Starting phenix.real_space_refine on Thu Mar 5 20:20:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhk_31997/03_2026/7vhk_31997.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhk_31997/03_2026/7vhk_31997.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 { model { file = "/net/cci-nas-00/data/ceres_data/7vhk_31997/03_2026/7vhk_31997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhk_31997/03_2026/7vhk_31997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vhk_31997/03_2026/7vhk_31997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhk_31997/03_2026/7vhk_31997.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 114 5.16 5 C 16056 2.51 5 N 4203 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25191 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: A, C Time building chain proxies: 9.90, per 1000 atoms: 0.39 Number of scatterers: 25191 At special positions: 0 Unit cell: (149.76, 157.04, 174.72, 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 114 16.00 O 4818 8.00 N 4203 7.00 C 16056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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=2.38 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=2.13 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.97 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.38 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.38 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.13 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.13 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.97 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.97 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " 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: 2.05 Conformation dependent library (CDL) restraints added in 993.8 milliseconds 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6036 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 54 sheets defined 22.9% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.678A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.963A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.347A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.756A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 740 through 750 removed outlier: 3.684A pdb=" N GLY B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.663A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 879 through 884 removed outlier: 4.258A pdb=" N ALA B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 902 Processing helix chain 'B' and resid 905 through 912 removed outlier: 4.279A pdb=" N LEU B 909 " --> pdb=" O THR B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 932 Processing helix chain 'B' and resid 933 through 939 removed outlier: 6.902A pdb=" N SER B 936 " --> pdb=" O SER B 933 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 937 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 957 removed outlier: 4.131A pdb=" N ASN B 946 " --> pdb=" O GLN B 942 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 948 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 950 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1025 removed outlier: 4.780A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1140 removed outlier: 3.895A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.678A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.963A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.348A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.756A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 740 through 750 removed outlier: 3.684A pdb=" N GLY A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 775 removed outlier: 3.663A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 859 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.258A pdb=" N ALA A 883 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.280A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 932 Processing helix chain 'A' and resid 933 through 939 removed outlier: 6.903A pdb=" N SER A 936 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 937 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 removed outlier: 4.130A pdb=" N ASN A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 950 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 4.779A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.895A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.677A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.964A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.347A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.756A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 740 through 750 removed outlier: 3.684A pdb=" N GLY C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 775 removed outlier: 3.664A pdb=" N PHE C 775 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 814 Processing helix chain 'C' and resid 842 through 849 Processing helix chain 'C' and resid 859 through 876 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.259A pdb=" N ALA C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 902 Processing helix chain 'C' and resid 905 through 912 removed outlier: 4.280A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 932 Processing helix chain 'C' and resid 933 through 939 removed outlier: 6.903A pdb=" N SER C 936 " --> pdb=" O SER C 933 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 937 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 957 removed outlier: 4.130A pdb=" N ASN C 946 " --> pdb=" O GLN C 942 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN C 948 " --> pdb=" O VAL C 944 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 950 " --> pdb=" O ASN C 946 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.780A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1140 removed outlier: 3.895A pdb=" N SER C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.531A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 230 removed outlier: 7.203A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.768A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.707A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.529A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.067A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.675A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.765A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 684 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 688 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 704 through 706 Processing sheet with id=AB4, first strand: chain 'B' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B1059 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B1059 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B1052 " --> pdb=" O ALA B1049 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B1049 " --> pdb=" O GLY B1052 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 727 through 729 removed outlier: 3.576A pdb=" N SER B 728 " --> pdb=" O THR B 852 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1074 through 1075 Processing sheet with id=AB8, first strand: chain 'B' and resid 1079 through 1083 removed outlier: 4.315A pdb=" N ALA B1080 " --> pdb=" O SER B1116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B1116 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1087 through 1089 Processing sheet with id=AC1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.531A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AC4, first strand: chain 'A' and resid 224 through 230 removed outlier: 7.203A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.769A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.706A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.529A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.068A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.675A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.765A pdb=" N VAL A 656 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR A 689 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 684 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 688 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 704 through 706 Processing sheet with id=AD4, first strand: chain 'A' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A1059 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A1059 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A1052 " --> pdb=" O ALA A1049 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1049 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 727 through 729 removed outlier: 3.576A pdb=" N SER A 728 " --> pdb=" O THR A 852 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1074 through 1075 Processing sheet with id=AD8, first strand: chain 'A' and resid 1079 through 1083 removed outlier: 4.315A pdb=" N ALA A1080 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A1116 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1087 through 1089 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.531A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE4, first strand: chain 'C' and resid 224 through 230 removed outlier: 7.202A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.768A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.706A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.529A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.067A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.675A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.766A pdb=" N VAL C 656 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 689 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 684 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 688 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 704 through 706 Processing sheet with id=AF4, first strand: chain 'C' and resid 710 through 721 removed outlier: 6.513A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C1059 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR C1060 " --> pdb=" O HIS C1041 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS C1041 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 710 through 721 removed outlier: 6.513A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C1059 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY C1052 " --> pdb=" O ALA C1049 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C1049 " --> pdb=" O GLY C1052 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 727 through 729 removed outlier: 3.577A pdb=" N SER C 728 " --> pdb=" O THR C 852 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AF8, first strand: chain 'C' and resid 1079 through 1083 removed outlier: 4.316A pdb=" N ALA C1080 " --> pdb=" O SER C1116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C1116 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1087 through 1089 783 hydrogen bonds defined for protein. 2178 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: 5.04 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8184 1.35 - 1.48: 6623 1.48 - 1.60: 10825 1.60 - 1.73: 0 1.73 - 1.85: 144 Bond restraints: 25776 Sorted by residual: bond pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CA SER B 596 " pdb=" C SER B 596 " ideal model delta sigma weight residual 1.529 1.515 0.014 1.04e-02 9.25e+03 1.78e+00 bond pdb=" CB CYS C 731 " pdb=" SG CYS C 731 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.76e+00 ... (remaining 25771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 33458 1.52 - 3.05: 1385 3.05 - 4.57: 176 4.57 - 6.09: 54 6.09 - 7.61: 12 Bond angle restraints: 35085 Sorted by residual: angle pdb=" N GLY B 750 " pdb=" CA GLY B 750 " pdb=" C GLY B 750 " ideal model delta sigma weight residual 110.20 117.39 -7.19 1.32e+00 5.74e-01 2.97e+01 angle pdb=" N GLY C 750 " pdb=" CA GLY C 750 " pdb=" C GLY C 750 " ideal model delta sigma weight residual 110.20 117.38 -7.18 1.32e+00 5.74e-01 2.96e+01 angle pdb=" N GLY A 750 " pdb=" CA GLY A 750 " pdb=" C GLY A 750 " ideal model delta sigma weight residual 110.20 117.36 -7.16 1.32e+00 5.74e-01 2.94e+01 angle pdb=" C PHE B 562 " pdb=" N GLN B 563 " pdb=" CA GLN B 563 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C PHE C 562 " pdb=" N GLN C 563 " pdb=" CA GLN C 563 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 ... (remaining 35080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 13755 17.63 - 35.27: 1293 35.27 - 52.90: 249 52.90 - 70.53: 28 70.53 - 88.17: 29 Dihedral angle restraints: 15354 sinusoidal: 5955 harmonic: 9399 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.80 87.80 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.79 87.79 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.78 87.78 1 1.00e+01 1.00e-02 9.23e+01 ... (remaining 15351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2407 0.035 - 0.070: 1090 0.070 - 0.105: 364 0.105 - 0.141: 96 0.141 - 0.176: 15 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CA PRO C 463 " pdb=" N PRO C 463 " pdb=" C PRO C 463 " pdb=" CB PRO C 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA PRO A 463 " pdb=" N PRO A 463 " pdb=" C PRO A 463 " pdb=" CB PRO A 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA PRO B 463 " pdb=" N PRO B 463 " pdb=" C PRO B 463 " pdb=" CB PRO B 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 3969 not shown) Planarity restraints: 4563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 173 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO B 174 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 174 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 173 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 174 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " 0.023 5.00e-02 4.00e+02 ... (remaining 4560 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 382 2.63 - 3.20: 23919 3.20 - 3.76: 36930 3.76 - 4.33: 53435 4.33 - 4.90: 87074 Nonbonded interactions: 201740 Sorted by model distance: nonbonded pdb=" OG1 THR B 385 " pdb=" OG1 THR A 415 " model vdw 2.059 3.040 nonbonded pdb=" OG1 THR A 385 " pdb=" OG1 THR C 415 " model vdw 2.117 3.040 nonbonded pdb=" OE2 GLU C 654 " pdb=" OG SER C 684 " model vdw 2.137 3.040 nonbonded pdb=" OE2 GLU B 654 " pdb=" OG SER B 684 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU A 654 " pdb=" OG SER A 684 " model vdw 2.138 3.040 ... (remaining 201735 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' 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: 2.710 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.230 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.007 0.350 25815 Z= 0.311 Angle : 0.792 20.687 35163 Z= 0.450 Chirality : 0.045 0.176 3972 Planarity : 0.004 0.041 4563 Dihedral : 14.124 88.168 9201 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.12), residues: 3213 helix: -1.90 (0.16), residues: 702 sheet: -3.42 (0.18), residues: 606 loop : -3.56 (0.12), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.012 0.001 TYR B 749 PHE 0.011 0.001 PHE B 541 TRP 0.017 0.002 TRP C 436 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00525 (25776) covalent geometry : angle 0.73068 (35085) SS BOND : bond 0.10184 ( 39) SS BOND : angle 6.55244 ( 78) hydrogen bonds : bond 0.23169 ( 753) hydrogen bonds : angle 9.69087 ( 2178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.873 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: B 64 TRP cc_start: 0.7707 (t60) cc_final: 0.7358 (t60) REVERT: B 655 HIS cc_start: 0.8254 (t70) cc_final: 0.8018 (t70) REVERT: B 847 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7575 (tttm) REVERT: B 1043 MET cc_start: 0.8174 (ptp) cc_final: 0.7962 (ptm) REVERT: A 65 PHE cc_start: 0.7213 (m-80) cc_final: 0.6767 (m-10) REVERT: A 104 TRP cc_start: 0.7420 (m-90) cc_final: 0.6979 (m-90) REVERT: A 191 GLU cc_start: 0.7148 (mp0) cc_final: 0.6239 (mt-10) REVERT: A 206 LYS cc_start: 0.8602 (tptt) cc_final: 0.8221 (tptt) REVERT: A 505 TYR cc_start: 0.6494 (m-80) cc_final: 0.6146 (m-80) REVERT: A 927 ILE cc_start: 0.8849 (tp) cc_final: 0.8595 (tp) REVERT: C 190 ARG cc_start: 0.6678 (mtm180) cc_final: 0.5306 (mtt180) REVERT: C 297 SER cc_start: 0.7953 (m) cc_final: 0.7711 (t) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1567 time to fit residues: 98.3357 Evaluate side-chains 237 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 207 HIS B 448 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 ASN B1081 HIS A 165 ASN A 448 ASN A 544 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 HIS A1101 ASN C 115 GLN C 165 ASN C 207 HIS C 211 ASN C 448 ASN C 544 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN C1081 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.166613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137044 restraints weight = 39058.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136017 restraints weight = 50327.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137155 restraints weight = 50624.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138613 restraints weight = 32228.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138890 restraints weight = 28598.096| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25815 Z= 0.181 Angle : 0.637 7.489 35163 Z= 0.333 Chirality : 0.045 0.185 3972 Planarity : 0.004 0.061 4563 Dihedral : 5.277 26.812 3468 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.92 % Allowed : 10.39 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.13), residues: 3213 helix: -0.77 (0.18), residues: 708 sheet: -2.85 (0.19), residues: 654 loop : -2.96 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.025 0.001 TYR C1060 PHE 0.023 0.002 PHE C 429 TRP 0.020 0.002 TRP C 436 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00429 (25776) covalent geometry : angle 0.62800 (35085) SS BOND : bond 0.00600 ( 39) SS BOND : angle 2.34505 ( 78) hydrogen bonds : bond 0.04600 ( 753) hydrogen bonds : angle 6.11382 ( 2178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5535 (t80) cc_final: 0.5074 (t80) REVERT: B 165 ASN cc_start: 0.5059 (OUTLIER) cc_final: 0.4432 (t0) REVERT: B 655 HIS cc_start: 0.8303 (t70) cc_final: 0.8099 (t70) REVERT: B 987 ASP cc_start: 0.6648 (m-30) cc_final: 0.6068 (m-30) REVERT: B 1010 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 1043 MET cc_start: 0.7832 (ptp) cc_final: 0.7588 (ptm) REVERT: A 65 PHE cc_start: 0.7471 (m-80) cc_final: 0.6805 (m-10) REVERT: A 104 TRP cc_start: 0.7267 (m-90) cc_final: 0.6794 (m-90) REVERT: A 121 ASN cc_start: 0.5040 (t0) cc_final: 0.4730 (m-40) REVERT: A 165 ASN cc_start: 0.5026 (OUTLIER) cc_final: 0.4532 (t0) REVERT: A 177 MET cc_start: 0.4975 (tmm) cc_final: 0.4670 (tmm) REVERT: A 927 ILE cc_start: 0.8737 (tp) cc_final: 0.8459 (tp) REVERT: C 65 PHE cc_start: 0.7586 (m-10) cc_final: 0.7349 (m-10) REVERT: C 297 SER cc_start: 0.8010 (m) cc_final: 0.7709 (t) REVERT: C 598 ILE cc_start: 0.8966 (mt) cc_final: 0.8660 (mt) outliers start: 54 outliers final: 35 residues processed: 325 average time/residue: 0.1412 time to fit residues: 77.8751 Evaluate side-chains 266 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 868 SER Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 75 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 165 optimal weight: 0.0980 chunk 240 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 316 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 317 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 409 GLN A 519 HIS ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN C 207 HIS C 519 HIS C 658 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142390 restraints weight = 38868.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141949 restraints weight = 51354.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143166 restraints weight = 44287.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143849 restraints weight = 31115.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144261 restraints weight = 31207.290| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25815 Z= 0.114 Angle : 0.548 7.731 35163 Z= 0.286 Chirality : 0.042 0.171 3972 Planarity : 0.004 0.062 4563 Dihedral : 4.711 23.816 3468 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.56 % Allowed : 13.48 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.14), residues: 3213 helix: 0.06 (0.19), residues: 711 sheet: -2.43 (0.19), residues: 651 loop : -2.62 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.020 0.001 TYR C1060 PHE 0.019 0.001 PHE A 562 TRP 0.017 0.001 TRP C 436 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00265 (25776) covalent geometry : angle 0.54293 (35085) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.72810 ( 78) hydrogen bonds : bond 0.03719 ( 753) hydrogen bonds : angle 5.26448 ( 2178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 289 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.4998 (t80) cc_final: 0.4718 (t80) REVERT: B 514 SER cc_start: 0.8010 (m) cc_final: 0.7603 (p) REVERT: B 987 ASP cc_start: 0.6393 (m-30) cc_final: 0.5984 (m-30) REVERT: B 1010 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 1022 MET cc_start: 0.8150 (tpp) cc_final: 0.7689 (ttm) REVERT: B 1043 MET cc_start: 0.7539 (ptp) cc_final: 0.7337 (ptm) REVERT: A 121 ASN cc_start: 0.4716 (t0) cc_final: 0.4484 (m-40) REVERT: A 552 LEU cc_start: 0.8720 (mm) cc_final: 0.8512 (mp) REVERT: A 774 VAL cc_start: 0.8951 (t) cc_final: 0.8625 (t) REVERT: A 927 ILE cc_start: 0.8600 (tp) cc_final: 0.8352 (tp) REVERT: A 950 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8280 (tm-30) REVERT: A 1022 MET cc_start: 0.8519 (tpp) cc_final: 0.7636 (ttm) REVERT: C 297 SER cc_start: 0.7809 (m) cc_final: 0.7574 (t) REVERT: C 449 TYR cc_start: 0.6259 (m-80) cc_final: 0.6015 (m-80) REVERT: C 658 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6792 (p0) REVERT: C 1043 MET cc_start: 0.7514 (ptp) cc_final: 0.7252 (ptm) outliers start: 72 outliers final: 47 residues processed: 339 average time/residue: 0.1320 time to fit residues: 76.9857 Evaluate side-chains 280 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 868 SER Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 301 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 544 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS A 115 GLN A 460 ASN A 658 ASN A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.165812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136687 restraints weight = 39079.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134918 restraints weight = 52265.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136205 restraints weight = 51173.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137363 restraints weight = 31896.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137677 restraints weight = 29811.542| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25815 Z= 0.214 Angle : 0.637 9.805 35163 Z= 0.326 Chirality : 0.045 0.210 3972 Planarity : 0.004 0.065 4563 Dihedral : 5.023 24.957 3468 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.45 % Allowed : 15.26 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.14), residues: 3213 helix: 0.01 (0.19), residues: 711 sheet: -2.28 (0.19), residues: 666 loop : -2.57 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.024 0.001 TYR A1060 PHE 0.031 0.002 PHE B 392 TRP 0.019 0.002 TRP B 436 HIS 0.005 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00512 (25776) covalent geometry : angle 0.62986 (35085) SS BOND : bond 0.00562 ( 39) SS BOND : angle 2.04876 ( 78) hydrogen bonds : bond 0.04233 ( 753) hydrogen bonds : angle 5.48013 ( 2178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 247 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5523 (t80) cc_final: 0.5241 (t80) REVERT: B 436 TRP cc_start: 0.6412 (OUTLIER) cc_final: 0.5665 (p-90) REVERT: B 514 SER cc_start: 0.8316 (m) cc_final: 0.7850 (p) REVERT: B 987 ASP cc_start: 0.6509 (m-30) cc_final: 0.6074 (m-30) REVERT: B 1043 MET cc_start: 0.7681 (ptp) cc_final: 0.7438 (ptm) REVERT: A 104 TRP cc_start: 0.6952 (m-90) cc_final: 0.6416 (m-90) REVERT: A 552 LEU cc_start: 0.8803 (mm) cc_final: 0.8554 (mp) REVERT: A 927 ILE cc_start: 0.8669 (tp) cc_final: 0.8397 (tp) REVERT: A 950 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 436 TRP cc_start: 0.6208 (OUTLIER) cc_final: 0.4382 (p-90) REVERT: C 660 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: C 950 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7993 (tm-30) REVERT: C 1043 MET cc_start: 0.7745 (ptp) cc_final: 0.7482 (ptm) outliers start: 97 outliers final: 72 residues processed: 312 average time/residue: 0.1230 time to fit residues: 67.1011 Evaluate side-chains 296 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 276 optimal weight: 1.9990 chunk 312 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 310 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139693 restraints weight = 38927.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139332 restraints weight = 49693.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140219 restraints weight = 42927.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141386 restraints weight = 30876.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141646 restraints weight = 28842.663| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25815 Z= 0.140 Angle : 0.569 9.447 35163 Z= 0.293 Chirality : 0.043 0.196 3972 Planarity : 0.004 0.066 4563 Dihedral : 4.700 24.688 3468 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.20 % Allowed : 17.04 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3213 helix: 0.32 (0.20), residues: 711 sheet: -2.10 (0.20), residues: 642 loop : -2.43 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.021 0.001 TYR A1060 PHE 0.022 0.001 PHE A 643 TRP 0.019 0.001 TRP B 353 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00336 (25776) covalent geometry : angle 0.56324 (35085) SS BOND : bond 0.00390 ( 39) SS BOND : angle 1.75318 ( 78) hydrogen bonds : bond 0.03694 ( 753) hydrogen bonds : angle 5.09373 ( 2178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 258 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5192 (t80) cc_final: 0.4947 (t80) REVERT: B 177 MET cc_start: 0.3933 (mmm) cc_final: 0.1253 (tmm) REVERT: B 436 TRP cc_start: 0.6382 (OUTLIER) cc_final: 0.5372 (p-90) REVERT: B 987 ASP cc_start: 0.6500 (m-30) cc_final: 0.6049 (m-30) REVERT: B 1010 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 1043 MET cc_start: 0.7582 (ptp) cc_final: 0.7357 (ptm) REVERT: A 552 LEU cc_start: 0.8773 (mm) cc_final: 0.8570 (mp) REVERT: A 927 ILE cc_start: 0.8617 (tp) cc_final: 0.8336 (tp) REVERT: A 950 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8055 (tm-30) REVERT: C 950 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 1043 MET cc_start: 0.7654 (ptp) cc_final: 0.7398 (ptm) REVERT: C 1103 TYR cc_start: 0.8610 (t80) cc_final: 0.8360 (t80) outliers start: 90 outliers final: 76 residues processed: 321 average time/residue: 0.1335 time to fit residues: 73.5885 Evaluate side-chains 305 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 228 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 123 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 302 optimal weight: 0.5980 chunk 305 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138848 restraints weight = 39139.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138667 restraints weight = 53795.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139775 restraints weight = 53899.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140553 restraints weight = 33003.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141275 restraints weight = 29577.191| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25815 Z= 0.150 Angle : 0.572 9.638 35163 Z= 0.293 Chirality : 0.044 0.174 3972 Planarity : 0.004 0.068 4563 Dihedral : 4.659 24.285 3468 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.74 % Allowed : 17.86 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 3213 helix: 0.43 (0.20), residues: 711 sheet: -2.00 (0.20), residues: 657 loop : -2.35 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.021 0.001 TYR A1060 PHE 0.023 0.001 PHE A 643 TRP 0.018 0.001 TRP B 436 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00359 (25776) covalent geometry : angle 0.56684 (35085) SS BOND : bond 0.00420 ( 39) SS BOND : angle 1.72269 ( 78) hydrogen bonds : bond 0.03695 ( 753) hydrogen bonds : angle 5.02827 ( 2178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 245 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5187 (t80) cc_final: 0.4711 (t80) REVERT: B 177 MET cc_start: 0.4270 (mmm) cc_final: 0.1361 (tmm) REVERT: B 353 TRP cc_start: 0.8098 (p90) cc_final: 0.7728 (p90) REVERT: B 436 TRP cc_start: 0.6420 (OUTLIER) cc_final: 0.5321 (p-90) REVERT: B 514 SER cc_start: 0.8108 (m) cc_final: 0.7757 (p) REVERT: B 946 ASN cc_start: 0.8296 (t0) cc_final: 0.8032 (t0) REVERT: B 987 ASP cc_start: 0.6468 (m-30) cc_final: 0.6031 (m-30) REVERT: B 1010 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 177 MET cc_start: 0.4734 (tmm) cc_final: 0.4475 (tmm) REVERT: A 552 LEU cc_start: 0.8774 (mm) cc_final: 0.8563 (mp) REVERT: A 927 ILE cc_start: 0.8549 (tp) cc_final: 0.8262 (tp) REVERT: C 190 ARG cc_start: 0.7056 (mtm180) cc_final: 0.5378 (mtt180) REVERT: C 436 TRP cc_start: 0.6208 (OUTLIER) cc_final: 0.4235 (p-90) REVERT: C 950 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 1043 MET cc_start: 0.7671 (ptp) cc_final: 0.7387 (ptm) outliers start: 105 outliers final: 85 residues processed: 324 average time/residue: 0.1257 time to fit residues: 70.4710 Evaluate side-chains 314 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 227 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 282 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 174 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141641 restraints weight = 38960.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141287 restraints weight = 53971.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142185 restraints weight = 47029.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143892 restraints weight = 33271.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144008 restraints weight = 28577.293| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25815 Z= 0.121 Angle : 0.546 8.850 35163 Z= 0.280 Chirality : 0.043 0.176 3972 Planarity : 0.004 0.065 4563 Dihedral : 4.458 23.790 3468 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.45 % Allowed : 18.57 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 3213 helix: 0.66 (0.20), residues: 711 sheet: -1.87 (0.20), residues: 657 loop : -2.25 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.020 0.001 TYR A1060 PHE 0.023 0.001 PHE A 643 TRP 0.016 0.001 TRP B 436 HIS 0.004 0.000 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00289 (25776) covalent geometry : angle 0.54136 (35085) SS BOND : bond 0.00418 ( 39) SS BOND : angle 1.60060 ( 78) hydrogen bonds : bond 0.03472 ( 753) hydrogen bonds : angle 4.82616 ( 2178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 262 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.4973 (t80) cc_final: 0.4678 (t80) REVERT: B 177 MET cc_start: 0.4011 (mmm) cc_final: 0.1395 (tmm) REVERT: B 353 TRP cc_start: 0.7997 (p90) cc_final: 0.7711 (p90) REVERT: B 355 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7721 (mmm160) REVERT: B 436 TRP cc_start: 0.6413 (OUTLIER) cc_final: 0.5353 (p-90) REVERT: B 514 SER cc_start: 0.8087 (m) cc_final: 0.7781 (p) REVERT: B 946 ASN cc_start: 0.8191 (t0) cc_final: 0.7867 (t0) REVERT: B 987 ASP cc_start: 0.6306 (m-30) cc_final: 0.5898 (m-30) REVERT: B 1010 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 1043 MET cc_start: 0.7505 (ptp) cc_final: 0.7210 (ptp) REVERT: A 143 VAL cc_start: 0.6767 (OUTLIER) cc_final: 0.6306 (t) REVERT: A 206 LYS cc_start: 0.8382 (tppt) cc_final: 0.8099 (tptp) REVERT: A 927 ILE cc_start: 0.8544 (tp) cc_final: 0.8264 (tp) REVERT: A 950 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 967 SER cc_start: 0.8057 (t) cc_final: 0.7112 (m) REVERT: A 1022 MET cc_start: 0.8606 (tpp) cc_final: 0.7640 (ttm) REVERT: C 190 ARG cc_start: 0.6952 (mtm180) cc_final: 0.5317 (mtt180) REVERT: C 436 TRP cc_start: 0.6242 (OUTLIER) cc_final: 0.4123 (p-90) REVERT: C 950 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 1043 MET cc_start: 0.7602 (ptp) cc_final: 0.7323 (ptm) outliers start: 97 outliers final: 85 residues processed: 332 average time/residue: 0.1361 time to fit residues: 76.3605 Evaluate side-chains 333 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 245 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 38 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 218 optimal weight: 30.0000 chunk 291 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.163122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133754 restraints weight = 39310.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133288 restraints weight = 54402.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134639 restraints weight = 55854.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135135 restraints weight = 33664.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136537 restraints weight = 29736.324| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 25815 Z= 0.300 Angle : 0.712 14.932 35163 Z= 0.365 Chirality : 0.048 0.192 3972 Planarity : 0.005 0.070 4563 Dihedral : 5.270 27.818 3468 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.09 % Allowed : 18.57 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.14), residues: 3213 helix: 0.14 (0.20), residues: 696 sheet: -2.07 (0.20), residues: 675 loop : -2.39 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 898 TYR 0.028 0.002 TYR B1060 PHE 0.028 0.002 PHE A 643 TRP 0.022 0.002 TRP B 436 HIS 0.009 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00721 (25776) covalent geometry : angle 0.70573 (35085) SS BOND : bond 0.00512 ( 39) SS BOND : angle 2.16273 ( 78) hydrogen bonds : bond 0.04579 ( 753) hydrogen bonds : angle 5.51140 ( 2178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 229 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5468 (t80) cc_final: 0.5186 (t80) REVERT: B 177 MET cc_start: 0.4485 (mmm) cc_final: 0.1680 (tmm) REVERT: B 436 TRP cc_start: 0.6782 (OUTLIER) cc_final: 0.5465 (p-90) REVERT: B 514 SER cc_start: 0.8559 (m) cc_final: 0.8085 (p) REVERT: B 987 ASP cc_start: 0.6525 (m-30) cc_final: 0.6058 (m-30) REVERT: A 104 TRP cc_start: 0.7060 (m-90) cc_final: 0.6567 (m-90) REVERT: A 143 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6502 (t) REVERT: A 927 ILE cc_start: 0.8665 (tp) cc_final: 0.8342 (tp) REVERT: C 143 VAL cc_start: 0.7569 (OUTLIER) cc_final: 0.7331 (t) REVERT: C 190 ARG cc_start: 0.7094 (mtm180) cc_final: 0.5409 (mtt180) REVERT: C 436 TRP cc_start: 0.6751 (OUTLIER) cc_final: 0.4593 (p-90) REVERT: C 895 MET cc_start: 0.8561 (tpp) cc_final: 0.8230 (tpt) REVERT: C 950 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 115 outliers final: 93 residues processed: 308 average time/residue: 0.1318 time to fit residues: 69.2368 Evaluate side-chains 316 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 219 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 150 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 299 optimal weight: 0.6980 chunk 304 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.168768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140275 restraints weight = 39244.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139924 restraints weight = 52654.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141201 restraints weight = 53542.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142004 restraints weight = 32018.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142767 restraints weight = 28920.891| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25815 Z= 0.120 Angle : 0.569 11.893 35163 Z= 0.291 Chirality : 0.043 0.160 3972 Planarity : 0.004 0.067 4563 Dihedral : 4.663 26.768 3468 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.34 % Allowed : 19.46 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.15), residues: 3213 helix: 0.57 (0.20), residues: 711 sheet: -1.81 (0.20), residues: 654 loop : -2.28 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.019 0.001 TYR A1060 PHE 0.027 0.001 PHE A 515 TRP 0.017 0.001 TRP B 436 HIS 0.004 0.000 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00284 (25776) covalent geometry : angle 0.56404 (35085) SS BOND : bond 0.00437 ( 39) SS BOND : angle 1.69905 ( 78) hydrogen bonds : bond 0.03526 ( 753) hydrogen bonds : angle 4.84079 ( 2178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 255 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5281 (t80) cc_final: 0.4960 (t80) REVERT: B 177 MET cc_start: 0.4194 (mmm) cc_final: 0.1504 (tmm) REVERT: B 353 TRP cc_start: 0.8030 (p90) cc_final: 0.7708 (p90) REVERT: B 436 TRP cc_start: 0.6615 (OUTLIER) cc_final: 0.5279 (p-90) REVERT: B 655 HIS cc_start: 0.7902 (t70) cc_final: 0.7459 (t70) REVERT: B 946 ASN cc_start: 0.8182 (t0) cc_final: 0.7914 (t0) REVERT: B 987 ASP cc_start: 0.6426 (m-30) cc_final: 0.5975 (m-30) REVERT: A 104 TRP cc_start: 0.6904 (m-90) cc_final: 0.6481 (m-90) REVERT: A 143 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6217 (t) REVERT: A 206 LYS cc_start: 0.8430 (tppt) cc_final: 0.8107 (tptt) REVERT: A 927 ILE cc_start: 0.8527 (tp) cc_final: 0.8301 (tp) REVERT: A 967 SER cc_start: 0.8155 (t) cc_final: 0.7224 (m) REVERT: A 1022 MET cc_start: 0.8625 (tpp) cc_final: 0.7707 (ttm) REVERT: C 143 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7276 (t) REVERT: C 190 ARG cc_start: 0.7106 (mtm180) cc_final: 0.5413 (mtt180) REVERT: C 436 TRP cc_start: 0.6515 (OUTLIER) cc_final: 0.4251 (p-90) REVERT: C 950 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 1043 MET cc_start: 0.7630 (ptp) cc_final: 0.7353 (ptm) outliers start: 94 outliers final: 78 residues processed: 326 average time/residue: 0.1379 time to fit residues: 75.4711 Evaluate side-chains 313 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 231 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 57 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 309 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN C 422 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.166945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136709 restraints weight = 39551.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135819 restraints weight = 52966.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137587 restraints weight = 48771.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138045 restraints weight = 31466.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139512 restraints weight = 27991.271| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25815 Z= 0.147 Angle : 0.587 11.406 35163 Z= 0.299 Chirality : 0.043 0.201 3972 Planarity : 0.004 0.068 4563 Dihedral : 4.663 25.118 3468 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.27 % Allowed : 19.74 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 3213 helix: 0.73 (0.20), residues: 693 sheet: -1.82 (0.20), residues: 669 loop : -2.20 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.020 0.001 TYR A1060 PHE 0.026 0.001 PHE A 65 TRP 0.017 0.001 TRP B 436 HIS 0.004 0.000 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00353 (25776) covalent geometry : angle 0.58163 (35085) SS BOND : bond 0.00449 ( 39) SS BOND : angle 1.74535 ( 78) hydrogen bonds : bond 0.03628 ( 753) hydrogen bonds : angle 4.87500 ( 2178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 236 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5404 (t80) cc_final: 0.5072 (t80) REVERT: B 177 MET cc_start: 0.4154 (mmm) cc_final: 0.1433 (tmm) REVERT: B 436 TRP cc_start: 0.6675 (OUTLIER) cc_final: 0.5284 (p-90) REVERT: B 465 GLU cc_start: 0.4287 (pm20) cc_final: 0.3575 (pt0) REVERT: B 946 ASN cc_start: 0.8237 (t0) cc_final: 0.7993 (t0) REVERT: B 987 ASP cc_start: 0.6483 (m-30) cc_final: 0.6040 (m-30) REVERT: A 104 TRP cc_start: 0.6842 (m-90) cc_final: 0.6417 (m-90) REVERT: A 143 VAL cc_start: 0.6694 (OUTLIER) cc_final: 0.6226 (t) REVERT: A 206 LYS cc_start: 0.8475 (tppt) cc_final: 0.8053 (tptp) REVERT: A 927 ILE cc_start: 0.8539 (tp) cc_final: 0.8246 (tp) REVERT: A 967 SER cc_start: 0.8278 (t) cc_final: 0.7320 (m) REVERT: C 143 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7301 (t) REVERT: C 190 ARG cc_start: 0.7189 (mtm180) cc_final: 0.5415 (mtt180) REVERT: C 436 TRP cc_start: 0.6595 (OUTLIER) cc_final: 0.4277 (p-90) REVERT: C 950 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 1043 MET cc_start: 0.7588 (ptp) cc_final: 0.7321 (ptm) outliers start: 92 outliers final: 83 residues processed: 305 average time/residue: 0.1344 time to fit residues: 69.9307 Evaluate side-chains 316 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 229 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1104 GLU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 280 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 99 optimal weight: 0.6980 chunk 168 optimal weight: 0.0770 chunk 238 optimal weight: 9.9990 chunk 303 optimal weight: 0.6980 chunk 271 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 770 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN C 422 ASN C 894 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.169950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139450 restraints weight = 39262.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138930 restraints weight = 47896.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140783 restraints weight = 44758.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141130 restraints weight = 28990.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142643 restraints weight = 26254.337| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25815 Z= 0.105 Angle : 0.554 9.838 35163 Z= 0.282 Chirality : 0.042 0.157 3972 Planarity : 0.004 0.064 4563 Dihedral : 4.365 22.920 3468 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.74 % Allowed : 20.85 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.15), residues: 3213 helix: 1.09 (0.21), residues: 687 sheet: -1.78 (0.20), residues: 645 loop : -2.10 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.017 0.001 TYR A1060 PHE 0.022 0.001 PHE A 643 TRP 0.015 0.001 TRP B 436 HIS 0.004 0.000 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00247 (25776) covalent geometry : angle 0.54994 (35085) SS BOND : bond 0.00380 ( 39) SS BOND : angle 1.55824 ( 78) hydrogen bonds : bond 0.03278 ( 753) hydrogen bonds : angle 4.59398 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.36 seconds wall clock time: 60 minutes 20.64 seconds (3620.64 seconds total)