Starting phenix.real_space_refine on Fri Jun 13 22:28:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f56_28861/06_2025/8f56_28861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f56_28861/06_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_28861/06_2025/8f56_28861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f56_28861/06_2025/8f56_28861.map" model { file = "/net/cci-nas-00/data/ceres_data/8f56_28861/06_2025/8f56_28861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f56_28861/06_2025/8f56_28861.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.072 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.10, per 1000 atoms: 0.65 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: 4.17 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.18 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: 7.57 Time building geometry restraints manager: 4.88 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.180 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (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 TRP 0.013 0.001 TRP B 540 HIS 0.002 0.001 HIS A 686 PHE 0.011 0.001 PHE B 958 TYR 0.009 0.001 TYR A 77 ARG 0.003 0.000 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.16024 ( 1061) hydrogen bonds : angle 6.33225 ( 3186) covalent geometry : bond 0.00406 (15934) covalent geometry : angle 0.55687 (21639) *********************** 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 : 1.759 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: 1.1595 time to fit residues: 676.7520 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 : 1.704 ------------------------------------------------------------------------------- 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 171 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 103 optimal weight: 0.0040 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 319 HIS A 517 GLN A 584 GLN A 655 ASN A 686 HIS A 691 HIS A 716 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 213 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: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114378 restraints weight = 20383.726| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.57 r_work: 0.3192 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15934 Z= 0.144 Angle : 0.548 8.286 21639 Z= 0.287 Chirality : 0.039 0.156 2512 Planarity : 0.004 0.054 2786 Dihedral : 4.400 58.088 2201 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.73 % Allowed : 15.64 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2033 helix: 2.22 (0.15), residues: 1179 sheet: -0.14 (0.30), residues: 296 loop : -0.20 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 319 PHE 0.020 0.001 PHE A 4 TYR 0.015 0.002 TYR A 467 ARG 0.010 0.001 ARG A 732 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 1061) hydrogen bonds : angle 4.90816 ( 3186) covalent geometry : bond 0.00298 (15934) covalent geometry : angle 0.54805 (21639) *********************** 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 376 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.8119 (mt) cc_final: 0.7848 (mt) REVERT: A 28 PHE cc_start: 0.8189 (m-80) cc_final: 0.7921 (m-80) REVERT: A 151 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8124 (ptmm) REVERT: A 205 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: A 240 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 414 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8056 (tp30) REVERT: A 900 MET cc_start: 0.8462 (mmm) cc_final: 0.8252 (mmm) REVERT: B 108 GLN cc_start: 0.7177 (mt0) cc_final: 0.6713 (mm110) REVERT: B 115 MET cc_start: 0.7772 (ttp) cc_final: 0.7050 (tpp) REVERT: B 151 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7951 (ptpp) REVERT: B 182 TYR cc_start: 0.8291 (m-10) cc_final: 0.8072 (m-80) REVERT: B 259 GLU cc_start: 0.7063 (pt0) cc_final: 0.6676 (pt0) REVERT: B 346 GLU cc_start: 0.8058 (tt0) cc_final: 0.7845 (mt-10) REVERT: B 520 ASN cc_start: 0.7288 (m-40) cc_final: 0.7038 (m110) REVERT: B 632 ASP cc_start: 0.8031 (t0) cc_final: 0.7732 (t70) REVERT: B 635 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8298 (mp0) REVERT: B 639 LYS cc_start: 0.8334 (mptt) cc_final: 0.7641 (mmmm) REVERT: B 701 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7843 (tt) REVERT: B 743 ASP cc_start: 0.7017 (m-30) cc_final: 0.6765 (m-30) REVERT: B 789 VAL cc_start: 0.7488 (t) cc_final: 0.7046 (p) outliers start: 79 outliers final: 27 residues processed: 349 average time/residue: 1.2275 time to fit residues: 478.2955 Evaluate side-chains 255 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 635 GLU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 811 SER 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 148 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 0.0050 chunk 194 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 123 GLN A 437 GLN A 604 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 67 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.109917 restraints weight = 20392.375| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.49 r_work: 0.3132 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15934 Z= 0.167 Angle : 0.556 8.142 21639 Z= 0.289 Chirality : 0.041 0.167 2512 Planarity : 0.004 0.038 2786 Dihedral : 4.395 55.238 2194 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.09 % Allowed : 17.38 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.19), residues: 2033 helix: 2.08 (0.15), residues: 1181 sheet: -0.36 (0.29), residues: 306 loop : -0.31 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 540 HIS 0.005 0.001 HIS A 716 PHE 0.014 0.001 PHE A 760 TYR 0.013 0.002 TYR A 544 ARG 0.016 0.001 ARG B1027 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 1061) hydrogen bonds : angle 4.69579 ( 3186) covalent geometry : bond 0.00392 (15934) covalent geometry : angle 0.55579 (21639) *********************** 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 355 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 270 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 3 ASN cc_start: 0.7710 (m-40) cc_final: 0.7340 (m-40) REVERT: A 28 PHE cc_start: 0.8320 (m-80) cc_final: 0.8088 (m-80) REVERT: A 63 GLN cc_start: 0.8110 (mt0) cc_final: 0.7872 (mt0) REVERT: A 68 ASN cc_start: 0.7873 (m110) cc_final: 0.7664 (m-40) REVERT: A 106 GLN cc_start: 0.8665 (mt0) cc_final: 0.8435 (mt0) REVERT: A 112 GLN cc_start: 0.7053 (mp10) cc_final: 0.6769 (mp10) REVERT: A 151 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8232 (ptmm) REVERT: A 184 MET cc_start: 0.8539 (mmt) cc_final: 0.8143 (tpt) REVERT: A 240 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 370 ILE cc_start: 0.8835 (mt) cc_final: 0.8598 (mm) REVERT: A 414 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 486 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8180 (mtp) REVERT: A 652 LYS cc_start: 0.8705 (mttm) cc_final: 0.8308 (mtpm) REVERT: A 656 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: A 970 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8060 (ttm-80) REVERT: B 81 GLN cc_start: 0.8487 (pt0) cc_final: 0.8118 (pt0) REVERT: B 108 GLN cc_start: 0.7232 (mt0) cc_final: 0.6814 (mm110) REVERT: B 152 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7513 (mm110) REVERT: B 269 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: B 398 MET cc_start: 0.8934 (tpp) cc_final: 0.8697 (mmt) REVERT: B 520 ASN cc_start: 0.7363 (m-40) cc_final: 0.7111 (m110) REVERT: B 632 ASP cc_start: 0.8241 (t0) cc_final: 0.7992 (t70) REVERT: B 635 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: B 639 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7597 (mmmm) REVERT: B 744 ILE cc_start: 0.7051 (pt) cc_final: 0.6786 (mt) outliers start: 85 outliers final: 35 residues processed: 324 average time/residue: 1.2997 time to fit residues: 465.9405 Evaluate side-chains 272 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR 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 970 ARG Chi-restraints excluded: chain A residue 994 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 269 GLU Chi-restraints excluded: chain B residue 278 LEU 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 635 GLU 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 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 49 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 63 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110493 restraints weight = 20324.481| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.55 r_work: 0.3141 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4210 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= 0.136 Angle : 0.527 9.507 21639 Z= 0.268 Chirality : 0.039 0.159 2512 Planarity : 0.004 0.038 2786 Dihedral : 4.331 56.938 2194 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.85 % Allowed : 18.99 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2033 helix: 2.18 (0.15), residues: 1177 sheet: -0.22 (0.29), residues: 308 loop : -0.33 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 540 HIS 0.003 0.001 HIS A 716 PHE 0.011 0.001 PHE A 760 TYR 0.012 0.001 TYR B 77 ARG 0.010 0.001 ARG A 732 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 1061) hydrogen bonds : angle 4.56832 ( 3186) covalent geometry : bond 0.00309 (15934) covalent geometry : angle 0.52676 (21639) *********************** 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 335 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASN cc_start: 0.7546 (m-40) cc_final: 0.7320 (m110) REVERT: A 28 PHE cc_start: 0.8388 (m-80) cc_final: 0.8087 (m-80) REVERT: A 112 GLN cc_start: 0.7122 (mp10) cc_final: 0.6833 (mp10) REVERT: A 151 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8185 (ptmm) REVERT: A 184 MET cc_start: 0.8554 (mmt) cc_final: 0.8151 (tpt) REVERT: A 370 ILE cc_start: 0.8837 (mt) cc_final: 0.8615 (mm) REVERT: A 414 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8159 (tm-30) REVERT: A 518 MET cc_start: 0.8609 (ppp) cc_final: 0.8268 (ppp) REVERT: A 536 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6880 (mtp180) REVERT: A 732 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7369 (ttm110) REVERT: A 860 MET cc_start: 0.8242 (tmm) cc_final: 0.7986 (tmt) REVERT: A 915 TRP cc_start: 0.8293 (t60) cc_final: 0.7903 (t-100) REVERT: A 950 MET cc_start: 0.7566 (mmm) cc_final: 0.7283 (mtp) REVERT: A 1029 ARG cc_start: 0.7656 (mmt180) cc_final: 0.6492 (mmm160) REVERT: B 59 ASN cc_start: 0.7283 (m-40) cc_final: 0.7038 (m110) REVERT: B 81 GLN cc_start: 0.8422 (pt0) cc_final: 0.8090 (pt0) REVERT: B 108 GLN cc_start: 0.7181 (mt0) cc_final: 0.6772 (mm110) REVERT: B 259 GLU cc_start: 0.6963 (pt0) cc_final: 0.6511 (pt0) REVERT: B 447 MET cc_start: 0.8115 (ttm) cc_final: 0.7599 (mtt) REVERT: B 520 ASN cc_start: 0.7381 (m-40) cc_final: 0.7105 (m110) REVERT: B 632 ASP cc_start: 0.8306 (t0) cc_final: 0.8093 (t70) REVERT: B 635 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: B 639 LYS cc_start: 0.8309 (mptt) cc_final: 0.7647 (mmmm) REVERT: B 743 ASP cc_start: 0.6388 (m-30) cc_final: 0.6187 (m-30) REVERT: B 856 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7938 (tp30) outliers start: 81 outliers final: 35 residues processed: 309 average time/residue: 1.3807 time to fit residues: 471.7824 Evaluate side-chains 268 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 659 GLU Chi-restraints excluded: chain A residue 757 VAL 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 994 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 213 GLN 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 635 GLU 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 1021 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 195 optimal weight: 0.4980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3495 r_free = 0.3495 target = 0.131546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109948 restraints weight = 20545.180| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.54 r_work: 0.3118 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15934 Z= 0.138 Angle : 0.525 9.183 21639 Z= 0.268 Chirality : 0.039 0.214 2512 Planarity : 0.004 0.039 2786 Dihedral : 4.321 58.078 2194 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 5.09 % Allowed : 19.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2033 helix: 2.19 (0.15), residues: 1177 sheet: -0.20 (0.29), residues: 313 loop : -0.36 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 540 HIS 0.003 0.001 HIS A 716 PHE 0.011 0.001 PHE A 571 TYR 0.012 0.001 TYR B 77 ARG 0.006 0.000 ARG A 732 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 1061) hydrogen bonds : angle 4.52546 ( 3186) covalent geometry : bond 0.00319 (15934) covalent geometry : angle 0.52516 (21639) *********************** 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 328 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 243 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8223 (ptmm) REVERT: A 184 MET cc_start: 0.8507 (mmt) cc_final: 0.8141 (tpt) REVERT: A 370 ILE cc_start: 0.8767 (mt) cc_final: 0.8567 (mm) REVERT: A 414 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 439 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 518 MET cc_start: 0.8610 (ppp) cc_final: 0.8215 (ppp) REVERT: A 656 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: A 732 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7450 (ttm110) REVERT: A 860 MET cc_start: 0.8218 (tmm) cc_final: 0.7900 (tmt) REVERT: A 915 TRP cc_start: 0.8320 (t60) cc_final: 0.7933 (t-100) REVERT: A 950 MET cc_start: 0.7600 (mmm) cc_final: 0.7353 (mtp) REVERT: A 970 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8078 (ttm-80) REVERT: A 1029 ARG cc_start: 0.7691 (mmt180) cc_final: 0.6552 (mmm160) REVERT: B 81 GLN cc_start: 0.8449 (pt0) cc_final: 0.8099 (pt0) REVERT: B 108 GLN cc_start: 0.7351 (mt0) cc_final: 0.6976 (mm110) REVERT: B 259 GLU cc_start: 0.7041 (pt0) cc_final: 0.6667 (pt0) REVERT: B 520 ASN cc_start: 0.7297 (m-40) cc_final: 0.7060 (m110) REVERT: B 623 VAL cc_start: 0.8616 (t) cc_final: 0.8287 (m) REVERT: B 856 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: B 885 CYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8441 (t) outliers start: 85 outliers final: 38 residues processed: 301 average time/residue: 1.3329 time to fit residues: 448.0603 Evaluate side-chains 269 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 182 TYR 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 439 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 757 VAL 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 167 SER Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 176 ASP 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 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU 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 676 SER Chi-restraints excluded: chain B residue 731 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 48 ASN A 63 GLN A 67 GLN A 74 ASN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN B 59 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104610 restraints weight = 20692.951| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.54 r_work: 0.3048 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15934 Z= 0.238 Angle : 0.612 8.934 21639 Z= 0.315 Chirality : 0.043 0.220 2512 Planarity : 0.004 0.041 2786 Dihedral : 4.592 57.345 2194 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.27 % Allowed : 19.77 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2033 helix: 1.89 (0.15), residues: 1171 sheet: -0.39 (0.29), residues: 303 loop : -0.42 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 540 HIS 0.006 0.001 HIS A 716 PHE 0.018 0.002 PHE A 981 TYR 0.014 0.002 TYR B 890 ARG 0.006 0.001 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 1061) hydrogen bonds : angle 4.74693 ( 3186) covalent geometry : bond 0.00576 (15934) covalent geometry : angle 0.61187 (21639) *********************** 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 328 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 240 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: A 151 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8275 (ptmm) REVERT: A 184 MET cc_start: 0.8548 (mmt) cc_final: 0.8163 (tpt) REVERT: A 205 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: A 414 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 497 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 518 MET cc_start: 0.8655 (ppp) cc_final: 0.8160 (ppp) REVERT: A 540 TRP cc_start: 0.9020 (m100) cc_final: 0.8814 (m100) REVERT: A 570 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.9000 (ptp) REVERT: A 595 LYS cc_start: 0.8425 (tttt) cc_final: 0.8098 (ttpt) REVERT: A 656 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: A 732 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7511 (ttm110) REVERT: A 915 TRP cc_start: 0.8504 (t60) cc_final: 0.8114 (t-100) REVERT: A 970 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8010 (ttm-80) REVERT: A 1029 ARG cc_start: 0.7972 (mmt180) cc_final: 0.6986 (mmm160) REVERT: B 7 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: B 81 GLN cc_start: 0.8573 (pt0) cc_final: 0.8104 (pt0) REVERT: B 108 GLN cc_start: 0.7407 (mt0) cc_final: 0.6998 (mm110) REVERT: B 152 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7610 (mm110) REVERT: B 520 ASN cc_start: 0.7384 (m-40) cc_final: 0.7146 (m110) REVERT: B 568 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8465 (mtt180) REVERT: B 602 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8174 (mptt) REVERT: B 675 SER cc_start: 0.8400 (p) cc_final: 0.8174 (t) REVERT: B 735 GLN cc_start: 0.7231 (tt0) cc_final: 0.6311 (pp30) REVERT: B 856 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: B 1027 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7543 (tpt170) outliers start: 88 outliers final: 41 residues processed: 303 average time/residue: 1.2892 time to fit residues: 431.1813 Evaluate side-chains 274 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 34 GLN 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 447 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 497 LEU 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 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 176 ASP Chi-restraints excluded: chain B residue 201 LYS 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 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 545 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 731 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 41 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 158 optimal weight: 0.3980 chunk 196 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 74 ASN A 245 GLN ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107761 restraints weight = 20509.483| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.54 r_work: 0.3091 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15934 Z= 0.139 Angle : 0.544 10.084 21639 Z= 0.279 Chirality : 0.040 0.185 2512 Planarity : 0.004 0.040 2786 Dihedral : 4.436 58.691 2194 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.07 % Allowed : 21.87 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 2033 helix: 2.10 (0.15), residues: 1169 sheet: -0.39 (0.29), residues: 323 loop : -0.37 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 540 HIS 0.003 0.001 HIS B 955 PHE 0.010 0.001 PHE A 571 TYR 0.010 0.001 TYR B 77 ARG 0.006 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 1061) hydrogen bonds : angle 4.60922 ( 3186) covalent geometry : bond 0.00316 (15934) covalent geometry : angle 0.54376 (21639) *********************** 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 298 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 230 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7633 (mp) REVERT: A 106 GLN cc_start: 0.8164 (mt0) cc_final: 0.7783 (mt0) REVERT: A 151 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8231 (ptmm) REVERT: A 414 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 518 MET cc_start: 0.8678 (ppp) cc_final: 0.8215 (ppp) REVERT: A 540 TRP cc_start: 0.8921 (m100) cc_final: 0.8698 (m100) REVERT: A 570 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8960 (ptp) REVERT: A 595 LYS cc_start: 0.8340 (tttt) cc_final: 0.8016 (ttpt) REVERT: A 656 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: A 732 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7520 (ttm110) REVERT: A 915 TRP cc_start: 0.8501 (t60) cc_final: 0.8095 (t-100) REVERT: A 970 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8082 (ttm-80) REVERT: A 1029 ARG cc_start: 0.7920 (mmt180) cc_final: 0.6939 (mmm160) REVERT: B 81 GLN cc_start: 0.8521 (pt0) cc_final: 0.8071 (pt0) REVERT: B 108 GLN cc_start: 0.7370 (mt0) cc_final: 0.6989 (mm110) REVERT: B 259 GLU cc_start: 0.7054 (pt0) cc_final: 0.6807 (pt0) REVERT: B 447 MET cc_start: 0.8388 (tpp) cc_final: 0.7981 (mtt) REVERT: B 520 ASN cc_start: 0.7422 (m-40) cc_final: 0.7098 (m110) REVERT: B 568 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8580 (mtt180) REVERT: B 602 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8151 (mptt) REVERT: B 623 VAL cc_start: 0.8615 (t) cc_final: 0.8318 (m) REVERT: B 675 SER cc_start: 0.8394 (p) cc_final: 0.8151 (t) REVERT: B 712 THR cc_start: 0.8941 (p) cc_final: 0.8720 (t) REVERT: B 735 GLN cc_start: 0.7277 (tt0) cc_final: 0.6355 (pp30) REVERT: B 765 ARG cc_start: 0.7311 (ttt-90) cc_final: 0.6539 (ttp-170) REVERT: B 856 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: B 866 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 885 CYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8465 (t) REVERT: B 893 TRP cc_start: 0.8345 (m100) cc_final: 0.7681 (m-90) outliers start: 68 outliers final: 37 residues processed: 279 average time/residue: 1.3874 time to fit residues: 426.3315 Evaluate side-chains 265 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 182 TYR 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 463 THR 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 804 THR Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 213 GLN 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 96 optimal weight: 0.0020 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 106 GLN A 245 GLN A 319 HIS ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 123 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109630 restraints weight = 20369.163| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.51 r_work: 0.3117 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5174 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= 0.124 Angle : 0.527 9.151 21639 Z= 0.270 Chirality : 0.040 0.191 2512 Planarity : 0.004 0.042 2786 Dihedral : 4.345 59.227 2194 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.83 % Allowed : 22.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2033 helix: 2.19 (0.15), residues: 1171 sheet: -0.27 (0.29), residues: 315 loop : -0.40 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 540 HIS 0.004 0.001 HIS B 955 PHE 0.009 0.001 PHE B 571 TYR 0.010 0.001 TYR B 77 ARG 0.005 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 1061) hydrogen bonds : angle 4.53232 ( 3186) covalent geometry : bond 0.00277 (15934) covalent geometry : angle 0.52712 (21639) *********************** 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 300 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7561 (mp) REVERT: A 151 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8266 (ptmm) REVERT: A 439 GLN cc_start: 0.7632 (tt0) cc_final: 0.7363 (tt0) REVERT: A 518 MET cc_start: 0.8681 (ppp) cc_final: 0.8224 (ppp) REVERT: A 595 LYS cc_start: 0.8295 (tttt) cc_final: 0.8000 (ttpt) REVERT: A 656 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: A 732 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7382 (ttm110) REVERT: A 860 MET cc_start: 0.8208 (tmm) cc_final: 0.7906 (tmt) REVERT: A 915 TRP cc_start: 0.8420 (t60) cc_final: 0.8038 (t-100) REVERT: A 974 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8504 (ptp) REVERT: A 1029 ARG cc_start: 0.7905 (mmt180) cc_final: 0.6957 (mmm160) REVERT: B 81 GLN cc_start: 0.8439 (pt0) cc_final: 0.7880 (pt0) REVERT: B 106 GLN cc_start: 0.7685 (mt0) cc_final: 0.7432 (mt0) REVERT: B 108 GLN cc_start: 0.7314 (mt0) cc_final: 0.6968 (mm110) REVERT: B 152 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7640 (mm110) REVERT: B 167 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8769 (t) REVERT: B 259 GLU cc_start: 0.6860 (pt0) cc_final: 0.6640 (pt0) REVERT: B 447 MET cc_start: 0.8336 (tpp) cc_final: 0.7877 (mtt) REVERT: B 520 ASN cc_start: 0.7466 (m-40) cc_final: 0.7161 (m110) REVERT: B 568 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8616 (mtt180) REVERT: B 602 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8158 (mptt) REVERT: B 623 VAL cc_start: 0.8550 (t) cc_final: 0.8323 (m) REVERT: B 639 LYS cc_start: 0.8411 (mmpt) cc_final: 0.7889 (tmtm) REVERT: B 675 SER cc_start: 0.8361 (p) cc_final: 0.8127 (t) REVERT: B 735 GLN cc_start: 0.7316 (tt0) cc_final: 0.6364 (pp30) REVERT: B 765 ARG cc_start: 0.7334 (ttt-90) cc_final: 0.6561 (ttp-170) REVERT: B 856 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: B 866 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8391 (mp) REVERT: B 885 CYS cc_start: 0.8781 (m) cc_final: 0.8461 (t) REVERT: B 893 TRP cc_start: 0.8358 (m100) cc_final: 0.7729 (m-90) outliers start: 64 outliers final: 36 residues processed: 284 average time/residue: 1.4082 time to fit residues: 444.7939 Evaluate side-chains 265 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 76 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 112 GLN 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 182 TYR 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 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 974 MET Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 176 ASP 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 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 731 GLN 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 990 THR Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 138 optimal weight: 2.9990 chunk 200 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 106 GLN A 123 GLN A 245 GLN A 319 HIS ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 ASN B 59 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.106567 restraints weight = 20534.553| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.53 r_work: 0.3077 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.004 0.051 15934 Z= 0.182 Angle : 0.572 9.470 21639 Z= 0.293 Chirality : 0.041 0.182 2512 Planarity : 0.004 0.042 2786 Dihedral : 4.453 58.937 2194 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.01 % Allowed : 22.83 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 2033 helix: 2.03 (0.15), residues: 1171 sheet: -0.45 (0.29), residues: 314 loop : -0.38 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 540 HIS 0.005 0.001 HIS B 955 PHE 0.013 0.001 PHE A 981 TYR 0.011 0.001 TYR B 77 ARG 0.008 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 1061) hydrogen bonds : angle 4.61161 ( 3186) covalent geometry : bond 0.00438 (15934) covalent geometry : angle 0.57202 (21639) *********************** 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 291 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7190 (mtp85) cc_final: 0.6905 (ptp90) REVERT: A 25 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 132 THR cc_start: 0.8060 (m) cc_final: 0.7776 (p) REVERT: A 151 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8274 (ptmm) REVERT: A 439 GLN cc_start: 0.7668 (tt0) cc_final: 0.7401 (tt0) REVERT: A 497 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 518 MET cc_start: 0.8668 (ppp) cc_final: 0.8140 (ppp) REVERT: A 595 LYS cc_start: 0.8368 (tttt) cc_final: 0.8062 (ttpt) REVERT: A 656 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: A 732 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7496 (ttm110) REVERT: A 799 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8822 (t80) REVERT: A 915 TRP cc_start: 0.8497 (t60) cc_final: 0.8087 (t-100) REVERT: A 1029 ARG cc_start: 0.7987 (mmt180) cc_final: 0.7043 (mmm160) REVERT: B 81 GLN cc_start: 0.8438 (pt0) cc_final: 0.8062 (pt0) REVERT: B 106 GLN cc_start: 0.7747 (mt0) cc_final: 0.7477 (mt0) REVERT: B 108 GLN cc_start: 0.7398 (mt0) cc_final: 0.7021 (mm110) REVERT: B 152 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7653 (mm110) REVERT: B 520 ASN cc_start: 0.7514 (m-40) cc_final: 0.7235 (m110) REVERT: B 568 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8550 (mtt180) REVERT: B 602 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8173 (mptt) REVERT: B 623 VAL cc_start: 0.8591 (t) cc_final: 0.8318 (m) REVERT: B 639 LYS cc_start: 0.8527 (mmpt) cc_final: 0.7931 (tmtm) REVERT: B 735 GLN cc_start: 0.7311 (tt0) cc_final: 0.6400 (pp30) REVERT: B 856 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 866 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 885 CYS cc_start: 0.8715 (m) cc_final: 0.8391 (t) REVERT: B 893 TRP cc_start: 0.8374 (m100) cc_final: 0.7759 (m-90) outliers start: 67 outliers final: 41 residues processed: 268 average time/residue: 1.3563 time to fit residues: 399.7425 Evaluate side-chains 270 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 27 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 112 GLN 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 182 TYR 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 447 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 497 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 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 152 GLN Chi-restraints excluded: chain B residue 198 MET 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 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 990 THR Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107238 restraints weight = 20600.630| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.52 r_work: 0.3109 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5324 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= 0.148 Angle : 0.552 9.367 21639 Z= 0.283 Chirality : 0.040 0.172 2512 Planarity : 0.004 0.042 2786 Dihedral : 4.413 58.194 2194 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.30 % Allowed : 23.43 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2033 helix: 2.06 (0.15), residues: 1171 sheet: -0.39 (0.29), residues: 308 loop : -0.43 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 540 HIS 0.005 0.001 HIS B 955 PHE 0.010 0.001 PHE B 571 TYR 0.013 0.001 TYR A 327 ARG 0.009 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1061) hydrogen bonds : angle 4.56580 ( 3186) covalent geometry : bond 0.00347 (15934) covalent geometry : angle 0.55184 (21639) ********************** 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 275 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6944 (ptp90) REVERT: A 25 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 151 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8274 (ptmm) REVERT: A 205 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: A 327 TYR cc_start: 0.8573 (t80) cc_final: 0.8357 (t80) REVERT: A 439 GLN cc_start: 0.7584 (tt0) cc_final: 0.7283 (tt0) REVERT: A 518 MET cc_start: 0.8652 (ppp) cc_final: 0.8112 (ppp) REVERT: A 570 MET cc_start: 0.9096 (ptp) cc_final: 0.8867 (pmt) REVERT: A 595 LYS cc_start: 0.8356 (tttt) cc_final: 0.8067 (ttpt) REVERT: A 656 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: A 732 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7572 (ttm110) REVERT: A 799 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8815 (t80) REVERT: A 915 TRP cc_start: 0.8483 (t60) cc_final: 0.8084 (t-100) REVERT: A 1029 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7025 (mmm160) REVERT: B 81 GLN cc_start: 0.8383 (pt0) cc_final: 0.8063 (pt0) REVERT: B 106 GLN cc_start: 0.7732 (mt0) cc_final: 0.7469 (mt0) REVERT: B 108 GLN cc_start: 0.7322 (mt0) cc_final: 0.6977 (mm110) REVERT: B 152 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7671 (mm110) REVERT: B 520 ASN cc_start: 0.7351 (m-40) cc_final: 0.7059 (m110) REVERT: B 568 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (mtt180) REVERT: B 602 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8179 (mptt) REVERT: B 623 VAL cc_start: 0.8546 (t) cc_final: 0.8324 (m) REVERT: B 639 LYS cc_start: 0.8516 (mmpt) cc_final: 0.7942 (tmtm) REVERT: B 735 GLN cc_start: 0.7308 (tt0) cc_final: 0.6378 (pp30) REVERT: B 765 ARG cc_start: 0.7410 (ttt-90) cc_final: 0.6585 (ttp-170) REVERT: B 856 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: B 866 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 885 CYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8363 (t) REVERT: B 893 TRP cc_start: 0.8374 (m100) cc_final: 0.7735 (m-90) outliers start: 55 outliers final: 35 residues processed: 260 average time/residue: 1.3379 time to fit residues: 384.4868 Evaluate side-chains 258 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 27 ILE Chi-restraints excluded: chain A residue 112 GLN 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 182 TYR 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 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 89 SER Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 198 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.0470 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 0.0060 overall best weight: 0.4094 ------------------------------------------------------------------------------- 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 686 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 = 0.3512 r_free = 0.3512 target = 0.132903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111549 restraints weight = 20408.218| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.52 r_work: 0.3157 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15934 Z= 0.114 Angle : 0.527 8.741 21639 Z= 0.269 Chirality : 0.040 0.250 2512 Planarity : 0.004 0.042 2786 Dihedral : 4.305 56.321 2194 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.82 % Allowed : 23.91 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 2033 helix: 2.19 (0.15), residues: 1173 sheet: -0.30 (0.30), residues: 301 loop : -0.41 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 540 HIS 0.003 0.001 HIS B 955 PHE 0.008 0.001 PHE B 571 TYR 0.008 0.001 TYR A 777 ARG 0.009 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 1061) hydrogen bonds : angle 4.45336 ( 3186) covalent geometry : bond 0.00246 (15934) covalent geometry : angle 0.52691 (21639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12032.86 seconds wall clock time: 208 minutes 3.96 seconds (12483.96 seconds total)