 0.005 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00422 (15934) covalent geometry : angle 0.55851 (21639) hydrogen bonds : bond 0.04572 ( 1061) hydrogen bonds : angle 4.61933 ( 3186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8014 (mt0) cc_final: 0.7782 (mt0) REVERT: A 106 GLN cc_start: 0.8681 (mt0) cc_final: 0.8443 (mt0) REVERT: A 151 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8237 (ptmm) REVERT: A 184 MET cc_start: 0.8528 (mmt) cc_final: 0.8129 (tpt) REVERT: A 270 MET cc_start: 0.8457 (mmm) cc_final: 0.8143 (tpt) REVERT: A 370 ILE cc_start: 0.8800 (mt) cc_final: 0.8584 (mm) REVERT: A 414 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 486 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: A 518 MET cc_start: 0.8650 (ppp) cc_final: 0.8191 (ppp) REVERT: A 540 TRP cc_start: 0.8826 (m100) cc_final: 0.8581 (m100) REVERT: A 570 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8943 (ptp) REVERT: A 595 LYS cc_start: 0.8206 (tttt) cc_final: 0.7919 (ttpt) REVERT: A 656 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: A 915 TRP cc_start: 0.8510 (t60) cc_final: 0.8031 (t-100) REVERT: A 950 MET cc_start: 0.7548 (mmm) cc_final: 0.7336 (mtp) REVERT: A 970 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: A 974 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8549 (ptp) REVERT: A 1029 ARG cc_start: 0.7708 (mmt180) cc_final: 0.6616 (mmm160) REVERT: B 59 ASN cc_start: 0.7285 (m-40) cc_final: 0.6906 (m110) REVERT: B 81 GLN cc_start: 0.8493 (pt0) cc_final: 0.8086 (pt0) REVERT: B 108 GLN cc_start: 0.7354 (mt0) cc_final: 0.6957 (mm110) REVERT: B 152 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7539 (mm110) REVERT: B 259 GLU cc_start: 0.7115 (pt0) cc_final: 0.6664 (pt0) REVERT: B 520 ASN cc_start: 0.7318 (m-40) cc_final: 0.7039 (m110) REVERT: B 602 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8091 (mptt) REVERT: B 623 VAL cc_start: 0.8633 (t) cc_final: 0.8303 (m) REVERT: B 885 CYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8390 (t) REVERT: B 1027 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6953 (tpt170) outliers start: 87 outliers final: 39 residues processed: 307 average time/residue: 0.6376 time to fit residues: 216.3172 Evaluate side-chains 274 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1027 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 120 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 68 ASN A 245 GLN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 213 GLN B 735 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108513 restraints weight = 20324.394| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.58 r_work: 0.3123 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15934 Z= 0.130 Angle : 0.517 7.925 21639 Z= 0.266 Chirality : 0.039 0.194 2512 Planarity : 0.004 0.040 2786 Dihedral : 4.324 58.609 2194 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.25 % Allowed : 21.15 % Favored : 74.60 % 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 aren not related in a simple way. whole: 1.64 (0.19), residues: 2033 helix: 2.17 (0.15), residues: 1176 sheet: -0.41 (0.29), residues: 315 loop : -0.32 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 130 TYR 0.011 0.001 TYR B 77 PHE 0.017 0.001 PHE B 853 TRP 0.018 0.001 TRP A 540 HIS 0.003 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00296 (15934) covalent geometry : angle 0.51742 (21639) hydrogen bonds : bond 0.04119 ( 1061) hydrogen bonds : angle 4.51423 ( 3186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.7986 (mt0) cc_final: 0.7749 (mt0) REVERT: A 151 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8265 (ptmm) REVERT: A 184 MET cc_start: 0.8517 (mmt) cc_final: 0.8132 (tpt) REVERT: A 205 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: A 270 MET cc_start: 0.8468 (mmm) cc_final: 0.8242 (tpt) REVERT: A 414 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 439 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 518 MET cc_start: 0.8616 (ppp) cc_final: 0.8215 (ppp) REVERT: A 533 ILE cc_start: 0.8085 (mp) cc_final: 0.7876 (mm) REVERT: A 595 LYS cc_start: 0.8214 (tttt) cc_final: 0.8005 (ttpt) REVERT: A 915 TRP cc_start: 0.8520 (t60) cc_final: 0.8074 (t-100) REVERT: A 950 MET cc_start: 0.7648 (mmm) cc_final: 0.7443 (mtp) REVERT: A 970 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8090 (ttm-80) REVERT: A 974 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8537 (ptp) REVERT: A 1029 ARG cc_start: 0.7720 (mmt180) cc_final: 0.6626 (mmm160) REVERT: B 59 ASN cc_start: 0.7201 (m-40) cc_final: 0.6988 (m110) REVERT: B 81 GLN cc_start: 0.8458 (pt0) cc_final: 0.8141 (pt0) REVERT: B 108 GLN cc_start: 0.7371 (mt0) cc_final: 0.7007 (mm110) REVERT: B 520 ASN cc_start: 0.7390 (m-40) cc_final: 0.7146 (m110) REVERT: B 568 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8567 (mtt180) REVERT: B 602 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8103 (mptt) REVERT: B 623 VAL cc_start: 0.8633 (t) cc_final: 0.8343 (m) REVERT: B 675 SER cc_start: 0.8348 (p) cc_final: 0.8118 (t) REVERT: B 735 GLN cc_start: 0.7349 (tt0) cc_final: 0.6476 (pp30) REVERT: B 856 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: B 866 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8479 (mp) REVERT: B 885 CYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8439 (t) REVERT: B 1027 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7048 (tpt170) outliers start: 71 outliers final: 32 residues processed: 286 average time/residue: 0.6612 time to fit residues: 208.9498 Evaluate side-chains 272 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1027 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 107 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 131 optimal weight: 0.0470 chunk 187 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 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 = 0.3455 r_free = 0.3455 target = 0.128167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106346 restraints weight = 20401.451| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.53 r_work: 0.3074 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15934 Z= 0.189 Angle : 0.568 10.685 21639 Z= 0.292 Chirality : 0.041 0.195 2512 Planarity : 0.004 0.042 2786 Dihedral : 4.462 58.604 2194 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.15 % Allowed : 20.07 % Favored : 74.78 % 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 aren not related in a simple way. whole: 1.47 (0.19), residues: 2033 helix: 2.00 (0.15), residues: 1176 sheet: -0.41 (0.29), residues: 313 loop : -0.35 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 732 TYR 0.012 0.002 TYR B 77 PHE 0.021 0.001 PHE B 853 TRP 0.025 0.001 TRP A 540 HIS 0.005 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00454 (15934) covalent geometry : angle 0.56764 (21639) hydrogen bonds : bond 0.04580 ( 1061) hydrogen bonds : angle 4.62117 ( 3186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 239 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7565 (mp) REVERT: A 63 GLN cc_start: 0.8047 (mt0) cc_final: 0.7825 (mt0) REVERT: A 132 THR cc_start: 0.7969 (m) cc_final: 0.7669 (p) REVERT: A 151 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8270 (ptmm) REVERT: A 184 MET cc_start: 0.8549 (mmt) cc_final: 0.8151 (tpt) REVERT: A 205 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: A 414 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 518 MET cc_start: 0.8633 (ppp) cc_final: 0.8266 (ppp) REVERT: A 570 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8968 (ptp) REVERT: A 595 LYS cc_start: 0.8369 (tttt) cc_final: 0.8064 (ttpt) REVERT: A 656 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: A 915 TRP cc_start: 0.8588 (t60) cc_final: 0.8120 (t-100) REVERT: A 970 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8078 (ttm-80) REVERT: A 1029 ARG cc_start: 0.7952 (mmt180) cc_final: 0.6938 (mmm160) REVERT: B 7 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: B 81 GLN cc_start: 0.8533 (pt0) cc_final: 0.8076 (pt0) REVERT: B 106 GLN cc_start: 0.7641 (mt0) cc_final: 0.7373 (mt0) REVERT: B 108 GLN cc_start: 0.7402 (mt0) cc_final: 0.7004 (mm110) REVERT: B 152 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7609 (mm110) REVERT: B 520 ASN cc_start: 0.7490 (m-40) cc_final: 0.7170 (m110) REVERT: B 568 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8552 (mtt180) REVERT: B 602 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8162 (mptt) REVERT: B 623 VAL cc_start: 0.8641 (t) cc_final: 0.8323 (m) REVERT: B 675 SER cc_start: 0.8357 (p) cc_final: 0.8134 (t) REVERT: B 735 GLN cc_start: 0.7296 (tt0) cc_final: 0.6399 (pp30) REVERT: B 856 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: B 1027 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7005 (tpt170) outliers start: 86 outliers final: 40 residues processed: 293 average time/residue: 0.6664 time to fit residues: 215.7837 Evaluate side-chains 278 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 986 MET Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1027 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 46 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 245 GLN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 124 ASN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108478 restraints weight = 20478.950| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.55 r_work: 0.3106 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15934 Z= 0.137 Angle : 0.539 9.232 21639 Z= 0.276 Chirality : 0.040 0.176 2512 Planarity : 0.004 0.044 2786 Dihedral : 4.379 59.690 2194 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.07 % Allowed : 21.75 % Favored : 74.18 % 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 aren not related in a simple way. whole: 1.60 (0.19), residues: 2033 helix: 2.13 (0.15), residues: 1171 sheet: -0.39 (0.29), residues: 309 loop : -0.32 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 432 TYR 0.009 0.001 TYR B 277 PHE 0.016 0.001 PHE B 853 TRP 0.023 0.001 TRP A 540 HIS 0.004 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00316 (15934) covalent geometry : angle 0.53935 (21639) hydrogen bonds : bond 0.04170 ( 1061) hydrogen bonds : angle 4.53195 ( 3186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7057 (mtp85) cc_final: 0.6718 (ptp90) REVERT: A 25 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7685 (mp) REVERT: A 63 GLN cc_start: 0.7997 (mt0) cc_final: 0.7767 (mt0) REVERT: A 151 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8238 (ptmm) REVERT: A 184 MET cc_start: 0.8539 (mmt) cc_final: 0.8173 (tpt) REVERT: A 205 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: A 414 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 518 MET cc_start: 0.8659 (ppp) cc_final: 0.8248 (ppp) REVERT: A 570 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8971 (ptp) REVERT: A 595 LYS cc_start: 0.8317 (tttt) cc_final: 0.8010 (ttpt) REVERT: A 656 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: A 915 TRP cc_start: 0.8548 (t60) cc_final: 0.8089 (t-100) REVERT: A 970 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8138 (ttm-80) REVERT: A 986 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8997 (ttt) REVERT: A 1029 ARG cc_start: 0.7917 (mmt180) cc_final: 0.6880 (mmm160) REVERT: B 7 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: B 81 GLN cc_start: 0.8470 (pt0) cc_final: 0.7876 (pt0) REVERT: B 108 GLN cc_start: 0.7378 (mt0) cc_final: 0.7011 (mm110) REVERT: B 152 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7624 (mm110) REVERT: B 447 MET cc_start: 0.8385 (tpp) cc_final: 0.8015 (mtt) REVERT: B 520 ASN cc_start: 0.7456 (m-40) cc_final: 0.7152 (m110) REVERT: B 568 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8586 (mtt180) REVERT: B 602 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8143 (mptt) REVERT: B 623 VAL cc_start: 0.8590 (t) cc_final: 0.8303 (m) REVERT: B 675 SER cc_start: 0.8330 (p) cc_final: 0.8105 (t) REVERT: B 735 GLN cc_start: 0.7293 (tt0) cc_final: 0.6397 (pp30) REVERT: B 856 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: B 866 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8416 (mp) REVERT: B 885 CYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8489 (t) REVERT: B 1027 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7075 (tpt170) outliers start: 68 outliers final: 35 residues processed: 282 average time/residue: 0.6597 time to fit residues: 206.2754 Evaluate side-chains 271 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1027 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 69 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109050 restraints weight = 20571.608| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.52 r_work: 0.3121 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15934 Z= 0.124 Angle : 0.529 8.910 21639 Z= 0.270 Chirality : 0.039 0.169 2512 Planarity : 0.004 0.048 2786 Dihedral : 4.312 58.301 2194 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.71 % Allowed : 22.65 % Favored : 73.64 % 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 aren not related in a simple way. whole: 1.62 (0.19), residues: 2033 helix: 2.16 (0.15), residues: 1178 sheet: -0.43 (0.29), residues: 315 loop : -0.34 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 732 TYR 0.010 0.001 TYR B 77 PHE 0.009 0.001 PHE A 571 TRP 0.021 0.001 TRP A 540 HIS 0.004 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00278 (15934) covalent geometry : angle 0.52862 (21639) hydrogen bonds : bond 0.03981 ( 1061) hydrogen bonds : angle 4.45880 ( 3186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7024 (mtp85) cc_final: 0.6631 (ptp90) REVERT: A 25 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 151 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8233 (ptmm) REVERT: A 184 MET cc_start: 0.8516 (mmt) cc_final: 0.8154 (tpt) REVERT: A 270 MET cc_start: 0.8414 (mmm) cc_final: 0.8088 (tpt) REVERT: A 486 MET cc_start: 0.8696 (mmm) cc_final: 0.8412 (mmt) REVERT: A 518 MET cc_start: 0.8663 (ppp) cc_final: 0.8265 (ppp) REVERT: A 595 LYS cc_start: 0.8287 (tttt) cc_final: 0.7982 (ttpt) REVERT: A 656 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: A 799 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8778 (t80) REVERT: A 860 MET cc_start: 0.8183 (tmm) cc_final: 0.7851 (tmt) REVERT: A 915 TRP cc_start: 0.8534 (t60) cc_final: 0.8081 (t-100) REVERT: A 1029 ARG cc_start: 0.7910 (mmt180) cc_final: 0.6882 (mmm160) REVERT: B 7 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: B 108 GLN cc_start: 0.7320 (mt0) cc_final: 0.7040 (mm-40) REVERT: B 152 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7631 (mm110) REVERT: B 398 MET cc_start: 0.8652 (mmt) cc_final: 0.8185 (mmt) REVERT: B 520 ASN cc_start: 0.7439 (m-40) cc_final: 0.7137 (m110) REVERT: B 568 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8604 (mtt180) REVERT: B 602 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8154 (mptt) REVERT: B 623 VAL cc_start: 0.8503 (t) cc_final: 0.8298 (m) REVERT: B 675 SER cc_start: 0.8300 (p) cc_final: 0.8076 (t) REVERT: B 735 GLN cc_start: 0.7421 (tt0) cc_final: 0.6456 (pp30) REVERT: B 779 MET cc_start: 0.6228 (tpp) cc_final: 0.5980 (tpt) REVERT: B 856 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: B 866 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8324 (mp) REVERT: B 885 CYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8460 (t) REVERT: B 893 TRP cc_start: 0.8377 (m100) cc_final: 0.7723 (m-90) REVERT: B 1027 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7066 (tpt170) outliers start: 62 outliers final: 29 residues processed: 276 average time/residue: 0.6537 time to fit residues: 199.8715 Evaluate side-chains 259 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1027 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 ASN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108622 restraints weight = 20434.214| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.53 r_work: 0.3107 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15934 Z= 0.147 Angle : 0.549 9.824 21639 Z= 0.280 Chirality : 0.040 0.166 2512 Planarity : 0.004 0.049 2786 Dihedral : 4.350 57.803 2194 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.24 % Allowed : 23.79 % Favored : 72.98 % 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 aren not related in a simple way. whole: 1.61 (0.19), residues: 2033 helix: 2.13 (0.15), residues: 1172 sheet: -0.38 (0.29), residues: 308 loop : -0.32 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 732 TYR 0.010 0.001 TYR B 277 PHE 0.025 0.001 PHE B 853 TRP 0.036 0.001 TRP A 540 HIS 0.005 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00346 (15934) covalent geometry : angle 0.54850 (21639) hydrogen bonds : bond 0.04161 ( 1061) hydrogen bonds : angle 4.49831 ( 3186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7145 (mtp85) cc_final: 0.6892 (ptp90) REVERT: A 25 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 151 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8248 (ptmm) REVERT: A 184 MET cc_start: 0.8523 (mmt) cc_final: 0.8153 (tpt) REVERT: A 486 MET cc_start: 0.8715 (mmm) cc_final: 0.8435 (mmt) REVERT: A 518 MET cc_start: 0.8662 (ppp) cc_final: 0.8282 (ppp) REVERT: A 556 LEU cc_start: 0.7989 (mm) cc_final: 0.7781 (mm) REVERT: A 570 MET cc_start: 0.9134 (ptp) cc_final: 0.8776 (pmm) REVERT: A 595 LYS cc_start: 0.8318 (tttt) cc_final: 0.8003 (ttpt) REVERT: A 600 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8281 (m90) REVERT: A 656 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: A 799 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8854 (t80) REVERT: A 915 TRP cc_start: 0.8547 (t60) cc_final: 0.8095 (t-100) REVERT: A 1029 ARG cc_start: 0.7961 (mmt180) cc_final: 0.7001 (mmm160) REVERT: B 7 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: B 108 GLN cc_start: 0.7278 (mt0) cc_final: 0.6997 (mm-40) REVERT: B 152 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7643 (mm110) REVERT: B 520 ASN cc_start: 0.7478 (m-40) cc_final: 0.7184 (m110) REVERT: B 568 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8594 (mtt180) REVERT: B 602 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8155 (mptt) REVERT: B 623 VAL cc_start: 0.8515 (t) cc_final: 0.8292 (m) REVERT: B 675 SER cc_start: 0.8321 (p) cc_final: 0.8098 (t) REVERT: B 735 GLN cc_start: 0.7390 (tt0) cc_final: 0.6445 (pp30) REVERT: B 856 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: B 866 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8392 (mp) REVERT: B 885 CYS cc_start: 0.8727 (m) cc_final: 0.8426 (t) REVERT: B 893 TRP cc_start: 0.8364 (m100) cc_final: 0.7692 (m-90) REVERT: B 1027 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7080 (tpt170) outliers start: 54 outliers final: 33 residues processed: 258 average time/residue: 0.6803 time to fit residues: 193.6378 Evaluate side-chains 260 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1027 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 0 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108022 restraints weight = 20460.985| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.48 r_work: 0.3109 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15934 Z= 0.148 Angle : 0.553 12.652 21639 Z= 0.281 Chirality : 0.040 0.163 2512 Planarity : 0.004 0.046 2786 Dihedral : 4.368 57.325 2194 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.30 % Allowed : 23.97 % Favored : 72.74 % 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 aren not related in a simple way. whole: 1.59 (0.19), residues: 2033 helix: 2.12 (0.15), residues: 1171 sheet: -0.41 (0.29), residues: 308 loop : -0.30 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 732 TYR 0.010 0.001 TYR B 277 PHE 0.026 0.001 PHE B 853 TRP 0.037 0.001 TRP A 540 HIS 0.004 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00348 (15934) covalent geometry : angle 0.55272 (21639) hydrogen bonds : bond 0.04175 ( 1061) hydrogen bonds : angle 4.50380 ( 3186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6007.35 seconds wall clock time: 103 minutes 24.74 seconds (6204.74 seconds total)