Starting phenix.real_space_refine on Sun Aug 24 23:17:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t21_40977/08_2025/8t21_40977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t21_40977/08_2025/8t21_40977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t21_40977/08_2025/8t21_40977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t21_40977/08_2025/8t21_40977.map" model { file = "/net/cci-nas-00/data/ceres_data/8t21_40977/08_2025/8t21_40977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t21_40977/08_2025/8t21_40977.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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 105 5.16 5 C 14970 2.51 5 N 3891 2.21 5 O 4464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23430 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Chain: "B" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Chain: "C" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Time building chain proxies: 4.46, per 1000 atoms: 0.19 Number of scatterers: 23430 At special positions: 0 Unit cell: (134.31, 144.3, 177.6, 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 105 16.00 O 4464 8.00 N 3891 7.00 C 14970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 732.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 34 sheets defined 24.0% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.951A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.942A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.717A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.721A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.796A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.740A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.816A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 5.688A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.938A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.654A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.667A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.841A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.302A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.675A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.651A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.582A pdb=" N ILE B 980 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1000 removed outlier: 5.533A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1033 removed outlier: 3.524A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.898A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.065A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.792A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.604A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.572A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.530A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.578A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.561A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.851A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.226A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.958A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.988A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1142 through 1147' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.579A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.620A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.614A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 538 removed outlier: 3.751A pdb=" N LEU A 552 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 655 through 660 removed outlier: 8.012A pdb=" N VAL A 656 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA A 694 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 658 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR A 696 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.922A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.237A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.672A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.859A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.907A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AB8, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 659 removed outlier: 5.964A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.902A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.902A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.759A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.802A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.811A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.409A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.090A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.816A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 433 through 434 Processing sheet with id=AD2, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AD3, first strand: chain 'C' and resid 655 through 660 removed outlier: 8.495A pdb=" N VAL C 656 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA C 694 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN C 658 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 696 " --> pdb=" O ASN C 658 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.789A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.545A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.531A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7540 1.35 - 1.50: 6672 1.50 - 1.65: 9623 1.65 - 1.80: 64 1.80 - 1.95: 65 Bond restraints: 23964 Sorted by residual: bond pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 1.523 1.598 -0.075 1.27e-02 6.20e+03 3.44e+01 bond pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.29e-02 6.01e+03 3.10e+01 bond pdb=" N PHE A 59 " pdb=" CA PHE A 59 " ideal model delta sigma weight residual 1.457 1.526 -0.068 1.29e-02 6.01e+03 2.80e+01 bond pdb=" CG PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 1.503 1.347 0.156 3.40e-02 8.65e+02 2.10e+01 bond pdb=" N ASN A 544 " pdb=" CA ASN A 544 " ideal model delta sigma weight residual 1.456 1.516 -0.059 1.31e-02 5.83e+03 2.03e+01 ... (remaining 23959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 32422 5.06 - 10.12: 163 10.12 - 15.18: 30 15.18 - 20.24: 2 20.24 - 25.30: 2 Bond angle restraints: 32619 Sorted by residual: angle pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 112.00 92.71 19.29 1.40e+00 5.10e-01 1.90e+02 angle pdb=" C VAL A 88 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta sigma weight residual 121.54 146.84 -25.30 1.91e+00 2.74e-01 1.76e+02 angle pdb=" C PHE A 58 " pdb=" N PHE A 59 " pdb=" CA PHE A 59 " ideal model delta sigma weight residual 121.54 142.17 -20.63 1.91e+00 2.74e-01 1.17e+02 angle pdb=" O LEU A 56 " pdb=" C LEU A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 121.32 109.82 11.50 1.15e+00 7.56e-01 1.00e+02 angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 110.28 124.60 -14.32 1.48e+00 4.57e-01 9.36e+01 ... (remaining 32614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12247 17.94 - 35.88: 1613 35.88 - 53.82: 349 53.82 - 71.76: 64 71.76 - 89.70: 40 Dihedral angle restraints: 14313 sinusoidal: 5586 harmonic: 8727 Sorted by residual: dihedral pdb=" CA PHE B 55 " pdb=" C PHE B 55 " pdb=" N LEU B 56 " pdb=" CA LEU B 56 " ideal model delta harmonic sigma weight residual 180.00 122.91 57.09 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA PHE A 92 " pdb=" C PHE A 92 " pdb=" N ALA A 93 " pdb=" CA ALA A 93 " ideal model delta harmonic sigma weight residual 180.00 123.09 56.91 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA VAL A 88 " pdb=" C VAL A 88 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual -180.00 -127.43 -52.57 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 14310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 3660 0.138 - 0.277: 57 0.277 - 0.415: 5 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 3723 Sorted by residual: chirality pdb=" CG LEU A 518 " pdb=" CB LEU A 518 " pdb=" CD1 LEU A 518 " pdb=" CD2 LEU A 518 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASN A 85 " pdb=" N ASN A 85 " pdb=" C ASN A 85 " pdb=" CB ASN A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CG LEU B 56 " pdb=" CB LEU B 56 " pdb=" CD1 LEU B 56 " pdb=" CD2 LEU B 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3720 not shown) Planarity restraints: 4236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 56 " -0.036 2.00e-02 2.50e+03 6.46e-02 4.18e+01 pdb=" C LEU A 56 " 0.112 2.00e-02 2.50e+03 pdb=" O LEU A 56 " -0.037 2.00e-02 2.50e+03 pdb=" N PRO A 57 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 38 " -0.110 5.00e-02 4.00e+02 1.48e-01 3.49e+01 pdb=" N PRO A 39 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 91 " -0.028 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" C TYR A 91 " 0.097 2.00e-02 2.50e+03 pdb=" O TYR A 91 " -0.037 2.00e-02 2.50e+03 pdb=" N PHE A 92 " -0.032 2.00e-02 2.50e+03 ... (remaining 4233 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 290 2.53 - 3.13: 18845 3.13 - 3.72: 36650 3.72 - 4.31: 47093 4.31 - 4.90: 75436 Nonbonded interactions: 178314 Sorted by model distance: nonbonded pdb=" N SER A 60 " pdb=" O VAL A 88 " model vdw 1.943 3.120 nonbonded pdb=" N TYR B 423 " pdb=" O ARG B 466 " model vdw 2.040 3.120 nonbonded pdb=" O LEU A 56 " pdb=" N GLY A 87 " model vdw 2.045 3.120 nonbonded pdb=" N HIS B 519 " pdb=" O PHE B 562 " model vdw 2.056 3.120 nonbonded pdb=" OG1 THR B 385 " pdb=" O LEU C 977 " model vdw 2.071 3.040 ... (remaining 178309 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue 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: 12.250 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.050 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.005 0.156 24003 Z= 0.283 Angle : 1.036 25.304 32697 Z= 0.589 Chirality : 0.053 0.691 3723 Planarity : 0.007 0.148 4236 Dihedral : 16.988 89.697 8574 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.64 % Favored : 88.02 % Rotamer: Outliers : 0.34 % Allowed : 24.06 % Favored : 75.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 1.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.15), residues: 2955 helix: 1.94 (0.22), residues: 557 sheet: -0.72 (0.28), residues: 359 loop : -2.86 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 34 TYR 0.039 0.002 TYR B 37 PHE 0.071 0.002 PHE B 55 TRP 0.034 0.002 TRP B 64 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00544 (23964) covalent geometry : angle 1.02861 (32619) SS BOND : bond 0.00355 ( 39) SS BOND : angle 2.75243 ( 78) hydrogen bonds : bond 0.21454 ( 653) hydrogen bonds : angle 7.51194 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7506 (t-90) cc_final: 0.7232 (t-170) REVERT: A 615 VAL cc_start: 0.9085 (t) cc_final: 0.8840 (m) REVERT: A 968 SER cc_start: 0.8404 (m) cc_final: 0.8155 (p) REVERT: A 1138 TYR cc_start: 0.7609 (t80) cc_final: 0.7228 (t80) REVERT: B 113 LYS cc_start: 0.5418 (tptp) cc_final: 0.5216 (mmtm) REVERT: B 133 PHE cc_start: 0.5331 (t80) cc_final: 0.4947 (m-80) REVERT: B 206 LYS cc_start: 0.7959 (tptt) cc_final: 0.7353 (mtpt) REVERT: B 731 MET cc_start: 0.8894 (pmm) cc_final: 0.8001 (pmm) REVERT: B 960 ASN cc_start: 0.7876 (m-40) cc_final: 0.7600 (t0) REVERT: B 979 ASP cc_start: 0.4949 (t0) cc_final: 0.4171 (t0) REVERT: B 1029 MET cc_start: 0.7212 (tmm) cc_final: 0.6759 (ttm) REVERT: C 191 GLU cc_start: 0.8247 (mp0) cc_final: 0.7917 (mp0) REVERT: C 900 MET cc_start: 0.7770 (mmp) cc_final: 0.7368 (mtt) REVERT: C 973 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.6001 (tt) REVERT: C 995 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7563 (ptm-80) REVERT: C 1002 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7971 (tm-30) REVERT: C 1050 MET cc_start: 0.7078 (mmp) cc_final: 0.6499 (mmp) outliers start: 9 outliers final: 1 residues processed: 272 average time/residue: 0.1457 time to fit residues: 61.2038 Evaluate side-chains 149 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN B 165 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 969 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.165276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.127101 restraints weight = 65866.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124639 restraints weight = 42920.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125410 restraints weight = 40358.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.125894 restraints weight = 31490.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126113 restraints weight = 29407.256| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 24003 Z= 0.241 Angle : 0.933 23.463 32697 Z= 0.499 Chirality : 0.052 0.363 3723 Planarity : 0.006 0.099 4236 Dihedral : 7.496 58.504 3205 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.59 % Favored : 89.07 % Rotamer: Outliers : 3.72 % Allowed : 22.20 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.15), residues: 2955 helix: 1.94 (0.22), residues: 563 sheet: -0.68 (0.26), residues: 371 loop : -2.84 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 328 TYR 0.030 0.002 TYR B 204 PHE 0.057 0.002 PHE A 392 TRP 0.019 0.002 TRP C 64 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00464 (23964) covalent geometry : angle 0.92231 (32619) SS BOND : bond 0.00663 ( 39) SS BOND : angle 3.00980 ( 78) hydrogen bonds : bond 0.06271 ( 653) hydrogen bonds : angle 5.75865 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 164 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.1727 (t80) cc_final: 0.0844 (m-80) REVERT: A 190 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5618 (mmm-85) REVERT: A 382 VAL cc_start: 0.1912 (OUTLIER) cc_final: 0.1651 (m) REVERT: A 544 ASN cc_start: 0.6671 (OUTLIER) cc_final: 0.6302 (m110) REVERT: A 740 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8434 (tmm) REVERT: A 894 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 55 PHE cc_start: 0.4814 (m-80) cc_final: 0.4337 (m-80) REVERT: B 206 LYS cc_start: 0.8886 (tptt) cc_final: 0.8523 (tttt) REVERT: B 452 LEU cc_start: 0.0423 (OUTLIER) cc_final: 0.0085 (tp) REVERT: B 1029 MET cc_start: 0.8293 (tmm) cc_final: 0.7800 (ttm) REVERT: C 360 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.6864 (t0) REVERT: C 402 ILE cc_start: -0.1497 (OUTLIER) cc_final: -0.1973 (tt) REVERT: C 449 TYR cc_start: 0.7369 (t80) cc_final: 0.7141 (t80) REVERT: C 754 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9166 (tp) REVERT: C 995 ARG cc_start: 0.7580 (ptm160) cc_final: 0.7206 (ptm-80) REVERT: C 1050 MET cc_start: 0.7247 (mmp) cc_final: 0.6756 (mmp) outliers start: 98 outliers final: 41 residues processed: 254 average time/residue: 0.1097 time to fit residues: 46.8762 Evaluate side-chains 173 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 216 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 230 optimal weight: 0.1980 chunk 217 optimal weight: 0.0050 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 450 ASN B 519 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** 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 = 0.4338 r_free = 0.4338 target = 0.161530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117005 restraints weight = 61831.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115285 restraints weight = 50002.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115462 restraints weight = 38715.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.115909 restraints weight = 33967.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116408 restraints weight = 29148.755| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 24003 Z= 0.222 Angle : 0.862 22.437 32697 Z= 0.463 Chirality : 0.050 0.374 3723 Planarity : 0.006 0.102 4236 Dihedral : 7.026 51.096 3203 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.98 % Favored : 89.75 % Rotamer: Outliers : 4.68 % Allowed : 22.12 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.78 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.15), residues: 2955 helix: 1.97 (0.22), residues: 559 sheet: -0.71 (0.25), residues: 388 loop : -2.83 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.023 0.001 TYR B 380 PHE 0.042 0.001 PHE A 329 TRP 0.027 0.001 TRP C 64 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00427 (23964) covalent geometry : angle 0.84980 (32619) SS BOND : bond 0.00766 ( 39) SS BOND : angle 3.07592 ( 78) hydrogen bonds : bond 0.05844 ( 653) hydrogen bonds : angle 5.32312 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 143 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: A 110 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.4155 (mt) REVERT: A 409 GLN cc_start: 0.2330 (OUTLIER) cc_final: 0.1741 (pm20) REVERT: A 655 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.7044 (t-90) REVERT: A 740 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8127 (tmm) REVERT: A 894 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8755 (mt) REVERT: B 169 GLU cc_start: 0.4585 (OUTLIER) cc_final: 0.4272 (mm-30) REVERT: B 206 LYS cc_start: 0.8964 (tptt) cc_final: 0.8455 (ttmt) REVERT: B 452 LEU cc_start: -0.0076 (OUTLIER) cc_final: -0.0407 (tp) REVERT: B 731 MET cc_start: 0.8586 (pmm) cc_final: 0.7331 (ptt) REVERT: C 166 CYS cc_start: 0.7806 (OUTLIER) cc_final: 0.6569 (t) REVERT: C 233 ILE cc_start: 0.2607 (OUTLIER) cc_final: 0.1693 (tt) REVERT: C 449 TYR cc_start: 0.7654 (t80) cc_final: 0.7405 (t80) REVERT: C 1050 MET cc_start: 0.7206 (mmp) cc_final: 0.6832 (mmp) outliers start: 123 outliers final: 57 residues processed: 256 average time/residue: 0.1077 time to fit residues: 46.7689 Evaluate side-chains 180 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 113 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 158 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 216 optimal weight: 0.4980 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 286 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1106 GLN B 188 ASN B 271 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1106 GLN C 115 GLN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.158021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114641 restraints weight = 62627.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.111968 restraints weight = 50315.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112533 restraints weight = 38988.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.112898 restraints weight = 35803.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.113246 restraints weight = 29839.030| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 24003 Z= 0.226 Angle : 0.871 20.984 32697 Z= 0.462 Chirality : 0.051 0.446 3723 Planarity : 0.006 0.099 4236 Dihedral : 6.863 51.364 3201 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.52 % Favored : 89.20 % Rotamer: Outliers : 5.78 % Allowed : 21.13 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.15), residues: 2955 helix: 1.95 (0.22), residues: 564 sheet: -0.66 (0.26), residues: 376 loop : -2.78 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 273 TYR 0.026 0.001 TYR B1138 PHE 0.055 0.001 PHE A 59 TRP 0.014 0.001 TRP C 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00450 (23964) covalent geometry : angle 0.85865 (32619) SS BOND : bond 0.00812 ( 39) SS BOND : angle 3.08153 ( 78) hydrogen bonds : bond 0.06194 ( 653) hydrogen bonds : angle 5.19847 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 126 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: A 110 LEU cc_start: 0.4382 (OUTLIER) cc_final: 0.4110 (mt) REVERT: A 133 PHE cc_start: 0.3461 (OUTLIER) cc_final: 0.3028 (m-80) REVERT: A 190 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5751 (mmm-85) REVERT: A 409 GLN cc_start: 0.1939 (OUTLIER) cc_final: 0.1436 (pm20) REVERT: A 655 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.7085 (t-90) REVERT: A 740 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8160 (tmm) REVERT: A 894 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8837 (mt) REVERT: A 1094 VAL cc_start: 0.9339 (OUTLIER) cc_final: 0.9096 (m) REVERT: B 55 PHE cc_start: 0.5471 (m-80) cc_final: 0.4838 (m-80) REVERT: B 169 GLU cc_start: 0.4738 (OUTLIER) cc_final: 0.4343 (mm-30) REVERT: B 206 LYS cc_start: 0.8953 (tptt) cc_final: 0.8533 (tttt) REVERT: B 207 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7214 (t-90) REVERT: B 382 VAL cc_start: 0.5182 (OUTLIER) cc_final: 0.4965 (t) REVERT: B 418 ILE cc_start: 0.2664 (OUTLIER) cc_final: 0.2453 (mm) REVERT: B 452 LEU cc_start: 0.0252 (OUTLIER) cc_final: -0.0188 (tp) REVERT: B 731 MET cc_start: 0.8637 (pmm) cc_final: 0.7635 (ptt) REVERT: B 1029 MET cc_start: 0.8359 (tmm) cc_final: 0.7625 (tmm) REVERT: C 115 GLN cc_start: 0.4134 (OUTLIER) cc_final: 0.3865 (tt0) REVERT: C 166 CYS cc_start: 0.7783 (OUTLIER) cc_final: 0.6393 (t) REVERT: C 360 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7460 (t0) REVERT: C 402 ILE cc_start: -0.1521 (OUTLIER) cc_final: -0.2104 (tt) REVERT: C 449 TYR cc_start: 0.7561 (t80) cc_final: 0.7301 (t80) REVERT: C 1050 MET cc_start: 0.7326 (mmp) cc_final: 0.7009 (mmp) outliers start: 152 outliers final: 77 residues processed: 263 average time/residue: 0.1068 time to fit residues: 47.4060 Evaluate side-chains 207 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 112 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 206 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 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 = 0.4285 r_free = 0.4285 target = 0.158341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.115783 restraints weight = 61427.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112570 restraints weight = 44185.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113037 restraints weight = 37051.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113844 restraints weight = 30120.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113917 restraints weight = 25990.953| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 24003 Z= 0.232 Angle : 0.863 20.485 32697 Z= 0.461 Chirality : 0.050 0.448 3723 Planarity : 0.006 0.095 4236 Dihedral : 6.833 46.861 3201 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.86 % Favored : 88.90 % Rotamer: Outliers : 5.36 % Allowed : 20.68 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.82 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.15), residues: 2955 helix: 1.80 (0.22), residues: 576 sheet: -0.78 (0.25), residues: 391 loop : -2.82 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 995 TYR 0.021 0.002 TYR A 266 PHE 0.045 0.002 PHE A 59 TRP 0.012 0.001 TRP A 436 HIS 0.009 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00480 (23964) covalent geometry : angle 0.85195 (32619) SS BOND : bond 0.00827 ( 39) SS BOND : angle 2.99712 ( 78) hydrogen bonds : bond 0.06745 ( 653) hydrogen bonds : angle 5.23878 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 113 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: A 84 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.4912 (p90) REVERT: A 190 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5888 (mmm-85) REVERT: A 655 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.7374 (t-90) REVERT: A 740 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8123 (tmm) REVERT: A 894 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8865 (mt) REVERT: A 902 MET cc_start: 0.8742 (tpp) cc_final: 0.8381 (mmt) REVERT: A 912 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8501 (p) REVERT: A 1094 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9036 (m) REVERT: B 55 PHE cc_start: 0.5079 (m-80) cc_final: 0.4649 (m-80) REVERT: B 169 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.4311 (mm-30) REVERT: B 206 LYS cc_start: 0.9062 (tptt) cc_final: 0.8560 (tttt) REVERT: B 207 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7255 (t-90) REVERT: B 418 ILE cc_start: 0.2628 (OUTLIER) cc_final: 0.2416 (mm) REVERT: B 731 MET cc_start: 0.8641 (pmm) cc_final: 0.7897 (ptt) REVERT: B 1029 MET cc_start: 0.8404 (tmm) cc_final: 0.7842 (ttm) REVERT: C 64 TRP cc_start: 0.6737 (t60) cc_final: 0.6515 (t60) REVERT: C 104 TRP cc_start: 0.6592 (p90) cc_final: 0.5870 (p90) REVERT: C 166 CYS cc_start: 0.7185 (OUTLIER) cc_final: 0.5567 (t) REVERT: C 360 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7472 (t0) REVERT: C 402 ILE cc_start: -0.1525 (OUTLIER) cc_final: -0.2113 (tt) REVERT: C 449 TYR cc_start: 0.7490 (t80) cc_final: 0.7251 (t80) REVERT: C 708 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8475 (m) REVERT: C 1050 MET cc_start: 0.7538 (mmp) cc_final: 0.7183 (mmp) outliers start: 141 outliers final: 90 residues processed: 243 average time/residue: 0.1184 time to fit residues: 48.8125 Evaluate side-chains 211 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 106 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 47 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 226 optimal weight: 0.0570 chunk 123 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 166 optimal weight: 0.0980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.162824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116052 restraints weight = 64929.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.119329 restraints weight = 40959.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.119803 restraints weight = 23353.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120443 restraints weight = 21263.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120474 restraints weight = 19870.892| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 24003 Z= 0.202 Angle : 0.834 19.008 32697 Z= 0.438 Chirality : 0.049 0.441 3723 Planarity : 0.006 0.087 4236 Dihedral : 6.602 49.371 3201 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.71 % Favored : 90.02 % Rotamer: Outliers : 4.22 % Allowed : 21.85 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.15), residues: 2955 helix: 1.87 (0.22), residues: 579 sheet: -0.56 (0.26), residues: 375 loop : -2.76 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.017 0.001 TYR A 266 PHE 0.031 0.001 PHE A 329 TRP 0.012 0.001 TRP A 436 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00388 (23964) covalent geometry : angle 0.82332 (32619) SS BOND : bond 0.00859 ( 39) SS BOND : angle 2.85551 ( 78) hydrogen bonds : bond 0.05357 ( 653) hydrogen bonds : angle 4.92978 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 116 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: A 84 PHE cc_start: 0.5570 (OUTLIER) cc_final: 0.4631 (p90) REVERT: A 170 TYR cc_start: 0.8748 (m-80) cc_final: 0.8384 (m-80) REVERT: A 190 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.5701 (mmm-85) REVERT: A 409 GLN cc_start: 0.1691 (OUTLIER) cc_final: 0.1068 (pm20) REVERT: A 655 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.7093 (t-90) REVERT: A 740 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8138 (tmm) REVERT: A 902 MET cc_start: 0.8670 (tpp) cc_final: 0.8312 (mmt) REVERT: A 912 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 1094 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8987 (m) REVERT: B 169 GLU cc_start: 0.4678 (OUTLIER) cc_final: 0.4275 (mm-30) REVERT: B 206 LYS cc_start: 0.8955 (tptt) cc_final: 0.8501 (tttt) REVERT: B 207 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7430 (t-90) REVERT: B 418 ILE cc_start: 0.2637 (OUTLIER) cc_final: 0.2433 (mm) REVERT: B 731 MET cc_start: 0.8586 (pmm) cc_final: 0.7857 (ptt) REVERT: B 1029 MET cc_start: 0.8357 (tmm) cc_final: 0.7671 (ttm) REVERT: C 64 TRP cc_start: 0.6806 (t60) cc_final: 0.6533 (t60) REVERT: C 104 TRP cc_start: 0.6544 (p90) cc_final: 0.5704 (p90) REVERT: C 200 TYR cc_start: 0.7124 (m-80) cc_final: 0.6790 (m-80) REVERT: C 360 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7472 (t0) REVERT: C 449 TYR cc_start: 0.7407 (t80) cc_final: 0.7157 (t80) REVERT: C 708 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8227 (m) outliers start: 111 outliers final: 74 residues processed: 214 average time/residue: 0.1165 time to fit residues: 41.8548 Evaluate side-chains 190 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 103 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 85 optimal weight: 0.9980 chunk 258 optimal weight: 0.4980 chunk 122 optimal weight: 0.1980 chunk 225 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.161494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114550 restraints weight = 64865.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.116875 restraints weight = 44671.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.118697 restraints weight = 26129.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.118747 restraints weight = 22060.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.118923 restraints weight = 20030.310| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 24003 Z= 0.198 Angle : 0.819 18.487 32697 Z= 0.431 Chirality : 0.049 0.442 3723 Planarity : 0.006 0.087 4236 Dihedral : 6.499 58.582 3201 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.05 % Favored : 89.68 % Rotamer: Outliers : 4.22 % Allowed : 21.78 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.15), residues: 2955 helix: 2.02 (0.22), residues: 579 sheet: -0.64 (0.25), residues: 381 loop : -2.73 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.021 0.001 TYR A 266 PHE 0.030 0.001 PHE A 329 TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00388 (23964) covalent geometry : angle 0.80795 (32619) SS BOND : bond 0.00861 ( 39) SS BOND : angle 2.80210 ( 78) hydrogen bonds : bond 0.05331 ( 653) hydrogen bonds : angle 4.83727 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 116 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: A 84 PHE cc_start: 0.5419 (OUTLIER) cc_final: 0.4506 (p90) REVERT: A 170 TYR cc_start: 0.8878 (m-80) cc_final: 0.8531 (m-80) REVERT: A 190 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5689 (mmm-85) REVERT: A 386 LYS cc_start: 0.8079 (tttm) cc_final: 0.7310 (tptp) REVERT: A 655 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.7296 (t-90) REVERT: A 894 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8742 (mt) REVERT: A 902 MET cc_start: 0.8723 (tpp) cc_final: 0.8373 (mmt) REVERT: B 169 GLU cc_start: 0.4721 (OUTLIER) cc_final: 0.4312 (mm-30) REVERT: B 206 LYS cc_start: 0.8958 (tptt) cc_final: 0.8403 (ttmt) REVERT: B 207 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7387 (t-90) REVERT: B 731 MET cc_start: 0.8572 (pmm) cc_final: 0.8022 (ptt) REVERT: B 935 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7360 (tp-100) REVERT: B 1029 MET cc_start: 0.8493 (tmm) cc_final: 0.8116 (ttp) REVERT: C 64 TRP cc_start: 0.6822 (t60) cc_final: 0.6464 (t60) REVERT: C 104 TRP cc_start: 0.6582 (p90) cc_final: 0.5744 (p90) REVERT: C 200 TYR cc_start: 0.7140 (m-80) cc_final: 0.6776 (m-80) REVERT: C 360 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7533 (t0) REVERT: C 449 TYR cc_start: 0.7400 (t80) cc_final: 0.7149 (t80) REVERT: C 697 MET cc_start: 0.8071 (mmm) cc_final: 0.7757 (mmm) REVERT: C 708 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8325 (m) outliers start: 111 outliers final: 75 residues processed: 215 average time/residue: 0.1187 time to fit residues: 42.2996 Evaluate side-chains 195 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 110 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 289 optimal weight: 0.9980 chunk 114 optimal weight: 0.0970 chunk 283 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 151 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 448 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.161595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.114651 restraints weight = 64869.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117545 restraints weight = 37340.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118933 restraints weight = 23472.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.118957 restraints weight = 22611.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.119231 restraints weight = 20058.239| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.206 24003 Z= 0.195 Angle : 0.813 17.914 32697 Z= 0.425 Chirality : 0.049 0.450 3723 Planarity : 0.006 0.087 4236 Dihedral : 6.421 57.352 3201 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.17 % Favored : 90.52 % Rotamer: Outliers : 4.18 % Allowed : 21.97 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.15), residues: 2955 helix: 2.06 (0.22), residues: 579 sheet: -0.50 (0.26), residues: 373 loop : -2.66 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.017 0.001 TYR A 266 PHE 0.043 0.001 PHE B 55 TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00377 (23964) covalent geometry : angle 0.80275 (32619) SS BOND : bond 0.00844 ( 39) SS BOND : angle 2.77818 ( 78) hydrogen bonds : bond 0.05048 ( 653) hydrogen bonds : angle 4.78878 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 120 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6362 (m-10) REVERT: A 84 PHE cc_start: 0.5210 (OUTLIER) cc_final: 0.4388 (p90) REVERT: A 190 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5593 (mmm-85) REVERT: A 386 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7305 (tptp) REVERT: A 655 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7313 (t-90) REVERT: A 894 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (mt) REVERT: A 902 MET cc_start: 0.8654 (tpp) cc_final: 0.8289 (mmt) REVERT: B 53 ASP cc_start: 0.7396 (t0) cc_final: 0.7193 (t0) REVERT: B 169 GLU cc_start: 0.4738 (OUTLIER) cc_final: 0.4330 (mm-30) REVERT: B 190 ARG cc_start: 0.6532 (ptt180) cc_final: 0.6088 (ptt90) REVERT: B 206 LYS cc_start: 0.8992 (tptt) cc_final: 0.8422 (ttmt) REVERT: B 207 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7307 (t-90) REVERT: B 731 MET cc_start: 0.8625 (pmm) cc_final: 0.8091 (ptt) REVERT: B 935 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: B 1029 MET cc_start: 0.8482 (tmm) cc_final: 0.8071 (ttp) REVERT: C 64 TRP cc_start: 0.6784 (t60) cc_final: 0.6387 (t60) REVERT: C 104 TRP cc_start: 0.6523 (p90) cc_final: 0.5701 (p90) REVERT: C 200 TYR cc_start: 0.7211 (m-80) cc_final: 0.6729 (m-80) REVERT: C 360 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7492 (t0) REVERT: C 449 TYR cc_start: 0.7390 (t80) cc_final: 0.7137 (t80) REVERT: C 697 MET cc_start: 0.8036 (mmm) cc_final: 0.7766 (mmm) REVERT: C 708 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8320 (m) outliers start: 110 outliers final: 79 residues processed: 219 average time/residue: 0.1117 time to fit residues: 41.3288 Evaluate side-chains 201 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 111 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1045 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 143 optimal weight: 0.5980 chunk 239 optimal weight: 0.0070 chunk 275 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 250 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 274 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.159494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118047 restraints weight = 62436.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114430 restraints weight = 44225.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.114738 restraints weight = 40632.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115126 restraints weight = 38624.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115725 restraints weight = 30065.861| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 24003 Z= 0.191 Angle : 0.808 17.815 32697 Z= 0.422 Chirality : 0.048 0.436 3723 Planarity : 0.006 0.080 4236 Dihedral : 6.300 57.004 3201 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.02 % Favored : 89.75 % Rotamer: Outliers : 3.88 % Allowed : 22.08 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.15), residues: 2955 helix: 1.93 (0.22), residues: 591 sheet: -0.43 (0.26), residues: 372 loop : -2.60 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.015 0.001 TYR A 266 PHE 0.035 0.001 PHE B 55 TRP 0.011 0.001 TRP A 436 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00373 (23964) covalent geometry : angle 0.79755 (32619) SS BOND : bond 0.00841 ( 39) SS BOND : angle 2.72768 ( 78) hydrogen bonds : bond 0.04876 ( 653) hydrogen bonds : angle 4.72970 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 116 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6391 (m-10) REVERT: A 170 TYR cc_start: 0.9056 (m-80) cc_final: 0.8816 (m-80) REVERT: A 190 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5621 (mmm-85) REVERT: A 386 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7217 (tptp) REVERT: A 655 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7366 (t-90) REVERT: A 894 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 902 MET cc_start: 0.8731 (tpp) cc_final: 0.8328 (mmt) REVERT: B 53 ASP cc_start: 0.7400 (t0) cc_final: 0.7192 (t0) REVERT: B 55 PHE cc_start: 0.4460 (m-80) cc_final: 0.3834 (m-80) REVERT: B 169 GLU cc_start: 0.4726 (OUTLIER) cc_final: 0.4329 (mm-30) REVERT: B 190 ARG cc_start: 0.6499 (ptt180) cc_final: 0.6267 (ptt180) REVERT: B 207 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7461 (t-90) REVERT: B 731 MET cc_start: 0.8596 (pmm) cc_final: 0.8077 (ptt) REVERT: B 935 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: B 1029 MET cc_start: 0.8477 (tmm) cc_final: 0.8058 (ttp) REVERT: C 64 TRP cc_start: 0.6774 (t60) cc_final: 0.6365 (t60) REVERT: C 104 TRP cc_start: 0.6540 (p90) cc_final: 0.5790 (p90) REVERT: C 189 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7650 (mm) REVERT: C 200 TYR cc_start: 0.7008 (m-80) cc_final: 0.6606 (m-80) REVERT: C 360 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7506 (t0) REVERT: C 449 TYR cc_start: 0.7320 (t80) cc_final: 0.7062 (t80) REVERT: C 697 MET cc_start: 0.8210 (mmm) cc_final: 0.7864 (mmm) REVERT: C 708 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8378 (m) outliers start: 102 outliers final: 81 residues processed: 208 average time/residue: 0.1193 time to fit residues: 41.2853 Evaluate side-chains 202 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 110 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 0.0030 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** 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 = 0.4262 r_free = 0.4262 target = 0.159307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110209 restraints weight = 63715.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113322 restraints weight = 31343.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.115502 restraints weight = 20266.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116704 restraints weight = 15210.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117582 restraints weight = 12917.451| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 24003 Z= 0.211 Angle : 0.834 17.741 32697 Z= 0.437 Chirality : 0.049 0.500 3723 Planarity : 0.006 0.080 4236 Dihedral : 6.401 55.810 3201 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.32 % Favored : 89.44 % Rotamer: Outliers : 3.46 % Allowed : 22.69 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.15), residues: 2955 helix: 1.98 (0.22), residues: 582 sheet: -0.52 (0.26), residues: 361 loop : -2.58 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 273 TYR 0.022 0.001 TYR A 396 PHE 0.051 0.002 PHE A 92 TRP 0.012 0.001 TRP A 436 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00444 (23964) covalent geometry : angle 0.82375 (32619) SS BOND : bond 0.00870 ( 39) SS BOND : angle 2.77087 ( 78) hydrogen bonds : bond 0.06271 ( 653) hydrogen bonds : angle 4.93452 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 122 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6206 (m-10) REVERT: A 170 TYR cc_start: 0.8920 (m-80) cc_final: 0.8707 (m-80) REVERT: A 190 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5332 (mmm-85) REVERT: A 275 PHE cc_start: 0.6182 (m-10) cc_final: 0.5788 (m-10) REVERT: A 894 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8763 (mt) REVERT: A 902 MET cc_start: 0.8896 (tpp) cc_final: 0.8530 (mmt) REVERT: B 53 ASP cc_start: 0.7247 (t0) cc_final: 0.7038 (t0) REVERT: B 55 PHE cc_start: 0.4740 (m-80) cc_final: 0.4058 (m-80) REVERT: B 169 GLU cc_start: 0.4457 (OUTLIER) cc_final: 0.4088 (mm-30) REVERT: B 190 ARG cc_start: 0.6602 (ptt180) cc_final: 0.6252 (ptt90) REVERT: B 207 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7454 (t-90) REVERT: B 935 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7403 (tp-100) REVERT: B 1029 MET cc_start: 0.8602 (tmm) cc_final: 0.7964 (ttt) REVERT: C 64 TRP cc_start: 0.6972 (t60) cc_final: 0.6574 (t60) REVERT: C 104 TRP cc_start: 0.6624 (p90) cc_final: 0.5772 (p90) REVERT: C 360 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7418 (t0) REVERT: C 449 TYR cc_start: 0.7422 (t80) cc_final: 0.7196 (t80) REVERT: C 697 MET cc_start: 0.8507 (mmm) cc_final: 0.8265 (mmm) REVERT: C 1031 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7894 (tm-30) outliers start: 91 outliers final: 76 residues processed: 206 average time/residue: 0.1099 time to fit residues: 38.8525 Evaluate side-chains 197 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 114 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 32 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 45 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** 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 = 0.4274 r_free = 0.4274 target = 0.160431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111568 restraints weight = 63390.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114683 restraints weight = 31129.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116874 restraints weight = 20045.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118021 restraints weight = 15124.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.118921 restraints weight = 12790.269| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 24003 Z= 0.195 Angle : 0.813 17.311 32697 Z= 0.424 Chirality : 0.049 0.416 3723 Planarity : 0.006 0.080 4236 Dihedral : 6.308 55.591 3201 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.75 % Favored : 90.02 % Rotamer: Outliers : 3.53 % Allowed : 22.69 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.15), residues: 2955 helix: 1.94 (0.22), residues: 588 sheet: -0.47 (0.26), residues: 356 loop : -2.54 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.020 0.001 TYR A 396 PHE 0.030 0.001 PHE B 55 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00392 (23964) covalent geometry : angle 0.80308 (32619) SS BOND : bond 0.00865 ( 39) SS BOND : angle 2.66052 ( 78) hydrogen bonds : bond 0.05577 ( 653) hydrogen bonds : angle 4.82695 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3687.91 seconds wall clock time: 64 minutes 27.33 seconds (3867.33 seconds total)