Starting phenix.real_space_refine on Fri Jun 20 10:34:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t21_40977/06_2025/8t21_40977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t21_40977/06_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_40977/06_2025/8t21_40977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t21_40977/06_2025/8t21_40977.map" model { file = "/net/cci-nas-00/data/ceres_data/8t21_40977/06_2025/8t21_40977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t21_40977/06_2025/8t21_40977.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.61, per 1000 atoms: 0.67 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: 5.66 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.66 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: 8.27 Time building geometry restraints manager: 6.82 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: 0.08 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: 8.390 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: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 55.170 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.002 TRP B 64 HIS 0.005 0.001 HIS C 519 PHE 0.071 0.002 PHE B 55 TYR 0.039 0.002 TYR B 37 ARG 0.011 0.001 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.21454 ( 653) hydrogen bonds : angle 7.51194 ( 1815) SS BOND : bond 0.00355 ( 39) SS BOND : angle 2.75243 ( 78) covalent geometry : bond 0.00544 (23964) covalent geometry : angle 1.02861 (32619) *********************** 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 : 2.357 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: 0.4255 (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: 0.3779 time to fit residues: 159.3580 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 : 2.710 ------------------------------------------------------------------------------- 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 253 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 235 optimal weight: 20.0000 chunk 90 optimal weight: 0.1980 chunk 142 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 272 optimal weight: 0.0470 overall best weight: 1.2484 ------------------------------------------------------------------------------- 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 450 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.158526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.115371 restraints weight = 62448.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.112752 restraints weight = 46617.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112892 restraints weight = 39485.051| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 24003 Z= 0.251 Angle : 0.946 23.372 32697 Z= 0.506 Chirality : 0.053 0.376 3723 Planarity : 0.007 0.104 4236 Dihedral : 7.539 59.089 3205 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.76 % Favored : 88.90 % Rotamer: Outliers : 4.26 % Allowed : 21.89 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.15), residues: 2955 helix: 1.85 (0.22), residues: 563 sheet: -0.75 (0.26), residues: 361 loop : -2.86 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.005 0.001 HIS A 655 PHE 0.057 0.002 PHE A 392 TYR 0.030 0.002 TYR C 396 ARG 0.006 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.06620 ( 653) hydrogen bonds : angle 5.64894 ( 1815) SS BOND : bond 0.00687 ( 39) SS BOND : angle 3.05333 ( 78) covalent geometry : bond 0.00499 (23964) covalent geometry : angle 0.93553 (32619) *********************** 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 274 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 162 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.1896 (t80) cc_final: 0.0991 (m-80) REVERT: A 190 ARG cc_start: 0.5764 (OUTLIER) cc_final: 0.5289 (mmm-85) REVERT: A 382 VAL cc_start: 0.2506 (OUTLIER) cc_final: 0.2256 (m) REVERT: A 544 ASN cc_start: 0.6621 (OUTLIER) cc_final: 0.6415 (m110) REVERT: A 553 THR cc_start: 0.5484 (OUTLIER) cc_final: 0.5167 (p) REVERT: A 740 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8188 (tmm) REVERT: A 894 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8770 (mt) REVERT: B 55 PHE cc_start: 0.4884 (m-80) cc_final: 0.4400 (m-80) REVERT: B 169 GLU cc_start: 0.4548 (OUTLIER) cc_final: 0.4167 (mm-30) REVERT: B 206 LYS cc_start: 0.8870 (tptt) cc_final: 0.8280 (mttt) REVERT: B 452 LEU cc_start: -0.0037 (OUTLIER) cc_final: -0.0341 (tp) REVERT: B 1029 MET cc_start: 0.8267 (tmm) cc_final: 0.7915 (ttm) REVERT: C 353 TRP cc_start: 0.7405 (p-90) cc_final: 0.7199 (p-90) REVERT: C 360 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.6751 (t0) REVERT: C 402 ILE cc_start: -0.1901 (OUTLIER) cc_final: -0.2414 (tt) REVERT: C 449 TYR cc_start: 0.7675 (t80) cc_final: 0.7177 (t80) REVERT: C 489 TYR cc_start: 0.6809 (p90) cc_final: 0.6475 (m-80) REVERT: C 995 ARG cc_start: 0.7939 (ptm160) cc_final: 0.7483 (ptm-80) REVERT: C 1050 MET cc_start: 0.7351 (mmp) cc_final: 0.6955 (mmp) outliers start: 112 outliers final: 49 residues processed: 264 average time/residue: 0.2940 time to fit residues: 129.6960 Evaluate side-chains 176 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 117 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL 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 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE 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 518 LEU 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 553 THR 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 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 169 GLU 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 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 569 ILE Chi-restraints excluded: chain B residue 598 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 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 511 VAL Chi-restraints excluded: chain C residue 547 THR 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 736 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU 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 225 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 211 optimal weight: 0.4980 chunk 255 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 218 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 519 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.158582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115196 restraints weight = 62396.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.112299 restraints weight = 48613.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.112833 restraints weight = 39134.423| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 24003 Z= 0.228 Angle : 0.872 22.365 32697 Z= 0.468 Chirality : 0.051 0.377 3723 Planarity : 0.006 0.101 4236 Dihedral : 7.090 50.651 3203 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.81 % Favored : 89.88 % Rotamer: Outliers : 4.68 % Allowed : 22.23 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2955 helix: 1.87 (0.22), residues: 564 sheet: -0.67 (0.26), residues: 377 loop : -2.84 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 64 HIS 0.004 0.001 HIS A 207 PHE 0.041 0.001 PHE A 329 TYR 0.026 0.001 TYR B 380 ARG 0.007 0.001 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.06425 ( 653) hydrogen bonds : angle 5.34910 ( 1815) SS BOND : bond 0.00962 ( 39) SS BOND : angle 3.03329 ( 78) covalent geometry : bond 0.00444 (23964) covalent geometry : angle 0.85992 (32619) *********************** 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 257 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 134 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: A 409 GLN cc_start: 0.2165 (OUTLIER) cc_final: 0.1660 (pm20) REVERT: A 655 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7296 (t-90) REVERT: A 740 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8172 (tmm) REVERT: A 894 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8829 (mt) REVERT: B 169 GLU cc_start: 0.4688 (OUTLIER) cc_final: 0.4326 (mm-30) REVERT: B 206 LYS cc_start: 0.8904 (tptt) cc_final: 0.8355 (ttmt) REVERT: B 207 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7157 (t-90) REVERT: B 270 LEU cc_start: -0.1998 (OUTLIER) cc_final: -0.2229 (mt) REVERT: B 271 GLN cc_start: 0.2796 (OUTLIER) cc_final: 0.2525 (tt0) REVERT: B 418 ILE cc_start: 0.2765 (OUTLIER) cc_final: 0.2563 (mm) REVERT: B 452 LEU cc_start: 0.0051 (OUTLIER) cc_final: -0.0265 (tp) REVERT: B 731 MET cc_start: 0.8634 (pmm) cc_final: 0.7544 (ptt) REVERT: B 1029 MET cc_start: 0.8173 (tmm) cc_final: 0.7740 (ttm) REVERT: C 166 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6634 (t) REVERT: C 233 ILE cc_start: 0.2714 (OUTLIER) cc_final: 0.1812 (tt) REVERT: C 449 TYR cc_start: 0.7616 (t80) cc_final: 0.7367 (t80) REVERT: C 489 TYR cc_start: 0.6581 (p90) cc_final: 0.6289 (m-80) REVERT: C 1050 MET cc_start: 0.7578 (mmp) cc_final: 0.7180 (mmp) outliers start: 123 outliers final: 57 residues processed: 244 average time/residue: 0.2944 time to fit residues: 122.0288 Evaluate side-chains 181 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 111 time to evaluate : 2.660 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL 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 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 655 HIS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR 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 1132 ILE Chi-restraints excluded: chain B residue 49 HIS 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 270 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE 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 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 560 LEU 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 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL 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 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 222 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 289 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 280 ASN A 519 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** C 115 GLN ** 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 = 0.4302 r_free = 0.4302 target = 0.158304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114048 restraints weight = 62513.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112156 restraints weight = 47611.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112379 restraints weight = 37386.486| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 24003 Z= 0.223 Angle : 0.865 21.212 32697 Z= 0.460 Chirality : 0.050 0.420 3723 Planarity : 0.006 0.094 4236 Dihedral : 6.919 50.230 3201 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.39 % Favored : 89.34 % Rotamer: Outliers : 5.21 % Allowed : 21.70 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2955 helix: 1.86 (0.22), residues: 570 sheet: -0.69 (0.26), residues: 375 loop : -2.82 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.003 0.001 HIS A1088 PHE 0.044 0.001 PHE B 55 TYR 0.026 0.001 TYR B1138 ARG 0.005 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.06281 ( 653) hydrogen bonds : angle 5.17831 ( 1815) SS BOND : bond 0.00836 ( 39) SS BOND : angle 3.10358 ( 78) covalent geometry : bond 0.00441 (23964) covalent geometry : angle 0.85266 (32619) *********************** 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 258 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 121 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: A 62 VAL cc_start: 0.1229 (OUTLIER) cc_final: 0.0945 (t) REVERT: A 95 THR cc_start: 0.3795 (OUTLIER) cc_final: 0.3553 (p) REVERT: A 394 ASN cc_start: 0.2363 (OUTLIER) cc_final: 0.2133 (p0) REVERT: A 409 GLN cc_start: 0.2027 (OUTLIER) cc_final: 0.1475 (pm20) REVERT: A 655 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.7097 (t-90) REVERT: A 740 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: A 894 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8792 (mt) REVERT: A 912 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 1106 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: B 55 PHE cc_start: 0.5490 (m-80) cc_final: 0.5050 (m-80) REVERT: B 169 GLU cc_start: 0.4707 (OUTLIER) cc_final: 0.4352 (mm-30) REVERT: B 206 LYS cc_start: 0.8916 (tptt) cc_final: 0.8535 (tppt) REVERT: B 382 VAL cc_start: 0.4942 (OUTLIER) cc_final: 0.4713 (t) REVERT: B 452 LEU cc_start: 0.0066 (OUTLIER) cc_final: -0.0351 (tp) REVERT: B 731 MET cc_start: 0.8555 (pmm) cc_final: 0.7662 (ptt) REVERT: B 1029 MET cc_start: 0.8155 (tmm) cc_final: 0.7814 (ttm) REVERT: C 166 CYS cc_start: 0.7825 (OUTLIER) cc_final: 0.6478 (t) REVERT: C 218 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7510 (mm-40) REVERT: C 360 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7338 (t0) REVERT: C 402 ILE cc_start: -0.1560 (OUTLIER) cc_final: -0.2129 (tt) REVERT: C 449 TYR cc_start: 0.7594 (t80) cc_final: 0.7335 (t80) REVERT: C 488 CYS cc_start: 0.3476 (OUTLIER) cc_final: 0.1730 (m) REVERT: C 489 TYR cc_start: 0.6594 (p90) cc_final: 0.6319 (m-80) REVERT: C 1050 MET cc_start: 0.7433 (mmp) cc_final: 0.7052 (mmp) outliers start: 137 outliers final: 68 residues processed: 245 average time/residue: 0.2924 time to fit residues: 122.4484 Evaluate side-chains 194 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 108 time to evaluate : 2.978 ------------------------------------------------------------------------------- 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 171 VAL 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 345 THR 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 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 655 HIS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR 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 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN 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 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE 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 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 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE 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 218 GLN 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 367 VAL 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 458 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 488 CYS 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 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 786 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 142 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 273 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 448 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B1106 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.157498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.117973 restraints weight = 63947.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115237 restraints weight = 48431.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116085 restraints weight = 45255.330| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 24003 Z= 0.283 Angle : 0.924 21.058 32697 Z= 0.497 Chirality : 0.052 0.429 3723 Planarity : 0.007 0.102 4236 Dihedral : 7.189 48.419 3201 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.44 % Favored : 88.29 % Rotamer: Outliers : 6.31 % Allowed : 20.56 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.15), residues: 2955 helix: 1.44 (0.22), residues: 584 sheet: -0.90 (0.24), residues: 404 loop : -2.97 (0.12), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.007 0.002 HIS C1058 PHE 0.046 0.002 PHE A 59 TYR 0.021 0.002 TYR A 279 ARG 0.009 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.08737 ( 653) hydrogen bonds : angle 5.58771 ( 1815) SS BOND : bond 0.00945 ( 39) SS BOND : angle 3.04309 ( 78) covalent geometry : bond 0.00620 (23964) covalent geometry : angle 0.91276 (32619) *********************** 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 276 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 110 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: A 508 TYR cc_start: 0.2889 (OUTLIER) cc_final: 0.1491 (m-80) REVERT: A 544 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6848 (m110) REVERT: A 655 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7508 (t-90) REVERT: A 740 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7994 (tmm) REVERT: A 894 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8895 (mt) REVERT: A 912 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 1094 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9130 (m) REVERT: B 55 PHE cc_start: 0.5270 (m-80) cc_final: 0.4794 (m-80) REVERT: B 169 GLU cc_start: 0.5162 (OUTLIER) cc_final: 0.4718 (mm-30) REVERT: B 207 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7426 (t-90) REVERT: B 382 VAL cc_start: 0.4763 (OUTLIER) cc_final: 0.4552 (t) REVERT: B 418 ILE cc_start: 0.2753 (OUTLIER) cc_final: 0.2532 (mm) REVERT: B 565 PHE cc_start: 0.5206 (t80) cc_final: 0.4992 (t80) REVERT: B 731 MET cc_start: 0.8578 (pmm) cc_final: 0.8100 (ptt) REVERT: B 935 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7875 (tp-100) REVERT: C 104 TRP cc_start: 0.6703 (p90) cc_final: 0.5961 (p90) REVERT: C 166 CYS cc_start: 0.7207 (OUTLIER) cc_final: 0.5829 (t) REVERT: C 218 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7458 (mm-40) REVERT: C 360 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7412 (t0) REVERT: C 402 ILE cc_start: -0.0834 (OUTLIER) cc_final: -0.1422 (tt) REVERT: C 449 TYR cc_start: 0.7393 (t80) cc_final: 0.7169 (t80) REVERT: C 488 CYS cc_start: 0.3486 (OUTLIER) cc_final: 0.2618 (m) REVERT: C 1050 MET cc_start: 0.7907 (mmp) cc_final: 0.7531 (mmp) outliers start: 166 outliers final: 95 residues processed: 265 average time/residue: 0.2887 time to fit residues: 129.0693 Evaluate side-chains 211 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 98 time to evaluate : 2.957 ------------------------------------------------------------------------------- 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 62 VAL 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 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 274 THR 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 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 508 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 559 PHE 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 778 THR 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 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 85 ASN 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 400 PHE 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 656 VAL Chi-restraints excluded: chain B residue 696 THR 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 878 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 993 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 108 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 218 GLN 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 367 VAL 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 423 TYR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 488 CYS 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 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 1116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 195 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 224 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.158336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111277 restraints weight = 63780.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114357 restraints weight = 38678.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114410 restraints weight = 24539.573| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 24003 Z= 0.227 Angle : 0.858 20.004 32697 Z= 0.457 Chirality : 0.050 0.458 3723 Planarity : 0.006 0.098 4236 Dihedral : 6.934 49.255 3201 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.42 % Favored : 89.31 % Rotamer: Outliers : 5.21 % Allowed : 21.40 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2955 helix: 1.61 (0.22), residues: 581 sheet: -0.89 (0.25), residues: 384 loop : -2.91 (0.12), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.007 0.001 HIS B 66 PHE 0.031 0.002 PHE A 329 TYR 0.021 0.001 TYR A 37 ARG 0.004 0.001 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.07164 ( 653) hydrogen bonds : angle 5.25569 ( 1815) SS BOND : bond 0.00852 ( 39) SS BOND : angle 2.97079 ( 78) covalent geometry : bond 0.00464 (23964) covalent geometry : angle 0.84698 (32619) *********************** 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 257 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 120 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6862 (m-80) REVERT: A 62 VAL cc_start: 0.1344 (OUTLIER) cc_final: 0.1120 (t) REVERT: A 95 THR cc_start: 0.3238 (OUTLIER) cc_final: 0.3008 (p) REVERT: A 409 GLN cc_start: 0.1731 (OUTLIER) cc_final: 0.1014 (pm20) REVERT: A 508 TYR cc_start: 0.2260 (OUTLIER) cc_final: 0.0979 (m-80) REVERT: A 655 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7639 (t-90) REVERT: A 740 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8041 (tmm) REVERT: A 894 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8900 (mt) REVERT: A 902 MET cc_start: 0.8653 (tpp) cc_final: 0.8318 (mmt) REVERT: B 53 ASP cc_start: 0.7474 (t0) cc_final: 0.7271 (t0) REVERT: B 55 PHE cc_start: 0.5126 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: B 169 GLU cc_start: 0.4519 (OUTLIER) cc_final: 0.4113 (mm-30) REVERT: B 207 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7536 (t-90) REVERT: B 731 MET cc_start: 0.8622 (pmm) cc_final: 0.8250 (ptt) REVERT: C 104 TRP cc_start: 0.6632 (p90) cc_final: 0.6230 (p90) REVERT: C 200 TYR cc_start: 0.7320 (m-80) cc_final: 0.6999 (m-80) REVERT: C 218 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7495 (mm-40) REVERT: C 360 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7426 (t0) REVERT: C 402 ILE cc_start: -0.1190 (OUTLIER) cc_final: -0.1851 (tt) REVERT: C 449 TYR cc_start: 0.7580 (t80) cc_final: 0.7336 (t80) REVERT: C 781 VAL cc_start: 0.8491 (t) cc_final: 0.8238 (t) REVERT: C 1029 MET cc_start: 0.8683 (ttp) cc_final: 0.8423 (tmm) REVERT: C 1050 MET cc_start: 0.7700 (mmp) cc_final: 0.7334 (mmp) outliers start: 137 outliers final: 86 residues processed: 244 average time/residue: 0.3570 time to fit residues: 149.6272 Evaluate side-chains 206 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 106 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 207 HIS 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 361 CYS 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 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR 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 559 PHE 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 778 THR 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 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 55 PHE 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 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 516 GLU 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 705 VAL 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 982 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 218 GLN 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 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 462 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 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 Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 265 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 171 optimal weight: 0.0050 chunk 84 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 273 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 overall best weight: 0.7174 ------------------------------------------------------------------------------- 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 540 ASN ** 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 = 0.4279 r_free = 0.4279 target = 0.160523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.121310 restraints weight = 64784.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118733 restraints weight = 41804.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.119305 restraints weight = 42512.472| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4410 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= 0.205 Angle : 0.829 18.568 32697 Z= 0.440 Chirality : 0.049 0.409 3723 Planarity : 0.006 0.094 4236 Dihedral : 6.707 52.248 3201 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.05 % Favored : 89.68 % Rotamer: Outliers : 4.10 % Allowed : 22.54 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2955 helix: 1.72 (0.22), residues: 585 sheet: -0.63 (0.25), residues: 377 loop : -2.83 (0.12), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.005 0.001 HIS A 519 PHE 0.030 0.001 PHE A 329 TYR 0.024 0.001 TYR A 37 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.05903 ( 653) hydrogen bonds : angle 4.98557 ( 1815) SS BOND : bond 0.00912 ( 39) SS BOND : angle 2.82586 ( 78) covalent geometry : bond 0.00402 (23964) covalent geometry : angle 0.81888 (32619) *********************** 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 230 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 122 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: A 62 VAL cc_start: 0.1096 (OUTLIER) cc_final: 0.0857 (t) REVERT: A 95 THR cc_start: 0.3471 (OUTLIER) cc_final: 0.3203 (p) REVERT: A 528 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.5349 (ptmm) REVERT: A 655 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7450 (t-90) REVERT: A 894 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8882 (mt) REVERT: B 169 GLU cc_start: 0.4829 (OUTLIER) cc_final: 0.4412 (mm-30) REVERT: B 207 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7400 (t-90) REVERT: B 731 MET cc_start: 0.8508 (pmm) cc_final: 0.8129 (ptt) REVERT: C 64 TRP cc_start: 0.6912 (t60) cc_final: 0.6675 (t60) REVERT: C 104 TRP cc_start: 0.6561 (p90) cc_final: 0.5812 (p90) REVERT: C 200 TYR cc_start: 0.7188 (m-80) cc_final: 0.6916 (m-80) REVERT: C 218 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7520 (mm-40) REVERT: C 360 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7453 (t0) REVERT: C 378 LYS cc_start: 0.8500 (pttm) cc_final: 0.8276 (pttt) REVERT: C 449 TYR cc_start: 0.7368 (t80) cc_final: 0.7129 (t80) REVERT: C 708 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8431 (m) outliers start: 108 outliers final: 72 residues processed: 219 average time/residue: 0.2930 time to fit residues: 109.3964 Evaluate side-chains 192 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 109 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 207 HIS 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 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 528 LYS Chi-restraints excluded: chain A residue 546 LEU 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 778 THR 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 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 242 LEU 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 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 516 GLU 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 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 464 PHE 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 571 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 59 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 161 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.160177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114121 restraints weight = 64728.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116694 restraints weight = 40700.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.116938 restraints weight = 26075.353| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 24003 Z= 0.202 Angle : 0.830 17.723 32697 Z= 0.436 Chirality : 0.049 0.401 3723 Planarity : 0.006 0.094 4236 Dihedral : 6.628 60.728 3201 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.81 % Favored : 89.92 % Rotamer: Outliers : 4.37 % Allowed : 22.23 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2955 helix: 1.80 (0.22), residues: 585 sheet: -0.51 (0.26), residues: 363 loop : -2.78 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 104 HIS 0.004 0.001 HIS A 519 PHE 0.030 0.001 PHE A 92 TYR 0.022 0.001 TYR A 37 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 653) hydrogen bonds : angle 4.85945 ( 1815) SS BOND : bond 0.00905 ( 39) SS BOND : angle 2.88264 ( 78) covalent geometry : bond 0.00397 (23964) covalent geometry : angle 0.81872 (32619) *********************** 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 237 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 122 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6409 (m-10) REVERT: A 170 TYR cc_start: 0.8920 (m-80) cc_final: 0.8675 (m-80) REVERT: A 195 LYS cc_start: 0.5999 (mmmt) cc_final: 0.4454 (ttpt) REVERT: A 508 TYR cc_start: 0.2360 (OUTLIER) cc_final: 0.1015 (m-80) REVERT: A 528 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.5728 (ptmm) REVERT: A 655 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: A 894 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 55 PHE cc_start: 0.5644 (m-80) cc_final: 0.4770 (m-80) REVERT: B 169 GLU cc_start: 0.4702 (OUTLIER) cc_final: 0.4293 (mm-30) REVERT: B 207 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7519 (t-90) REVERT: B 731 MET cc_start: 0.8517 (pmm) cc_final: 0.8119 (ptt) REVERT: B 935 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: C 64 TRP cc_start: 0.6864 (t60) cc_final: 0.6563 (t60) REVERT: C 104 TRP cc_start: 0.6542 (p90) cc_final: 0.5780 (p90) REVERT: C 200 TYR cc_start: 0.7234 (m-80) cc_final: 0.6887 (m-80) REVERT: C 218 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7502 (mm-40) REVERT: C 360 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7370 (t0) REVERT: C 449 TYR cc_start: 0.7359 (t80) cc_final: 0.7128 (t80) REVERT: C 708 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8297 (m) REVERT: C 1029 MET cc_start: 0.8672 (tmm) cc_final: 0.8470 (tmm) outliers start: 115 outliers final: 80 residues processed: 226 average time/residue: 0.3403 time to fit residues: 126.7814 Evaluate side-chains 207 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 116 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 274 THR 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 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 508 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 535 LYS 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 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 1001 LEU 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 242 LEU 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 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 569 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 785 VAL 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 1043 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 218 GLN 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 367 VAL 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 462 LYS 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 571 ASP 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 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 74 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 211 optimal weight: 0.0470 chunk 168 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 234 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 = 0.4280 r_free = 0.4280 target = 0.161208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122303 restraints weight = 64559.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119548 restraints weight = 43573.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120799 restraints weight = 44247.365| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 24003 Z= 0.203 Angle : 0.832 18.058 32697 Z= 0.436 Chirality : 0.049 0.399 3723 Planarity : 0.006 0.105 4236 Dihedral : 6.546 55.683 3201 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.08 % Favored : 89.61 % Rotamer: Outliers : 3.95 % Allowed : 22.84 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.15), residues: 2955 helix: 1.83 (0.22), residues: 585 sheet: -0.48 (0.26), residues: 368 loop : -2.75 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 104 HIS 0.004 0.001 HIS A 519 PHE 0.036 0.001 PHE B 55 TYR 0.023 0.001 TYR A 396 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.05702 ( 653) hydrogen bonds : angle 4.86357 ( 1815) SS BOND : bond 0.00948 ( 39) SS BOND : angle 2.88762 ( 78) covalent geometry : bond 0.00406 (23964) covalent geometry : angle 0.82106 (32619) *********************** 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 223 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 119 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6422 (m-10) REVERT: A 170 TYR cc_start: 0.8894 (m-80) cc_final: 0.8433 (m-80) REVERT: A 508 TYR cc_start: 0.2597 (OUTLIER) cc_final: 0.1232 (m-80) REVERT: A 655 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7633 (t-90) REVERT: A 894 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8900 (mt) REVERT: B 55 PHE cc_start: 0.5050 (m-80) cc_final: 0.4371 (m-80) REVERT: B 169 GLU cc_start: 0.4913 (OUTLIER) cc_final: 0.4480 (mm-30) REVERT: B 207 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7475 (t-90) REVERT: B 731 MET cc_start: 0.8500 (pmm) cc_final: 0.8145 (ptt) REVERT: B 935 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: C 64 TRP cc_start: 0.6950 (t60) cc_final: 0.6605 (t60) REVERT: C 104 TRP cc_start: 0.6533 (p90) cc_final: 0.5818 (p90) REVERT: C 200 TYR cc_start: 0.6981 (m-80) cc_final: 0.6655 (m-80) REVERT: C 218 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7522 (mm-40) REVERT: C 360 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7507 (t0) REVERT: C 449 TYR cc_start: 0.7190 (t80) cc_final: 0.6967 (t80) REVERT: C 708 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8388 (m) REVERT: C 1029 MET cc_start: 0.8760 (tmm) cc_final: 0.8501 (tmm) outliers start: 104 outliers final: 78 residues processed: 214 average time/residue: 0.3026 time to fit residues: 108.5644 Evaluate side-chains 205 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 117 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 274 THR 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 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 518 LEU 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 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 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 229 LEU Chi-restraints excluded: chain B residue 242 LEU 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 569 ILE Chi-restraints excluded: chain B residue 656 VAL 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 1043 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 218 GLN 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 367 VAL 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 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 571 ASP 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 761 THR Chi-restraints excluded: chain C residue 767 LEU 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 183 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 36 optimal weight: 0.0030 chunk 293 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 272 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 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 = 0.4272 r_free = 0.4272 target = 0.157060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106856 restraints weight = 61460.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110260 restraints weight = 30862.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112375 restraints weight = 20082.867| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.215 24003 Z= 0.196 Angle : 0.832 17.401 32697 Z= 0.433 Chirality : 0.050 0.399 3723 Planarity : 0.006 0.101 4236 Dihedral : 6.459 54.702 3201 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.61 % Favored : 90.08 % Rotamer: Outliers : 3.19 % Allowed : 23.68 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.15), residues: 2955 helix: 1.95 (0.22), residues: 579 sheet: -0.41 (0.26), residues: 378 loop : -2.70 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 104 HIS 0.006 0.001 HIS A 519 PHE 0.030 0.001 PHE A 329 TYR 0.030 0.001 TYR A 396 ARG 0.003 0.000 ARG C 466 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 653) hydrogen bonds : angle 4.74143 ( 1815) SS BOND : bond 0.00913 ( 39) SS BOND : angle 2.70009 ( 78) covalent geometry : bond 0.00385 (23964) covalent geometry : angle 0.82224 (32619) ********************** 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 207 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 123 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6784 (m-10) REVERT: A 195 LYS cc_start: 0.5833 (mmmt) cc_final: 0.4311 (ttpt) REVERT: A 508 TYR cc_start: 0.2672 (OUTLIER) cc_final: 0.1080 (m-80) REVERT: A 894 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8790 (mt) REVERT: B 55 PHE cc_start: 0.5199 (m-80) cc_final: 0.4653 (m-80) REVERT: B 169 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.4227 (mm-30) REVERT: B 207 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7461 (t-90) REVERT: B 935 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: C 64 TRP cc_start: 0.6938 (t60) cc_final: 0.6575 (t60) REVERT: C 104 TRP cc_start: 0.6524 (p90) cc_final: 0.5751 (p90) REVERT: C 200 TYR cc_start: 0.7342 (m-80) cc_final: 0.7031 (m-80) REVERT: C 218 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7484 (mm-40) REVERT: C 360 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7320 (t0) REVERT: C 449 TYR cc_start: 0.7456 (t80) cc_final: 0.7236 (t80) REVERT: C 1029 MET cc_start: 0.8737 (tmm) cc_final: 0.8370 (tmm) outliers start: 84 outliers final: 67 residues processed: 199 average time/residue: 0.3682 time to fit residues: 123.1496 Evaluate side-chains 192 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 117 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 207 HIS 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 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 549 THR 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 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 242 LEU 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 569 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 935 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 218 GLN 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 367 VAL 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 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 Chi-restraints excluded: chain C residue 1045 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 260 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.154288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103332 restraints weight = 59815.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106517 restraints weight = 30817.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108514 restraints weight = 20544.337| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.215 24003 Z= 0.253 Angle : 0.895 17.919 32697 Z= 0.472 Chirality : 0.052 0.480 3723 Planarity : 0.006 0.112 4236 Dihedral : 6.759 56.288 3201 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.17 % Favored : 88.49 % Rotamer: Outliers : 3.38 % Allowed : 23.76 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.15), residues: 2955 helix: 1.55 (0.22), residues: 592 sheet: -0.74 (0.25), residues: 373 loop : -2.72 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP A 104 HIS 0.008 0.002 HIS C 519 PHE 0.037 0.002 PHE C 559 TYR 0.027 0.002 TYR A 266 ARG 0.005 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.08131 ( 653) hydrogen bonds : angle 5.27418 ( 1815) SS BOND : bond 0.00932 ( 39) SS BOND : angle 2.87177 ( 78) covalent geometry : bond 0.00551 (23964) covalent geometry : angle 0.88487 (32619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9029.30 seconds wall clock time: 161 minutes 9.21 seconds (9669.21 seconds total)