Starting phenix.real_space_refine on Tue Mar 19 14:17:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz1_32901/03_2024/7wz1_32901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz1_32901/03_2024/7wz1_32901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz1_32901/03_2024/7wz1_32901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz1_32901/03_2024/7wz1_32901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz1_32901/03_2024/7wz1_32901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz1_32901/03_2024/7wz1_32901.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 111 5.16 5 C 15661 2.51 5 N 4033 2.21 5 O 4662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24467 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8032 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 973} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8000 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.50, per 1000 atoms: 0.51 Number of scatterers: 24467 At special positions: 0 Unit cell: (139.384, 145.768, 167.048, 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 111 16.00 O 4662 8.00 N 4033 7.00 C 15661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 9.71 Conformation dependent library (CDL) restraints added in 4.3 seconds 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 49 sheets defined 22.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.936A pdb=" N TYR A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.525A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.142A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.613A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.142A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.549A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 782 removed outlier: 3.555A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.721A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.363A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 937 removed outlier: 3.858A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.857A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.169A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.512A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.646A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.415A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.903A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.579A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 761 through 778 removed outlier: 3.817A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.640A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.926A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.629A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.579A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.518A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 979 through 983 removed outlier: 3.589A pdb=" N ARG B 983 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.528A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.980A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.913A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.863A pdb=" N GLY C 447 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 605 removed outlier: 3.858A pdb=" N THR C 604 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 605 " --> pdb=" O THR C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 601 through 605' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 761 through 780 Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 930 through 940 removed outlier: 3.602A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 945 No H-bonds generated for 'chain 'C' and resid 943 through 945' Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.034A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.182A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.995A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.510A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.652A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.984A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.792A pdb=" N ILE A 201 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.742A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 186 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.608A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.662A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.884A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.160A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 394 through 400 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.543A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.357A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.274A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.291A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.291A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.773A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AC3, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.343A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.161A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.618A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 90 through 94 removed outlier: 7.285A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.332A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.631A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.521A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.106A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD4, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.762A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.145A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.642A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B1086 " --> pdb=" O HIS B1083 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.764A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 226 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.538A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.556A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.842A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.502A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.511A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.462A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.859A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.972A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 722 removed outlier: 3.564A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.552A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1121 701 hydrogen bonds defined for protein. 1938 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: 9.51 Time building geometry restraints manager: 10.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7763 1.34 - 1.46: 4999 1.46 - 1.58: 12140 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25040 Sorted by residual: bond pdb=" CA VAL C 67 " pdb=" C VAL C 67 " ideal model delta sigma weight residual 1.526 1.490 0.035 1.13e-02 7.83e+03 9.83e+00 bond pdb=" CA SER A 937 " pdb=" C SER A 937 " ideal model delta sigma weight residual 1.522 1.486 0.037 1.43e-02 4.89e+03 6.60e+00 bond pdb=" CA HIS C 66 " pdb=" C HIS C 66 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.22e-02 6.72e+03 6.59e+00 bond pdb=" C GLN C 173 " pdb=" N PRO C 174 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.12e-02 7.97e+03 5.39e+00 bond pdb=" CA LEU A 938 " pdb=" C LEU A 938 " ideal model delta sigma weight residual 1.520 1.489 0.031 1.37e-02 5.33e+03 5.11e+00 ... (remaining 25035 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.12: 525 105.12 - 112.34: 12668 112.34 - 119.56: 7427 119.56 - 126.79: 13209 126.79 - 134.01: 266 Bond angle restraints: 34095 Sorted by residual: angle pdb=" N LEU A 938 " pdb=" CA LEU A 938 " pdb=" C LEU A 938 " ideal model delta sigma weight residual 114.64 97.90 16.74 1.52e+00 4.33e-01 1.21e+02 angle pdb=" C VAL C 67 " pdb=" CA VAL C 67 " pdb=" CB VAL C 67 " ideal model delta sigma weight residual 111.23 104.99 6.24 1.08e+00 8.57e-01 3.34e+01 angle pdb=" C PHE C 79 " pdb=" N ASP C 80 " pdb=" CA ASP C 80 " ideal model delta sigma weight residual 122.99 115.36 7.63 1.41e+00 5.03e-01 2.93e+01 angle pdb=" C ASP B 80 " pdb=" N ASN B 81 " pdb=" CA ASN B 81 " ideal model delta sigma weight residual 123.16 117.63 5.53 1.23e+00 6.61e-01 2.02e+01 angle pdb=" N ILE B 909 " pdb=" CA ILE B 909 " pdb=" C ILE B 909 " ideal model delta sigma weight residual 113.47 109.11 4.36 1.01e+00 9.80e-01 1.86e+01 ... (remaining 34090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14570 17.89 - 35.77: 614 35.77 - 53.66: 97 53.66 - 71.54: 19 71.54 - 89.43: 5 Dihedral angle restraints: 15305 sinusoidal: 6285 harmonic: 9020 Sorted by residual: dihedral pdb=" CA CYS A 291 " pdb=" C CYS A 291 " pdb=" N ALA A 292 " pdb=" CA ALA A 292 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -113.52 27.52 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CA SER B 112 " pdb=" C SER B 112 " pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 15302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3191 0.051 - 0.102: 657 0.102 - 0.152: 101 0.152 - 0.203: 5 0.203 - 0.254: 3 Chirality restraints: 3957 Sorted by residual: chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LEU A 938 " pdb=" N LEU A 938 " pdb=" C LEU A 938 " pdb=" CB LEU A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3954 not shown) Planarity restraints: 4407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 986 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO C 373 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 986 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.026 5.00e-02 4.00e+02 ... (remaining 4404 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2437 2.75 - 3.29: 24591 3.29 - 3.82: 40055 3.82 - 4.36: 46190 4.36 - 4.90: 79010 Nonbonded interactions: 192283 Sorted by model distance: nonbonded pdb=" O PHE A 106 " pdb=" OG SER A 116 " model vdw 2.212 2.440 nonbonded pdb=" OD2 ASP C 808 " pdb=" OG SER C 810 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR C 29 " pdb=" OD1 ASP C 215 " model vdw 2.250 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.260 2.440 nonbonded pdb=" O GLN B 957 " pdb=" OG1 THR B 961 " model vdw 2.262 2.440 ... (remaining 192278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 26 through 68 or resid 80 through 1147 or resid 1301 throu \ gh 1309)) selection = (chain 'C' and (resid 26 through 68 or resid 80 through 243 or resid 262 through \ 1147 or resid 1301 through 1309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 8.110 Check model and map are aligned: 0.320 Set scattering table: 0.250 Process input model: 65.190 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.003 0.043 25040 Z= 0.188 Angle : 0.658 16.744 34095 Z= 0.410 Chirality : 0.042 0.254 3957 Planarity : 0.004 0.055 4379 Dihedral : 9.689 89.429 9374 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.40 % Allowed : 8.25 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.13), residues: 3044 helix: -0.37 (0.20), residues: 645 sheet: -3.05 (0.19), residues: 530 loop : -3.76 (0.11), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 886 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.001 PHE C 375 TYR 0.008 0.001 TYR A 160 ARG 0.002 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 802 time to evaluate : 2.909 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7739 (m-80) cc_final: 0.6731 (m-80) REVERT: A 45 SER cc_start: 0.7843 (t) cc_final: 0.7639 (p) REVERT: A 52 GLN cc_start: 0.6968 (tp40) cc_final: 0.6725 (tm-30) REVERT: A 104 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.7362 (m-90) REVERT: A 129 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7300 (mtmm) REVERT: A 188 ARG cc_start: 0.7391 (ptp-110) cc_final: 0.7098 (ptp90) REVERT: A 235 ILE cc_start: 0.8470 (mm) cc_final: 0.8009 (mm) REVERT: A 237 ARG cc_start: 0.7340 (ttm110) cc_final: 0.7006 (mtp85) REVERT: A 238 PHE cc_start: 0.6719 (t80) cc_final: 0.6505 (t80) REVERT: A 267 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 269 TYR cc_start: 0.7780 (m-80) cc_final: 0.7557 (m-80) REVERT: A 280 ASN cc_start: 0.7510 (t0) cc_final: 0.7263 (t0) REVERT: A 281 GLU cc_start: 0.7475 (pp20) cc_final: 0.6993 (pp20) REVERT: A 340 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5790 (pm20) REVERT: A 351 TYR cc_start: 0.6501 (p90) cc_final: 0.6074 (p90) REVERT: A 380 TYR cc_start: 0.6929 (m-80) cc_final: 0.6492 (m-10) REVERT: A 452 LEU cc_start: 0.7930 (tt) cc_final: 0.7249 (mm) REVERT: A 546 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7707 (tm) REVERT: A 558 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7526 (mtpp) REVERT: A 565 PHE cc_start: 0.6229 (m-10) cc_final: 0.5956 (m-10) REVERT: A 574 ASP cc_start: 0.7682 (t70) cc_final: 0.7417 (t0) REVERT: A 578 ASP cc_start: 0.7183 (t0) cc_final: 0.6950 (t0) REVERT: A 586 ASP cc_start: 0.7163 (t0) cc_final: 0.6805 (t0) REVERT: A 599 THR cc_start: 0.8313 (m) cc_final: 0.7922 (t) REVERT: A 654 GLU cc_start: 0.6872 (pm20) cc_final: 0.6591 (pm20) REVERT: A 660 TYR cc_start: 0.8417 (m-80) cc_final: 0.7493 (m-80) REVERT: A 670 ILE cc_start: 0.8420 (mm) cc_final: 0.8065 (mt) REVERT: A 675 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6631 (mm-40) REVERT: A 691 SER cc_start: 0.8092 (t) cc_final: 0.7887 (p) REVERT: A 693 ILE cc_start: 0.8539 (pt) cc_final: 0.8297 (pt) REVERT: A 707 TYR cc_start: 0.7594 (t80) cc_final: 0.7334 (t80) REVERT: A 751 ASN cc_start: 0.7843 (m-40) cc_final: 0.7618 (m110) REVERT: A 768 THR cc_start: 0.8174 (m) cc_final: 0.7897 (p) REVERT: A 774 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6785 (mp10) REVERT: A 779 GLN cc_start: 0.7848 (tt0) cc_final: 0.7537 (mt0) REVERT: A 787 GLN cc_start: 0.7659 (mt0) cc_final: 0.7167 (mt0) REVERT: A 819 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6511 (mt-10) REVERT: A 825 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8232 (mtpp) REVERT: A 867 ASP cc_start: 0.7254 (m-30) cc_final: 0.7005 (m-30) REVERT: A 869 MET cc_start: 0.7895 (mtt) cc_final: 0.7680 (mtp) REVERT: A 904 TYR cc_start: 0.6676 (m-10) cc_final: 0.6307 (m-10) REVERT: A 918 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 949 GLN cc_start: 0.7550 (mm110) cc_final: 0.7200 (mm-40) REVERT: A 993 ILE cc_start: 0.8343 (tp) cc_final: 0.7783 (tp) REVERT: A 998 THR cc_start: 0.7934 (m) cc_final: 0.7660 (p) REVERT: A 1029 MET cc_start: 0.7863 (ttm) cc_final: 0.7663 (ttm) REVERT: A 1030 SER cc_start: 0.8746 (m) cc_final: 0.8209 (t) REVERT: A 1072 GLU cc_start: 0.7842 (pm20) cc_final: 0.7524 (pm20) REVERT: A 1073 LYS cc_start: 0.8162 (mtpm) cc_final: 0.7956 (mtpp) REVERT: A 1081 ILE cc_start: 0.8006 (pt) cc_final: 0.7793 (mt) REVERT: A 1097 SER cc_start: 0.8430 (t) cc_final: 0.8081 (p) REVERT: A 1102 TRP cc_start: 0.8570 (m100) cc_final: 0.8082 (m100) REVERT: A 1111 GLU cc_start: 0.7608 (tt0) cc_final: 0.7212 (tt0) REVERT: A 1125 ASN cc_start: 0.7410 (p0) cc_final: 0.6916 (p0) REVERT: B 83 VAL cc_start: 0.5712 (OUTLIER) cc_final: 0.5433 (t) REVERT: B 105 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7639 (pt) REVERT: B 106 PHE cc_start: 0.7818 (m-80) cc_final: 0.7569 (m-10) REVERT: B 169 GLU cc_start: 0.7077 (pm20) cc_final: 0.6810 (pm20) REVERT: B 201 ILE cc_start: 0.8500 (mt) cc_final: 0.7984 (tt) REVERT: B 202 TYR cc_start: 0.7675 (m-80) cc_final: 0.7465 (m-80) REVERT: B 224 GLU cc_start: 0.6684 (pm20) cc_final: 0.6401 (pm20) REVERT: B 289 VAL cc_start: 0.7477 (t) cc_final: 0.7131 (m) REVERT: B 290 ASP cc_start: 0.6967 (p0) cc_final: 0.6660 (p0) REVERT: B 356 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7872 (mtpp) REVERT: B 360 ASN cc_start: 0.8290 (m110) cc_final: 0.8068 (m110) REVERT: B 380 TYR cc_start: 0.7965 (m-80) cc_final: 0.7122 (m-80) REVERT: B 551 VAL cc_start: 0.8694 (t) cc_final: 0.8487 (p) REVERT: B 557 LYS cc_start: 0.8278 (ptpp) cc_final: 0.8037 (ptpt) REVERT: B 558 LYS cc_start: 0.8190 (mppt) cc_final: 0.7660 (mppt) REVERT: B 644 GLN cc_start: 0.8208 (tp40) cc_final: 0.7979 (tp40) REVERT: B 650 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 654 GLU cc_start: 0.7375 (pm20) cc_final: 0.7152 (pm20) REVERT: B 698 SER cc_start: 0.7918 (t) cc_final: 0.7185 (p) REVERT: B 699 LEU cc_start: 0.8223 (mt) cc_final: 0.7904 (mt) REVERT: B 705 VAL cc_start: 0.8642 (t) cc_final: 0.8270 (m) REVERT: B 736 VAL cc_start: 0.8582 (m) cc_final: 0.8296 (t) REVERT: B 810 SER cc_start: 0.8275 (t) cc_final: 0.8074 (p) REVERT: B 819 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 821 LEU cc_start: 0.8392 (tp) cc_final: 0.7940 (tt) REVERT: B 850 ILE cc_start: 0.8635 (mm) cc_final: 0.8360 (tp) REVERT: B 868 GLU cc_start: 0.6479 (tp30) cc_final: 0.6012 (tp30) REVERT: B 922 LEU cc_start: 0.8209 (tp) cc_final: 0.8002 (tt) REVERT: B 950 ASP cc_start: 0.6919 (t70) cc_final: 0.6537 (t70) REVERT: B 975 SER cc_start: 0.8453 (m) cc_final: 0.8190 (t) REVERT: B 988 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6694 (tp30) REVERT: B 990 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: B 993 ILE cc_start: 0.8414 (tp) cc_final: 0.8165 (tp) REVERT: B 1029 MET cc_start: 0.8273 (tpp) cc_final: 0.7902 (tpp) REVERT: B 1081 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7525 (pt) REVERT: B 1097 SER cc_start: 0.8855 (t) cc_final: 0.8487 (p) REVERT: B 1104 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 1111 GLU cc_start: 0.7654 (tt0) cc_final: 0.7433 (tt0) REVERT: C 40 ASP cc_start: 0.6741 (p0) cc_final: 0.6462 (p0) REVERT: C 51 THR cc_start: 0.8419 (p) cc_final: 0.8192 (p) REVERT: C 105 ILE cc_start: 0.7383 (mm) cc_final: 0.7133 (mp) REVERT: C 117 LEU cc_start: 0.7543 (mt) cc_final: 0.7190 (mt) REVERT: C 212 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4757 (pm20) REVERT: C 224 GLU cc_start: 0.7319 (pm20) cc_final: 0.7112 (pm20) REVERT: C 238 PHE cc_start: 0.7618 (t80) cc_final: 0.7311 (t80) REVERT: C 269 TYR cc_start: 0.8201 (m-80) cc_final: 0.7835 (m-80) REVERT: C 347 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6040 (t80) REVERT: C 349 SER cc_start: 0.7428 (p) cc_final: 0.7170 (t) REVERT: C 377 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: C 398 ASP cc_start: 0.6622 (t70) cc_final: 0.6401 (t70) REVERT: C 414 GLN cc_start: 0.7182 (mp-120) cc_final: 0.6838 (mp10) REVERT: C 420 ASP cc_start: 0.6935 (t0) cc_final: 0.6566 (t0) REVERT: C 427 ASP cc_start: 0.6600 (t70) cc_final: 0.6332 (t70) REVERT: C 442 ASP cc_start: 0.7161 (m-30) cc_final: 0.6932 (m-30) REVERT: C 553 THR cc_start: 0.8226 (p) cc_final: 0.8015 (t) REVERT: C 565 PHE cc_start: 0.6584 (m-10) cc_final: 0.6182 (m-10) REVERT: C 675 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6817 (mm-40) REVERT: C 707 TYR cc_start: 0.7533 (t80) cc_final: 0.6644 (t80) REVERT: C 725 GLU cc_start: 0.6769 (tt0) cc_final: 0.6225 (tt0) REVERT: C 750 SER cc_start: 0.8746 (m) cc_final: 0.8254 (p) REVERT: C 751 ASN cc_start: 0.7961 (m-40) cc_final: 0.7516 (m-40) REVERT: C 776 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8057 (tttp) REVERT: C 779 GLN cc_start: 0.6789 (tt0) cc_final: 0.6550 (tm-30) REVERT: C 788 ILE cc_start: 0.8369 (mm) cc_final: 0.8120 (mm) REVERT: C 825 LYS cc_start: 0.8249 (tppt) cc_final: 0.7907 (ttmm) REVERT: C 868 GLU cc_start: 0.7078 (tp30) cc_final: 0.6739 (tp30) REVERT: C 904 TYR cc_start: 0.6811 (m-10) cc_final: 0.6427 (m-10) REVERT: C 914 ASN cc_start: 0.7475 (p0) cc_final: 0.6940 (p0) REVERT: C 921 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8125 (mmmm) REVERT: C 964 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7886 (ttmm) REVERT: C 975 SER cc_start: 0.8527 (m) cc_final: 0.8304 (t) REVERT: C 983 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7857 (ttm110) REVERT: C 1018 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8016 (mt) REVERT: C 1105 THR cc_start: 0.7596 (t) cc_final: 0.7325 (t) REVERT: C 1111 GLU cc_start: 0.7003 (tt0) cc_final: 0.6746 (tt0) REVERT: C 1139 ASP cc_start: 0.7929 (t70) cc_final: 0.7719 (t0) outliers start: 144 outliers final: 46 residues processed: 909 average time/residue: 0.3805 time to fit residues: 540.9214 Evaluate side-chains 706 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 645 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 173 GLN A 181 GLN A 314 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 437 ASN A 450 ASN A 519 HIS A 540 ASN A 544 ASN A 563 GLN A 580 GLN A 613 GLN A 784 GLN A 853 GLN A 901 GLN A 907 ASN A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1083 HIS A1101 HIS B 99 ASN B 314 GLN B 317 ASN B 321 GLN B 334 ASN B 370 ASN B 409 GLN B 448 ASN B 580 GLN B 644 GLN B 779 GLN B 784 GLN B 853 GLN B 895 GLN B 901 GLN B 907 ASN B 955 ASN B 957 GLN B1005 GLN B1010 GLN B1048 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 321 GLN C 360 ASN C 394 ASN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 540 ASN C 563 GLN C 613 GLN C 658 ASN C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 853 GLN C 895 GLN C 901 GLN C 926 GLN C 965 GLN C1002 GLN C1011 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25040 Z= 0.352 Angle : 0.662 11.545 34095 Z= 0.339 Chirality : 0.048 0.324 3957 Planarity : 0.005 0.055 4379 Dihedral : 7.880 82.678 4029 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 6.00 % Allowed : 15.30 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.14), residues: 3044 helix: 0.27 (0.21), residues: 650 sheet: -2.74 (0.20), residues: 515 loop : -3.29 (0.12), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 104 HIS 0.011 0.002 HIS A 519 PHE 0.038 0.002 PHE C1121 TYR 0.024 0.002 TYR C 265 ARG 0.006 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 718 time to evaluate : 2.643 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8121 (mp) cc_final: 0.7920 (mt) REVERT: A 65 PHE cc_start: 0.7061 (m-10) cc_final: 0.6786 (m-10) REVERT: A 84 LEU cc_start: 0.8415 (pt) cc_final: 0.7986 (pt) REVERT: A 102 ARG cc_start: 0.6848 (mtm-85) cc_final: 0.6635 (mtm-85) REVERT: A 104 TRP cc_start: 0.7605 (OUTLIER) cc_final: 0.7367 (m-90) REVERT: A 129 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7220 (mtmm) REVERT: A 188 ARG cc_start: 0.7588 (ptp-110) cc_final: 0.7129 (ptp90) REVERT: A 238 PHE cc_start: 0.7259 (t80) cc_final: 0.7025 (t80) REVERT: A 267 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 269 TYR cc_start: 0.7985 (m-80) cc_final: 0.7571 (m-10) REVERT: A 281 GLU cc_start: 0.7650 (pp20) cc_final: 0.7445 (pp20) REVERT: A 287 ASP cc_start: 0.7625 (p0) cc_final: 0.7354 (p0) REVERT: A 307 THR cc_start: 0.8223 (m) cc_final: 0.7882 (p) REVERT: A 340 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6164 (pm20) REVERT: A 351 TYR cc_start: 0.6522 (p90) cc_final: 0.6037 (p90) REVERT: A 358 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6367 (pt) REVERT: A 380 TYR cc_start: 0.6913 (m-80) cc_final: 0.6486 (m-10) REVERT: A 386 LYS cc_start: 0.8305 (mttp) cc_final: 0.8049 (mttt) REVERT: A 452 LEU cc_start: 0.7980 (tt) cc_final: 0.7412 (mm) REVERT: A 468 ILE cc_start: 0.2421 (OUTLIER) cc_final: 0.2166 (pp) REVERT: A 546 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7940 (tm) REVERT: A 558 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7702 (mtpp) REVERT: A 562 PHE cc_start: 0.7709 (p90) cc_final: 0.7448 (p90) REVERT: A 569 ILE cc_start: 0.8020 (pt) cc_final: 0.7702 (mp) REVERT: A 588 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8584 (p) REVERT: A 599 THR cc_start: 0.8489 (m) cc_final: 0.8150 (t) REVERT: A 664 ILE cc_start: 0.8496 (mm) cc_final: 0.8273 (mt) REVERT: A 675 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7084 (mm-40) REVERT: A 692 ILE cc_start: 0.8133 (mt) cc_final: 0.7590 (mt) REVERT: A 693 ILE cc_start: 0.8313 (pt) cc_final: 0.8087 (pt) REVERT: A 707 TYR cc_start: 0.7795 (t80) cc_final: 0.7576 (t80) REVERT: A 751 ASN cc_start: 0.7936 (m-40) cc_final: 0.7641 (m-40) REVERT: A 774 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7092 (mp10) REVERT: A 808 ASP cc_start: 0.7666 (t0) cc_final: 0.7462 (t0) REVERT: A 855 PHE cc_start: 0.8186 (m-80) cc_final: 0.7348 (m-80) REVERT: A 949 GLN cc_start: 0.7845 (mm110) cc_final: 0.7399 (mm-40) REVERT: A 995 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7635 (ttm170) REVERT: A 998 THR cc_start: 0.7996 (m) cc_final: 0.7717 (p) REVERT: A 1094 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7839 (m) REVERT: A 1097 SER cc_start: 0.8413 (t) cc_final: 0.7794 (p) REVERT: B 83 VAL cc_start: 0.6092 (OUTLIER) cc_final: 0.5748 (t) REVERT: B 169 GLU cc_start: 0.7579 (pm20) cc_final: 0.7180 (pm20) REVERT: B 177 MET cc_start: 0.6430 (tmt) cc_final: 0.6049 (tmt) REVERT: B 201 ILE cc_start: 0.8353 (mt) cc_final: 0.7790 (tt) REVERT: B 224 GLU cc_start: 0.6600 (pm20) cc_final: 0.6257 (pm20) REVERT: B 228 ASP cc_start: 0.6427 (t0) cc_final: 0.5944 (t0) REVERT: B 319 ARG cc_start: 0.7586 (ttm110) cc_final: 0.7241 (ttm110) REVERT: B 362 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7703 (p) REVERT: B 537 LYS cc_start: 0.8158 (tttp) cc_final: 0.7945 (tttp) REVERT: B 547 LYS cc_start: 0.8086 (mttm) cc_final: 0.7662 (mttp) REVERT: B 551 VAL cc_start: 0.8937 (t) cc_final: 0.8519 (p) REVERT: B 557 LYS cc_start: 0.8430 (ptpp) cc_final: 0.8142 (ptpt) REVERT: B 558 LYS cc_start: 0.8332 (mppt) cc_final: 0.7889 (mppt) REVERT: B 589 PRO cc_start: 0.8802 (Cg_exo) cc_final: 0.8241 (Cg_endo) REVERT: B 604 THR cc_start: 0.8427 (p) cc_final: 0.8061 (t) REVERT: B 675 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7250 (mm-40) REVERT: B 698 SER cc_start: 0.8250 (t) cc_final: 0.7907 (p) REVERT: B 705 VAL cc_start: 0.8768 (t) cc_final: 0.8493 (m) REVERT: B 711 SER cc_start: 0.8480 (t) cc_final: 0.8248 (t) REVERT: B 773 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6181 (tm-30) REVERT: B 774 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7626 (mm-40) REVERT: B 821 LEU cc_start: 0.8455 (tp) cc_final: 0.7965 (tt) REVERT: B 868 GLU cc_start: 0.6728 (tp30) cc_final: 0.6222 (tp30) REVERT: B 918 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7135 (mt-10) REVERT: B 922 LEU cc_start: 0.8471 (tp) cc_final: 0.8252 (tt) REVERT: B 933 LYS cc_start: 0.7368 (mtpp) cc_final: 0.7128 (mtpp) REVERT: B 950 ASP cc_start: 0.7210 (t70) cc_final: 0.6727 (t70) REVERT: B 975 SER cc_start: 0.8646 (m) cc_final: 0.8258 (t) REVERT: B 990 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: B 993 ILE cc_start: 0.8543 (tp) cc_final: 0.8161 (tp) REVERT: B 1029 MET cc_start: 0.8376 (tpp) cc_final: 0.7897 (tpp) REVERT: B 1038 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8383 (mtpp) REVERT: B 1090 PRO cc_start: 0.8475 (Cg_exo) cc_final: 0.8262 (Cg_endo) REVERT: B 1097 SER cc_start: 0.8922 (t) cc_final: 0.8234 (p) REVERT: C 40 ASP cc_start: 0.7080 (p0) cc_final: 0.6863 (p0) REVERT: C 53 ASP cc_start: 0.6759 (t0) cc_final: 0.6511 (t0) REVERT: C 105 ILE cc_start: 0.7884 (mm) cc_final: 0.7460 (mm) REVERT: C 106 PHE cc_start: 0.7700 (m-80) cc_final: 0.7436 (m-10) REVERT: C 187 LEU cc_start: 0.8351 (tp) cc_final: 0.7995 (tp) REVERT: C 188 ARG cc_start: 0.7060 (ptp-170) cc_final: 0.6654 (ptp-170) REVERT: C 239 GLN cc_start: 0.7897 (tp40) cc_final: 0.7603 (tp40) REVERT: C 269 TYR cc_start: 0.8471 (m-80) cc_final: 0.8009 (m-80) REVERT: C 347 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6513 (t80) REVERT: C 349 SER cc_start: 0.7969 (p) cc_final: 0.7725 (t) REVERT: C 377 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 378 LYS cc_start: 0.7783 (mmmm) cc_final: 0.7582 (mmmm) REVERT: C 398 ASP cc_start: 0.6947 (t70) cc_final: 0.6713 (t0) REVERT: C 414 GLN cc_start: 0.7336 (mp10) cc_final: 0.7037 (mp10) REVERT: C 420 ASP cc_start: 0.7326 (t0) cc_final: 0.6835 (t0) REVERT: C 427 ASP cc_start: 0.6675 (t70) cc_final: 0.6333 (t70) REVERT: C 442 ASP cc_start: 0.7504 (m-30) cc_final: 0.7244 (m-30) REVERT: C 462 LYS cc_start: 0.8060 (tptt) cc_final: 0.7858 (tppt) REVERT: C 465 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 707 TYR cc_start: 0.7746 (t80) cc_final: 0.6866 (t80) REVERT: C 711 SER cc_start: 0.8596 (m) cc_final: 0.8326 (p) REVERT: C 750 SER cc_start: 0.8495 (m) cc_final: 0.8174 (p) REVERT: C 751 ASN cc_start: 0.7858 (m-40) cc_final: 0.7454 (m-40) REVERT: C 776 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8085 (tttp) REVERT: C 788 ILE cc_start: 0.8312 (mm) cc_final: 0.8098 (mm) REVERT: C 825 LYS cc_start: 0.8311 (tppt) cc_final: 0.7876 (ttmm) REVERT: C 851 CYS cc_start: 0.7730 (t) cc_final: 0.7434 (m) REVERT: C 868 GLU cc_start: 0.7231 (tp30) cc_final: 0.6668 (tp30) REVERT: C 900 MET cc_start: 0.7783 (mtp) cc_final: 0.7583 (ttm) REVERT: C 921 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8112 (mmmm) REVERT: C 933 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7405 (mttp) REVERT: C 964 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7958 (ttmm) REVERT: C 984 LEU cc_start: 0.7897 (mp) cc_final: 0.7677 (mt) REVERT: C 1038 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8237 (mtpp) REVERT: C 1066 THR cc_start: 0.7945 (p) cc_final: 0.7707 (p) REVERT: C 1127 ASP cc_start: 0.7390 (p0) cc_final: 0.7183 (p0) outliers start: 160 outliers final: 96 residues processed: 815 average time/residue: 0.3578 time to fit residues: 452.0780 Evaluate side-chains 756 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 645 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 232 optimal weight: 0.1980 chunk 190 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 205 HIS A 239 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 751 ASN B 955 ASN B 957 GLN B 992 GLN B1011 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 450 ASN C 536 ASN C 564 GLN C 613 GLN C 641 ASN C 784 GLN C 957 GLN C1002 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25040 Z= 0.292 Angle : 0.632 9.729 34095 Z= 0.324 Chirality : 0.047 0.371 3957 Planarity : 0.005 0.058 4379 Dihedral : 7.704 79.999 4014 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 6.37 % Allowed : 18.00 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.14), residues: 3044 helix: 0.59 (0.21), residues: 647 sheet: -2.21 (0.20), residues: 525 loop : -3.09 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.008 0.001 HIS C 519 PHE 0.031 0.002 PHE A 643 TYR 0.024 0.002 TYR B 707 ARG 0.006 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 672 time to evaluate : 2.564 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7712 (t-90) cc_final: 0.7365 (t-170) REVERT: A 65 PHE cc_start: 0.7054 (m-10) cc_final: 0.6777 (m-10) REVERT: A 84 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8132 (pp) REVERT: A 102 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6402 (mtm-85) REVERT: A 104 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.7336 (m-10) REVERT: A 129 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7285 (mtmm) REVERT: A 188 ARG cc_start: 0.7619 (ptp-110) cc_final: 0.7137 (ptp90) REVERT: A 224 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6395 (mm-30) REVERT: A 238 PHE cc_start: 0.7329 (t80) cc_final: 0.7111 (t80) REVERT: A 267 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 269 TYR cc_start: 0.8043 (m-80) cc_final: 0.7648 (m-80) REVERT: A 307 THR cc_start: 0.8253 (m) cc_final: 0.7929 (p) REVERT: A 340 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6242 (pm20) REVERT: A 358 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6316 (pt) REVERT: A 380 TYR cc_start: 0.6932 (m-80) cc_final: 0.6507 (m-10) REVERT: A 386 LYS cc_start: 0.8376 (mttp) cc_final: 0.8117 (mttt) REVERT: A 436 TRP cc_start: 0.6542 (p90) cc_final: 0.6100 (p90) REVERT: A 492 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6331 (tp) REVERT: A 542 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8647 (t0) REVERT: A 558 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7781 (mtpp) REVERT: A 562 PHE cc_start: 0.7782 (p90) cc_final: 0.7434 (p90) REVERT: A 569 ILE cc_start: 0.8050 (pt) cc_final: 0.7825 (mp) REVERT: A 643 PHE cc_start: 0.8210 (t80) cc_final: 0.7989 (t80) REVERT: A 675 GLN cc_start: 0.7332 (mm-40) cc_final: 0.7084 (mm-40) REVERT: A 745 ASP cc_start: 0.6917 (m-30) cc_final: 0.6691 (p0) REVERT: A 774 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7071 (mp10) REVERT: A 851 CYS cc_start: 0.7454 (t) cc_final: 0.7016 (p) REVERT: A 854 LYS cc_start: 0.8494 (tptp) cc_final: 0.8289 (tptp) REVERT: A 855 PHE cc_start: 0.8117 (m-80) cc_final: 0.7357 (m-80) REVERT: A 869 MET cc_start: 0.8097 (mtt) cc_final: 0.7883 (mtm) REVERT: A 918 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 937 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7438 (t) REVERT: A 949 GLN cc_start: 0.7893 (mm110) cc_final: 0.7493 (mm-40) REVERT: A 969 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8099 (mtmm) REVERT: A 998 THR cc_start: 0.8059 (m) cc_final: 0.7787 (p) REVERT: A 1029 MET cc_start: 0.8192 (ttm) cc_final: 0.7954 (ttm) REVERT: A 1097 SER cc_start: 0.8426 (t) cc_final: 0.7612 (p) REVERT: A 1139 ASP cc_start: 0.7720 (t70) cc_final: 0.7428 (t70) REVERT: B 52 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7404 (tp-100) REVERT: B 108 THR cc_start: 0.6022 (OUTLIER) cc_final: 0.5770 (m) REVERT: B 129 LYS cc_start: 0.7966 (tppt) cc_final: 0.7645 (tppt) REVERT: B 169 GLU cc_start: 0.7604 (pm20) cc_final: 0.7104 (pm20) REVERT: B 177 MET cc_start: 0.6536 (tmt) cc_final: 0.5965 (tmt) REVERT: B 201 ILE cc_start: 0.8349 (mt) cc_final: 0.7804 (tt) REVERT: B 224 GLU cc_start: 0.6554 (pm20) cc_final: 0.6240 (pm20) REVERT: B 236 THR cc_start: 0.6222 (OUTLIER) cc_final: 0.6013 (m) REVERT: B 360 ASN cc_start: 0.8189 (m110) cc_final: 0.7934 (m110) REVERT: B 362 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7675 (p) REVERT: B 406 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6147 (tm-30) REVERT: B 537 LYS cc_start: 0.8159 (tttp) cc_final: 0.7818 (tttm) REVERT: B 551 VAL cc_start: 0.8880 (t) cc_final: 0.8491 (p) REVERT: B 557 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8222 (ptpt) REVERT: B 558 LYS cc_start: 0.8339 (mppt) cc_final: 0.7887 (mppt) REVERT: B 564 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8191 (mm110) REVERT: B 571 ASP cc_start: 0.7274 (t70) cc_final: 0.7073 (t0) REVERT: B 580 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7785 (mm110) REVERT: B 589 PRO cc_start: 0.8664 (Cg_exo) cc_final: 0.7940 (Cg_endo) REVERT: B 604 THR cc_start: 0.8454 (p) cc_final: 0.8172 (t) REVERT: B 698 SER cc_start: 0.8344 (t) cc_final: 0.7916 (p) REVERT: B 705 VAL cc_start: 0.8702 (t) cc_final: 0.8459 (m) REVERT: B 711 SER cc_start: 0.8538 (t) cc_final: 0.8274 (t) REVERT: B 773 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6235 (tm-30) REVERT: B 774 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7316 (mm110) REVERT: B 796 TYR cc_start: 0.7008 (t80) cc_final: 0.6769 (t80) REVERT: B 821 LEU cc_start: 0.8529 (tp) cc_final: 0.8066 (tt) REVERT: B 918 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 933 LYS cc_start: 0.7391 (mtpp) cc_final: 0.7191 (mtpp) REVERT: B 950 ASP cc_start: 0.7185 (t70) cc_final: 0.6838 (t70) REVERT: B 975 SER cc_start: 0.8524 (m) cc_final: 0.8156 (t) REVERT: B 990 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: B 993 ILE cc_start: 0.8631 (tp) cc_final: 0.8384 (tp) REVERT: B 1029 MET cc_start: 0.8403 (tpp) cc_final: 0.7907 (tpp) REVERT: B 1038 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8275 (mtpp) REVERT: B 1086 LYS cc_start: 0.8305 (ptmt) cc_final: 0.8067 (mtpt) REVERT: B 1097 SER cc_start: 0.8837 (t) cc_final: 0.8156 (p) REVERT: B 1107 ARG cc_start: 0.7644 (ptt-90) cc_final: 0.6955 (ptt180) REVERT: C 40 ASP cc_start: 0.7141 (p0) cc_final: 0.6907 (p0) REVERT: C 41 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7803 (pttt) REVERT: C 53 ASP cc_start: 0.6883 (t0) cc_final: 0.6660 (t0) REVERT: C 105 ILE cc_start: 0.7935 (mm) cc_final: 0.7547 (mm) REVERT: C 106 PHE cc_start: 0.7698 (m-80) cc_final: 0.7381 (m-10) REVERT: C 187 LEU cc_start: 0.8302 (tp) cc_final: 0.7544 (tt) REVERT: C 188 ARG cc_start: 0.7008 (ptp-170) cc_final: 0.6586 (ptp-170) REVERT: C 200 LYS cc_start: 0.7944 (mttp) cc_final: 0.7728 (mttp) REVERT: C 204 LYS cc_start: 0.8354 (tttt) cc_final: 0.8006 (tttp) REVERT: C 216 LEU cc_start: 0.7615 (mt) cc_final: 0.7403 (mt) REVERT: C 224 GLU cc_start: 0.7286 (pm20) cc_final: 0.6823 (mp0) REVERT: C 239 GLN cc_start: 0.7756 (tp40) cc_final: 0.7498 (tp40) REVERT: C 269 TYR cc_start: 0.8534 (m-80) cc_final: 0.7981 (m-80) REVERT: C 307 THR cc_start: 0.7297 (m) cc_final: 0.7063 (p) REVERT: C 349 SER cc_start: 0.8155 (p) cc_final: 0.7675 (t) REVERT: C 350 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8697 (t) REVERT: C 378 LYS cc_start: 0.7754 (mmmm) cc_final: 0.7540 (mmmm) REVERT: C 380 TYR cc_start: 0.7476 (m-10) cc_final: 0.7269 (m-10) REVERT: C 398 ASP cc_start: 0.7009 (t70) cc_final: 0.6713 (t0) REVERT: C 420 ASP cc_start: 0.7205 (t0) cc_final: 0.6755 (t0) REVERT: C 427 ASP cc_start: 0.6675 (t70) cc_final: 0.6315 (t70) REVERT: C 462 LYS cc_start: 0.8136 (tptt) cc_final: 0.7931 (ttmm) REVERT: C 465 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7272 (tm-30) REVERT: C 516 GLU cc_start: 0.7011 (pt0) cc_final: 0.6809 (pt0) REVERT: C 537 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7735 (mtpp) REVERT: C 588 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8230 (p) REVERT: C 643 PHE cc_start: 0.8178 (t80) cc_final: 0.7779 (t80) REVERT: C 707 TYR cc_start: 0.7773 (t80) cc_final: 0.6974 (t80) REVERT: C 711 SER cc_start: 0.8666 (m) cc_final: 0.8383 (p) REVERT: C 729 VAL cc_start: 0.8485 (p) cc_final: 0.8264 (t) REVERT: C 751 ASN cc_start: 0.7864 (m-40) cc_final: 0.7455 (m-40) REVERT: C 752 LEU cc_start: 0.8859 (mm) cc_final: 0.8452 (mt) REVERT: C 755 GLN cc_start: 0.7691 (pp30) cc_final: 0.7126 (pp30) REVERT: C 776 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8134 (tttp) REVERT: C 804 GLN cc_start: 0.7644 (mt0) cc_final: 0.7362 (mt0) REVERT: C 825 LYS cc_start: 0.8227 (tppt) cc_final: 0.7933 (tppt) REVERT: C 868 GLU cc_start: 0.7254 (tp30) cc_final: 0.6937 (tp30) REVERT: C 921 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8073 (mmmm) REVERT: C 964 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7933 (ttmm) REVERT: C 984 LEU cc_start: 0.7947 (mp) cc_final: 0.7641 (mt) REVERT: C 1002 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: C 1014 ARG cc_start: 0.7353 (tpp80) cc_final: 0.7118 (ttm-80) REVERT: C 1018 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 1038 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8208 (mmtt) REVERT: C 1073 LYS cc_start: 0.8362 (mtpt) cc_final: 0.7895 (mtpp) REVERT: C 1144 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7417 (mm-30) outliers start: 170 outliers final: 94 residues processed: 768 average time/residue: 0.3666 time to fit residues: 434.0679 Evaluate side-chains 753 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 640 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 133 optimal weight: 0.0570 chunk 188 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 146 optimal weight: 0.0170 chunk 266 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 334 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 895 GLN B 955 ASN B 957 GLN B 965 GLN B1005 GLN C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 784 GLN C 935 GLN C1010 GLN C1101 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25040 Z= 0.201 Angle : 0.595 9.773 34095 Z= 0.302 Chirality : 0.046 0.326 3957 Planarity : 0.004 0.065 4379 Dihedral : 7.373 91.139 4006 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.92 % Allowed : 20.40 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.14), residues: 3044 helix: 0.88 (0.21), residues: 640 sheet: -1.93 (0.20), residues: 564 loop : -2.93 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 353 HIS 0.005 0.001 HIS C1083 PHE 0.034 0.001 PHE A 643 TYR 0.024 0.001 TYR B 707 ARG 0.008 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 644 time to evaluate : 2.108 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7329 (tm-30) cc_final: 0.7009 (tm-30) REVERT: A 65 PHE cc_start: 0.7048 (m-10) cc_final: 0.6791 (m-10) REVERT: A 84 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8113 (pp) REVERT: A 102 ARG cc_start: 0.6779 (mtm-85) cc_final: 0.6412 (mtm-85) REVERT: A 104 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.7317 (m-90) REVERT: A 129 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7246 (mtmm) REVERT: A 188 ARG cc_start: 0.7753 (ptp-110) cc_final: 0.7383 (ptp90) REVERT: A 224 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6452 (mm-30) REVERT: A 267 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 269 TYR cc_start: 0.7990 (m-80) cc_final: 0.7703 (m-80) REVERT: A 307 THR cc_start: 0.8259 (m) cc_final: 0.7929 (p) REVERT: A 340 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: A 356 LYS cc_start: 0.7857 (ptmm) cc_final: 0.7451 (pttm) REVERT: A 358 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6509 (pt) REVERT: A 360 ASN cc_start: 0.8121 (m110) cc_final: 0.7804 (m-40) REVERT: A 380 TYR cc_start: 0.6944 (m-80) cc_final: 0.6499 (m-10) REVERT: A 386 LYS cc_start: 0.8381 (mttp) cc_final: 0.7795 (mtmm) REVERT: A 396 TYR cc_start: 0.7621 (m-80) cc_final: 0.7398 (m-80) REVERT: A 436 TRP cc_start: 0.6574 (p90) cc_final: 0.6146 (p90) REVERT: A 452 LEU cc_start: 0.7846 (tt) cc_final: 0.7628 (tp) REVERT: A 558 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7755 (mtpp) REVERT: A 562 PHE cc_start: 0.7798 (p90) cc_final: 0.7441 (p90) REVERT: A 564 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 569 ILE cc_start: 0.7997 (pt) cc_final: 0.7762 (mp) REVERT: A 578 ASP cc_start: 0.7396 (t0) cc_final: 0.7191 (t0) REVERT: A 588 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 660 TYR cc_start: 0.8632 (m-80) cc_final: 0.8247 (m-80) REVERT: A 675 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6929 (mm-40) REVERT: A 702 GLU cc_start: 0.6946 (mp0) cc_final: 0.6611 (mp0) REVERT: A 745 ASP cc_start: 0.6928 (m-30) cc_final: 0.6694 (p0) REVERT: A 768 THR cc_start: 0.8245 (m) cc_final: 0.7969 (p) REVERT: A 774 GLN cc_start: 0.7641 (mm-40) cc_final: 0.6995 (mp10) REVERT: A 855 PHE cc_start: 0.8091 (m-80) cc_final: 0.7782 (m-80) REVERT: A 869 MET cc_start: 0.8105 (mtt) cc_final: 0.7883 (mtm) REVERT: A 937 SER cc_start: 0.7717 (OUTLIER) cc_final: 0.7459 (t) REVERT: A 949 GLN cc_start: 0.7844 (mm110) cc_final: 0.7386 (mm-40) REVERT: A 998 THR cc_start: 0.7977 (m) cc_final: 0.7747 (p) REVERT: A 1001 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 1005 GLN cc_start: 0.7987 (tp40) cc_final: 0.7738 (tp40) REVERT: A 1029 MET cc_start: 0.8121 (ttm) cc_final: 0.7904 (ttm) REVERT: A 1097 SER cc_start: 0.8388 (t) cc_final: 0.7550 (p) REVERT: A 1139 ASP cc_start: 0.7696 (t70) cc_final: 0.7434 (t70) REVERT: B 129 LYS cc_start: 0.7873 (tppt) cc_final: 0.7490 (tppt) REVERT: B 169 GLU cc_start: 0.7533 (pm20) cc_final: 0.7116 (pm20) REVERT: B 177 MET cc_start: 0.6512 (tmt) cc_final: 0.6098 (tmt) REVERT: B 224 GLU cc_start: 0.6656 (pm20) cc_final: 0.6316 (pm20) REVERT: B 236 THR cc_start: 0.6245 (OUTLIER) cc_final: 0.6023 (m) REVERT: B 279 TYR cc_start: 0.8150 (m-10) cc_final: 0.7944 (m-10) REVERT: B 528 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8310 (mmmt) REVERT: B 537 LYS cc_start: 0.8132 (tttp) cc_final: 0.7778 (tttm) REVERT: B 551 VAL cc_start: 0.8874 (t) cc_final: 0.8536 (p) REVERT: B 557 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8233 (ptpt) REVERT: B 558 LYS cc_start: 0.8321 (mppt) cc_final: 0.7875 (mppt) REVERT: B 564 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8214 (mm110) REVERT: B 571 ASP cc_start: 0.7279 (t70) cc_final: 0.6999 (t0) REVERT: B 604 THR cc_start: 0.8460 (p) cc_final: 0.8189 (t) REVERT: B 698 SER cc_start: 0.8357 (t) cc_final: 0.7918 (p) REVERT: B 705 VAL cc_start: 0.8662 (t) cc_final: 0.8402 (m) REVERT: B 711 SER cc_start: 0.8538 (t) cc_final: 0.8260 (t) REVERT: B 719 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8157 (p) REVERT: B 759 PHE cc_start: 0.7203 (m-80) cc_final: 0.6869 (m-80) REVERT: B 773 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6053 (tm-30) REVERT: B 774 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7533 (mm110) REVERT: B 777 ASN cc_start: 0.7920 (m-40) cc_final: 0.7224 (m110) REVERT: B 821 LEU cc_start: 0.8527 (tp) cc_final: 0.8058 (tt) REVERT: B 918 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 933 LYS cc_start: 0.7324 (mtpp) cc_final: 0.7112 (mtpp) REVERT: B 950 ASP cc_start: 0.7173 (t70) cc_final: 0.6835 (t70) REVERT: B 975 SER cc_start: 0.8492 (m) cc_final: 0.8094 (t) REVERT: B 990 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: B 993 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8419 (tp) REVERT: B 1029 MET cc_start: 0.8369 (tpp) cc_final: 0.7901 (tpp) REVERT: B 1038 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8266 (mtpp) REVERT: B 1086 LYS cc_start: 0.8280 (ptmt) cc_final: 0.8042 (mtpt) REVERT: B 1097 SER cc_start: 0.8797 (t) cc_final: 0.8120 (p) REVERT: B 1107 ARG cc_start: 0.7459 (ptt-90) cc_final: 0.6775 (ptt180) REVERT: C 40 ASP cc_start: 0.7124 (p0) cc_final: 0.6893 (p0) REVERT: C 41 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7784 (pttt) REVERT: C 53 ASP cc_start: 0.6896 (t0) cc_final: 0.6674 (t0) REVERT: C 105 ILE cc_start: 0.7923 (mm) cc_final: 0.7539 (mm) REVERT: C 106 PHE cc_start: 0.7689 (m-80) cc_final: 0.7417 (m-10) REVERT: C 187 LEU cc_start: 0.8310 (tp) cc_final: 0.7561 (tt) REVERT: C 188 ARG cc_start: 0.7002 (ptp-170) cc_final: 0.6600 (ptp-170) REVERT: C 200 LYS cc_start: 0.7865 (mttp) cc_final: 0.7639 (mttp) REVERT: C 204 LYS cc_start: 0.8357 (tttt) cc_final: 0.7803 (tttp) REVERT: C 224 GLU cc_start: 0.7239 (pm20) cc_final: 0.6774 (mp0) REVERT: C 239 GLN cc_start: 0.7666 (tp40) cc_final: 0.7410 (tp40) REVERT: C 269 TYR cc_start: 0.8532 (m-80) cc_final: 0.7994 (m-80) REVERT: C 327 VAL cc_start: 0.8552 (m) cc_final: 0.8104 (t) REVERT: C 349 SER cc_start: 0.8166 (p) cc_final: 0.7698 (t) REVERT: C 362 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7761 (p) REVERT: C 398 ASP cc_start: 0.6953 (t70) cc_final: 0.6709 (t0) REVERT: C 414 GLN cc_start: 0.7542 (mp10) cc_final: 0.7342 (mp10) REVERT: C 420 ASP cc_start: 0.7118 (t0) cc_final: 0.6549 (t0) REVERT: C 427 ASP cc_start: 0.6661 (t70) cc_final: 0.6281 (t70) REVERT: C 454 ARG cc_start: 0.7741 (ttt180) cc_final: 0.7441 (ttt180) REVERT: C 465 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7283 (tm-30) REVERT: C 537 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7720 (mtpp) REVERT: C 588 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8154 (p) REVERT: C 619 GLU cc_start: 0.6345 (tt0) cc_final: 0.6143 (tt0) REVERT: C 643 PHE cc_start: 0.8112 (t80) cc_final: 0.7813 (t80) REVERT: C 707 TYR cc_start: 0.7785 (t80) cc_final: 0.6966 (t80) REVERT: C 729 VAL cc_start: 0.8449 (p) cc_final: 0.8216 (t) REVERT: C 751 ASN cc_start: 0.7764 (m-40) cc_final: 0.7502 (m-40) REVERT: C 752 LEU cc_start: 0.8794 (mm) cc_final: 0.8300 (mt) REVERT: C 755 GLN cc_start: 0.7664 (pp30) cc_final: 0.7136 (pp30) REVERT: C 776 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8150 (tttp) REVERT: C 825 LYS cc_start: 0.8211 (tppt) cc_final: 0.7907 (tppt) REVERT: C 868 GLU cc_start: 0.7210 (tp30) cc_final: 0.6936 (tp30) REVERT: C 900 MET cc_start: 0.7737 (mtp) cc_final: 0.7508 (mtp) REVERT: C 921 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8051 (mmmm) REVERT: C 964 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7934 (ttmm) REVERT: C 1002 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 1014 ARG cc_start: 0.7312 (tpp80) cc_final: 0.7064 (ttm170) REVERT: C 1038 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (mmtt) REVERT: C 1073 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7918 (mtmt) REVERT: C 1123 SER cc_start: 0.8208 (t) cc_final: 0.7997 (t) REVERT: C 1144 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7389 (mm-30) outliers start: 158 outliers final: 105 residues processed: 735 average time/residue: 0.3614 time to fit residues: 410.8226 Evaluate side-chains 746 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 624 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 957 GLN B1011 GLN C 30 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 25040 Z= 0.354 Angle : 0.659 9.857 34095 Z= 0.337 Chirality : 0.049 0.365 3957 Planarity : 0.005 0.068 4379 Dihedral : 7.618 92.067 4005 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.10 % Favored : 88.86 % Rotamer: Outliers : 6.79 % Allowed : 20.40 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.14), residues: 3044 helix: 0.67 (0.21), residues: 655 sheet: -1.83 (0.20), residues: 576 loop : -2.90 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.010 0.001 HIS A 49 PHE 0.038 0.002 PHE A 643 TYR 0.026 0.002 TYR B 707 ARG 0.010 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 660 time to evaluate : 2.588 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: symmetry clash REVERT: A 49 HIS cc_start: 0.7694 (t70) cc_final: 0.7440 (t-170) REVERT: A 52 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 65 PHE cc_start: 0.7059 (m-10) cc_final: 0.6824 (m-10) REVERT: A 102 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6613 (mtm-85) REVERT: A 104 TRP cc_start: 0.7766 (OUTLIER) cc_final: 0.7230 (m-90) REVERT: A 129 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7161 (mtmm) REVERT: A 188 ARG cc_start: 0.7904 (ptp-110) cc_final: 0.7496 (ptp90) REVERT: A 190 PHE cc_start: 0.8126 (m-80) cc_final: 0.7794 (m-10) REVERT: A 203 SER cc_start: 0.8514 (p) cc_final: 0.7815 (m) REVERT: A 224 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6716 (mm-30) REVERT: A 267 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.8000 (p) REVERT: A 269 TYR cc_start: 0.7976 (m-80) cc_final: 0.7587 (m-80) REVERT: A 307 THR cc_start: 0.8364 (m) cc_final: 0.8044 (p) REVERT: A 340 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6456 (pm20) REVERT: A 356 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7879 (ptpp) REVERT: A 358 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.6857 (pt) REVERT: A 360 ASN cc_start: 0.8267 (m110) cc_final: 0.8010 (m110) REVERT: A 380 TYR cc_start: 0.6939 (m-80) cc_final: 0.6549 (m-10) REVERT: A 386 LYS cc_start: 0.8469 (mttp) cc_final: 0.7895 (mtmm) REVERT: A 436 TRP cc_start: 0.6677 (p90) cc_final: 0.5932 (p90) REVERT: A 542 ASN cc_start: 0.8841 (t0) cc_final: 0.8564 (t0) REVERT: A 558 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7857 (mtpp) REVERT: A 564 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7028 (tm-30) REVERT: A 588 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 675 GLN cc_start: 0.7260 (mm-40) cc_final: 0.7008 (mm-40) REVERT: A 698 SER cc_start: 0.8552 (t) cc_final: 0.8081 (p) REVERT: A 765 ARG cc_start: 0.7264 (ttp-170) cc_final: 0.6950 (mtp180) REVERT: A 773 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6381 (tm-30) REVERT: A 774 GLN cc_start: 0.7645 (mm-40) cc_final: 0.6913 (mp10) REVERT: A 820 ASP cc_start: 0.7829 (m-30) cc_final: 0.7578 (m-30) REVERT: A 854 LYS cc_start: 0.8530 (tptp) cc_final: 0.8321 (tptp) REVERT: A 855 PHE cc_start: 0.8251 (m-80) cc_final: 0.7980 (m-80) REVERT: A 869 MET cc_start: 0.8137 (mtt) cc_final: 0.7928 (mtm) REVERT: A 937 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7641 (t) REVERT: A 949 GLN cc_start: 0.7980 (mm110) cc_final: 0.7555 (mm-40) REVERT: A 992 GLN cc_start: 0.7976 (mm110) cc_final: 0.7467 (mm110) REVERT: A 997 ILE cc_start: 0.8680 (mm) cc_final: 0.8430 (mt) REVERT: A 1097 SER cc_start: 0.8385 (t) cc_final: 0.7556 (p) REVERT: A 1139 ASP cc_start: 0.7754 (t70) cc_final: 0.7425 (t70) REVERT: B 129 LYS cc_start: 0.7892 (tppt) cc_final: 0.7451 (tppt) REVERT: B 169 GLU cc_start: 0.7619 (pm20) cc_final: 0.7184 (pm20) REVERT: B 177 MET cc_start: 0.6620 (tmt) cc_final: 0.6190 (tmt) REVERT: B 188 ARG cc_start: 0.6449 (ttm-80) cc_final: 0.6129 (ttm-80) REVERT: B 201 ILE cc_start: 0.8360 (mt) cc_final: 0.7756 (tt) REVERT: B 224 GLU cc_start: 0.6744 (pm20) cc_final: 0.6484 (pm20) REVERT: B 279 TYR cc_start: 0.8170 (m-10) cc_final: 0.7861 (m-10) REVERT: B 362 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7890 (p) REVERT: B 406 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6671 (tt0) REVERT: B 528 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8514 (mmmt) REVERT: B 537 LYS cc_start: 0.8242 (tttp) cc_final: 0.7686 (tttm) REVERT: B 547 LYS cc_start: 0.8063 (mttm) cc_final: 0.7595 (mttp) REVERT: B 549 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8395 (p) REVERT: B 551 VAL cc_start: 0.8861 (t) cc_final: 0.8487 (p) REVERT: B 557 LYS cc_start: 0.8546 (ptpp) cc_final: 0.8267 (ptpp) REVERT: B 558 LYS cc_start: 0.8352 (mppt) cc_final: 0.7913 (mppt) REVERT: B 560 LEU cc_start: 0.8816 (mt) cc_final: 0.8592 (mp) REVERT: B 563 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: B 571 ASP cc_start: 0.7343 (t70) cc_final: 0.6982 (t0) REVERT: B 604 THR cc_start: 0.8464 (p) cc_final: 0.8210 (t) REVERT: B 705 VAL cc_start: 0.8677 (t) cc_final: 0.8431 (m) REVERT: B 711 SER cc_start: 0.8525 (t) cc_final: 0.8222 (t) REVERT: B 719 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8177 (p) REVERT: B 752 LEU cc_start: 0.8702 (mt) cc_final: 0.8414 (mp) REVERT: B 773 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6282 (tm-30) REVERT: B 774 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7449 (mm110) REVERT: B 821 LEU cc_start: 0.8520 (tp) cc_final: 0.8024 (tt) REVERT: B 895 GLN cc_start: 0.7864 (pt0) cc_final: 0.7633 (pt0) REVERT: B 918 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6975 (mt-10) REVERT: B 935 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7445 (tp-100) REVERT: B 950 ASP cc_start: 0.7219 (t70) cc_final: 0.6901 (t70) REVERT: B 957 GLN cc_start: 0.7774 (tt0) cc_final: 0.7500 (tt0) REVERT: B 975 SER cc_start: 0.8577 (m) cc_final: 0.8186 (t) REVERT: B 988 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7040 (tp30) REVERT: B 990 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: B 993 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 1038 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8297 (mtpp) REVERT: B 1086 LYS cc_start: 0.8280 (ptmt) cc_final: 0.8024 (mtpt) REVERT: B 1097 SER cc_start: 0.8794 (t) cc_final: 0.8161 (p) REVERT: C 41 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (pttt) REVERT: C 49 HIS cc_start: 0.7169 (t-90) cc_final: 0.6938 (t-90) REVERT: C 105 ILE cc_start: 0.7903 (mm) cc_final: 0.7687 (mm) REVERT: C 106 PHE cc_start: 0.7686 (m-80) cc_final: 0.7423 (m-80) REVERT: C 188 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6895 (ptp-170) REVERT: C 200 LYS cc_start: 0.7930 (mttp) cc_final: 0.7662 (mttp) REVERT: C 204 LYS cc_start: 0.8412 (tttt) cc_final: 0.8030 (tttp) REVERT: C 362 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8180 (p) REVERT: C 364 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.7155 (t0) REVERT: C 414 GLN cc_start: 0.7704 (mp10) cc_final: 0.7232 (mp10) REVERT: C 427 ASP cc_start: 0.6828 (t70) cc_final: 0.6512 (t70) REVERT: C 454 ARG cc_start: 0.7726 (ttt180) cc_final: 0.7443 (ttt180) REVERT: C 465 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7192 (tm-30) REVERT: C 537 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7804 (mtpp) REVERT: C 588 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8208 (p) REVERT: C 619 GLU cc_start: 0.6605 (tt0) cc_final: 0.6401 (tt0) REVERT: C 704 SER cc_start: 0.8459 (p) cc_final: 0.8218 (p) REVERT: C 707 TYR cc_start: 0.7821 (t80) cc_final: 0.7038 (t80) REVERT: C 711 SER cc_start: 0.8658 (m) cc_final: 0.8374 (p) REVERT: C 724 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8479 (p) REVERT: C 729 VAL cc_start: 0.8504 (p) cc_final: 0.8281 (t) REVERT: C 752 LEU cc_start: 0.8817 (mm) cc_final: 0.8378 (mt) REVERT: C 755 GLN cc_start: 0.7714 (pp30) cc_final: 0.7160 (pp30) REVERT: C 776 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8197 (tttp) REVERT: C 825 LYS cc_start: 0.8307 (tppt) cc_final: 0.7994 (tppt) REVERT: C 868 GLU cc_start: 0.7274 (tp30) cc_final: 0.6827 (tp30) REVERT: C 869 MET cc_start: 0.7725 (mmm) cc_final: 0.7511 (mmm) REVERT: C 921 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8064 (mmmm) REVERT: C 935 GLN cc_start: 0.7833 (mt0) cc_final: 0.7584 (mt0) REVERT: C 985 ASP cc_start: 0.7381 (p0) cc_final: 0.7160 (p0) REVERT: C 1002 GLN cc_start: 0.7458 (tm-30) cc_final: 0.7187 (tm-30) REVERT: C 1038 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8275 (mtpp) REVERT: C 1066 THR cc_start: 0.7875 (p) cc_final: 0.7637 (p) REVERT: C 1073 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7840 (mtpp) REVERT: C 1123 SER cc_start: 0.8287 (t) cc_final: 0.8077 (t) outliers start: 181 outliers final: 112 residues processed: 780 average time/residue: 0.3561 time to fit residues: 427.8654 Evaluate side-chains 767 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 635 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 156 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A1101 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 907 ASN B 935 GLN C 30 ASN C 52 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 613 GLN C 762 GLN C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25040 Z= 0.214 Angle : 0.617 9.790 34095 Z= 0.313 Chirality : 0.048 0.332 3957 Planarity : 0.004 0.070 4379 Dihedral : 7.259 92.472 3998 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.89 % Favored : 90.08 % Rotamer: Outliers : 5.96 % Allowed : 21.30 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.15), residues: 3044 helix: 0.91 (0.21), residues: 650 sheet: -1.67 (0.20), residues: 565 loop : -2.76 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 353 HIS 0.008 0.001 HIS A 49 PHE 0.045 0.002 PHE A 643 TYR 0.029 0.001 TYR C 904 ARG 0.012 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 639 time to evaluate : 2.613 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7686 (t70) cc_final: 0.7390 (t-170) REVERT: A 52 GLN cc_start: 0.7308 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 65 PHE cc_start: 0.7087 (m-10) cc_final: 0.6831 (m-10) REVERT: A 88 ASP cc_start: 0.8114 (m-30) cc_final: 0.7682 (m-30) REVERT: A 102 ARG cc_start: 0.6809 (mtm-85) cc_final: 0.6450 (mtm-85) REVERT: A 104 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.7082 (m-90) REVERT: A 119 ILE cc_start: 0.8729 (mt) cc_final: 0.8410 (mm) REVERT: A 188 ARG cc_start: 0.7797 (ptp-110) cc_final: 0.7387 (ptp90) REVERT: A 203 SER cc_start: 0.8505 (p) cc_final: 0.7767 (m) REVERT: A 224 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6579 (mm-30) REVERT: A 267 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8043 (p) REVERT: A 269 TYR cc_start: 0.7915 (m-80) cc_final: 0.7574 (m-80) REVERT: A 307 THR cc_start: 0.8353 (m) cc_final: 0.8029 (p) REVERT: A 328 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7560 (mtp180) REVERT: A 356 LYS cc_start: 0.7960 (ptmm) cc_final: 0.7591 (pttm) REVERT: A 358 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7077 (pt) REVERT: A 359 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7469 (t) REVERT: A 360 ASN cc_start: 0.8119 (m110) cc_final: 0.7786 (m110) REVERT: A 380 TYR cc_start: 0.6899 (m-80) cc_final: 0.6500 (m-10) REVERT: A 386 LYS cc_start: 0.8453 (mttp) cc_final: 0.7880 (mtmm) REVERT: A 542 ASN cc_start: 0.8870 (t0) cc_final: 0.8591 (t0) REVERT: A 558 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7827 (mtpp) REVERT: A 564 GLN cc_start: 0.7671 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 588 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8560 (p) REVERT: A 675 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6920 (mm-40) REVERT: A 698 SER cc_start: 0.8538 (t) cc_final: 0.8047 (p) REVERT: A 768 THR cc_start: 0.8261 (m) cc_final: 0.7988 (p) REVERT: A 770 ILE cc_start: 0.8517 (mt) cc_final: 0.8129 (mm) REVERT: A 774 GLN cc_start: 0.7597 (mm-40) cc_final: 0.6928 (mp10) REVERT: A 854 LYS cc_start: 0.8497 (tptp) cc_final: 0.8261 (tptp) REVERT: A 855 PHE cc_start: 0.8163 (m-80) cc_final: 0.7937 (m-80) REVERT: A 869 MET cc_start: 0.8108 (mtt) cc_final: 0.7895 (mtm) REVERT: A 949 GLN cc_start: 0.7864 (mm110) cc_final: 0.7457 (mm-40) REVERT: A 992 GLN cc_start: 0.7938 (mm110) cc_final: 0.7523 (mt0) REVERT: A 997 ILE cc_start: 0.8713 (mm) cc_final: 0.8464 (mt) REVERT: A 998 THR cc_start: 0.8097 (t) cc_final: 0.7758 (p) REVERT: A 1097 SER cc_start: 0.8330 (t) cc_final: 0.7530 (p) REVERT: A 1139 ASP cc_start: 0.7733 (t70) cc_final: 0.7415 (t70) REVERT: B 82 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8279 (Cg_exo) REVERT: B 91 TYR cc_start: 0.7875 (t80) cc_final: 0.7643 (t80) REVERT: B 102 ARG cc_start: 0.7390 (mmm-85) cc_final: 0.7141 (mmm-85) REVERT: B 129 LYS cc_start: 0.7847 (tppt) cc_final: 0.7415 (tppt) REVERT: B 169 GLU cc_start: 0.7534 (pm20) cc_final: 0.7023 (pm20) REVERT: B 177 MET cc_start: 0.6619 (tmt) cc_final: 0.6197 (tmt) REVERT: B 201 ILE cc_start: 0.8372 (mt) cc_final: 0.7760 (tt) REVERT: B 224 GLU cc_start: 0.6744 (pm20) cc_final: 0.6386 (pm20) REVERT: B 237 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6105 (mtp180) REVERT: B 239 GLN cc_start: 0.6837 (tp40) cc_final: 0.6466 (mm110) REVERT: B 279 TYR cc_start: 0.8105 (m-10) cc_final: 0.7862 (m-10) REVERT: B 362 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7625 (p) REVERT: B 406 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6586 (tt0) REVERT: B 537 LYS cc_start: 0.8242 (tttp) cc_final: 0.7913 (tttm) REVERT: B 549 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8429 (p) REVERT: B 551 VAL cc_start: 0.8879 (t) cc_final: 0.8543 (p) REVERT: B 558 LYS cc_start: 0.8304 (mppt) cc_final: 0.7892 (mppt) REVERT: B 560 LEU cc_start: 0.8757 (mt) cc_final: 0.8544 (mp) REVERT: B 563 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 571 ASP cc_start: 0.7344 (t70) cc_final: 0.6964 (t0) REVERT: B 580 GLN cc_start: 0.7999 (mm110) cc_final: 0.7787 (mm110) REVERT: B 604 THR cc_start: 0.8446 (p) cc_final: 0.8218 (t) REVERT: B 645 THR cc_start: 0.7930 (t) cc_final: 0.6872 (m) REVERT: B 711 SER cc_start: 0.8524 (t) cc_final: 0.8277 (t) REVERT: B 719 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8133 (p) REVERT: B 752 LEU cc_start: 0.8696 (mt) cc_final: 0.8333 (mp) REVERT: B 773 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6084 (tm-30) REVERT: B 774 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7276 (mm110) REVERT: B 777 ASN cc_start: 0.7824 (m-40) cc_final: 0.7155 (m110) REVERT: B 821 LEU cc_start: 0.8515 (tp) cc_final: 0.8014 (tt) REVERT: B 904 TYR cc_start: 0.7120 (m-80) cc_final: 0.6766 (m-80) REVERT: B 918 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6924 (mt-10) REVERT: B 950 ASP cc_start: 0.7131 (t70) cc_final: 0.6808 (t70) REVERT: B 975 SER cc_start: 0.8596 (m) cc_final: 0.8127 (t) REVERT: B 990 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: B 993 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8442 (tp) REVERT: B 1038 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8285 (mtpp) REVERT: B 1073 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8244 (mtpp) REVERT: B 1086 LYS cc_start: 0.8255 (ptmt) cc_final: 0.7987 (mtpt) REVERT: B 1097 SER cc_start: 0.8780 (t) cc_final: 0.8129 (p) REVERT: C 41 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7912 (pttt) REVERT: C 52 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7228 (tm130) REVERT: C 105 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7473 (mm) REVERT: C 106 PHE cc_start: 0.7691 (m-80) cc_final: 0.7370 (m-10) REVERT: C 204 LYS cc_start: 0.8452 (tttt) cc_final: 0.7999 (tttp) REVERT: C 224 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: C 269 TYR cc_start: 0.8555 (m-80) cc_final: 0.7970 (m-80) REVERT: C 307 THR cc_start: 0.7412 (m) cc_final: 0.7182 (p) REVERT: C 327 VAL cc_start: 0.8482 (m) cc_final: 0.8024 (t) REVERT: C 414 GLN cc_start: 0.7790 (mp10) cc_final: 0.7401 (mp10) REVERT: C 454 ARG cc_start: 0.7623 (ttt180) cc_final: 0.7311 (ttt180) REVERT: C 461 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7473 (mt) REVERT: C 465 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7214 (tm-30) REVERT: C 509 ARG cc_start: 0.6413 (mtm110) cc_final: 0.6127 (mtm110) REVERT: C 537 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7817 (mtpp) REVERT: C 588 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8120 (p) REVERT: C 655 TYR cc_start: 0.7800 (t80) cc_final: 0.7501 (t80) REVERT: C 704 SER cc_start: 0.8363 (p) cc_final: 0.8126 (p) REVERT: C 707 TYR cc_start: 0.7881 (t80) cc_final: 0.7050 (t80) REVERT: C 711 SER cc_start: 0.8672 (m) cc_final: 0.8368 (p) REVERT: C 724 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8417 (p) REVERT: C 729 VAL cc_start: 0.8472 (p) cc_final: 0.8220 (t) REVERT: C 752 LEU cc_start: 0.8769 (mm) cc_final: 0.8326 (mt) REVERT: C 755 GLN cc_start: 0.7631 (pp30) cc_final: 0.7107 (pp30) REVERT: C 776 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8164 (tttp) REVERT: C 825 LYS cc_start: 0.8291 (tppt) cc_final: 0.7983 (tppt) REVERT: C 868 GLU cc_start: 0.7253 (tp30) cc_final: 0.6950 (tp30) REVERT: C 869 MET cc_start: 0.7680 (mmm) cc_final: 0.7449 (mmm) REVERT: C 921 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8048 (mmmm) REVERT: C 927 PHE cc_start: 0.8662 (t80) cc_final: 0.8191 (t80) REVERT: C 1005 GLN cc_start: 0.7714 (tp40) cc_final: 0.7219 (tp40) REVERT: C 1038 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8184 (mmtt) REVERT: C 1073 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7840 (mtpp) REVERT: C 1123 SER cc_start: 0.8199 (t) cc_final: 0.7985 (t) outliers start: 159 outliers final: 99 residues processed: 737 average time/residue: 0.3678 time to fit residues: 419.8528 Evaluate side-chains 736 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 617 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 168 optimal weight: 0.0070 chunk 250 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1101 HIS ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 955 ASN B 957 GLN B1011 GLN C 30 ASN C 81 ASN C 121 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25040 Z= 0.251 Angle : 0.636 9.807 34095 Z= 0.324 Chirality : 0.048 0.346 3957 Planarity : 0.005 0.069 4379 Dihedral : 7.147 94.308 3987 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.78 % Favored : 89.19 % Rotamer: Outliers : 5.25 % Allowed : 22.76 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.15), residues: 3044 helix: 0.92 (0.21), residues: 650 sheet: -1.73 (0.20), residues: 568 loop : -2.64 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.010 0.001 HIS C1048 PHE 0.050 0.002 PHE A 643 TYR 0.026 0.001 TYR B 707 ARG 0.010 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 643 time to evaluate : 2.893 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7712 (t70) cc_final: 0.7422 (t-170) REVERT: A 52 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6865 (tm-30) REVERT: A 88 ASP cc_start: 0.8113 (m-30) cc_final: 0.7662 (m-30) REVERT: A 102 ARG cc_start: 0.6806 (mtm-85) cc_final: 0.6588 (mtm-85) REVERT: A 188 ARG cc_start: 0.7938 (ptp-110) cc_final: 0.7601 (ptp90) REVERT: A 224 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6602 (mm-30) REVERT: A 267 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.8058 (p) REVERT: A 307 THR cc_start: 0.8374 (m) cc_final: 0.8055 (p) REVERT: A 356 LYS cc_start: 0.7989 (ptmm) cc_final: 0.7708 (ptmm) REVERT: A 358 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7253 (pt) REVERT: A 359 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7648 (t) REVERT: A 360 ASN cc_start: 0.8165 (m110) cc_final: 0.7856 (m110) REVERT: A 380 TYR cc_start: 0.6909 (m-80) cc_final: 0.6551 (m-10) REVERT: A 386 LYS cc_start: 0.8473 (mttp) cc_final: 0.7893 (mtmm) REVERT: A 420 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6342 (m-30) REVERT: A 542 ASN cc_start: 0.8879 (t0) cc_final: 0.8540 (t0) REVERT: A 544 ASN cc_start: 0.7845 (m110) cc_final: 0.7465 (m-40) REVERT: A 558 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7967 (mtpp) REVERT: A 675 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6908 (mm-40) REVERT: A 698 SER cc_start: 0.8539 (t) cc_final: 0.8062 (p) REVERT: A 768 THR cc_start: 0.8277 (m) cc_final: 0.8002 (p) REVERT: A 854 LYS cc_start: 0.8515 (tptp) cc_final: 0.8153 (tptp) REVERT: A 855 PHE cc_start: 0.8215 (m-80) cc_final: 0.7978 (m-80) REVERT: A 918 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 949 GLN cc_start: 0.7949 (mm110) cc_final: 0.7516 (mm-40) REVERT: A 997 ILE cc_start: 0.8694 (mm) cc_final: 0.8483 (mt) REVERT: A 998 THR cc_start: 0.8122 (t) cc_final: 0.7781 (p) REVERT: A 1097 SER cc_start: 0.8418 (t) cc_final: 0.7584 (p) REVERT: A 1139 ASP cc_start: 0.7759 (t70) cc_final: 0.7438 (t70) REVERT: B 52 GLN cc_start: 0.7718 (tp40) cc_final: 0.7295 (tp40) REVERT: B 82 PRO cc_start: 0.8634 (Cg_endo) cc_final: 0.8281 (Cg_exo) REVERT: B 91 TYR cc_start: 0.7875 (t80) cc_final: 0.7674 (t80) REVERT: B 119 ILE cc_start: 0.8320 (mt) cc_final: 0.8118 (mm) REVERT: B 129 LYS cc_start: 0.7841 (tppt) cc_final: 0.7409 (tppt) REVERT: B 169 GLU cc_start: 0.7528 (pm20) cc_final: 0.7002 (pm20) REVERT: B 177 MET cc_start: 0.6654 (tmt) cc_final: 0.6237 (tmt) REVERT: B 188 ARG cc_start: 0.6376 (ttm-80) cc_final: 0.6152 (ttm-80) REVERT: B 190 PHE cc_start: 0.8136 (m-10) cc_final: 0.7828 (m-10) REVERT: B 194 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7087 (p0) REVERT: B 224 GLU cc_start: 0.6670 (pm20) cc_final: 0.6319 (pm20) REVERT: B 237 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.6133 (mtp180) REVERT: B 239 GLN cc_start: 0.6885 (tp40) cc_final: 0.6528 (mm110) REVERT: B 279 TYR cc_start: 0.8100 (m-10) cc_final: 0.7817 (m-10) REVERT: B 362 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7773 (p) REVERT: B 406 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6657 (tt0) REVERT: B 537 LYS cc_start: 0.8252 (tttp) cc_final: 0.7886 (tttm) REVERT: B 547 LYS cc_start: 0.8022 (mttm) cc_final: 0.7682 (mmtm) REVERT: B 549 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 551 VAL cc_start: 0.8865 (t) cc_final: 0.8514 (p) REVERT: B 556 ASN cc_start: 0.8284 (p0) cc_final: 0.7916 (p0) REVERT: B 558 LYS cc_start: 0.8378 (mppt) cc_final: 0.7925 (mppt) REVERT: B 560 LEU cc_start: 0.8780 (mt) cc_final: 0.8559 (mp) REVERT: B 563 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: B 571 ASP cc_start: 0.7359 (t70) cc_final: 0.6956 (t0) REVERT: B 580 GLN cc_start: 0.8068 (mm110) cc_final: 0.7864 (mm110) REVERT: B 604 THR cc_start: 0.8413 (p) cc_final: 0.8204 (t) REVERT: B 645 THR cc_start: 0.7938 (t) cc_final: 0.6886 (m) REVERT: B 711 SER cc_start: 0.8521 (t) cc_final: 0.8249 (t) REVERT: B 719 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 752 LEU cc_start: 0.8645 (mt) cc_final: 0.8312 (mp) REVERT: B 773 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6095 (tm-30) REVERT: B 774 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7213 (mm110) REVERT: B 777 ASN cc_start: 0.7885 (m-40) cc_final: 0.7165 (m110) REVERT: B 821 LEU cc_start: 0.8595 (tp) cc_final: 0.8093 (tt) REVERT: B 904 TYR cc_start: 0.7213 (m-80) cc_final: 0.6857 (m-80) REVERT: B 918 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6916 (mt-10) REVERT: B 950 ASP cc_start: 0.7168 (t70) cc_final: 0.6847 (t70) REVERT: B 975 SER cc_start: 0.8619 (m) cc_final: 0.8157 (t) REVERT: B 984 LEU cc_start: 0.7986 (tp) cc_final: 0.7723 (tp) REVERT: B 988 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6845 (tp30) REVERT: B 990 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: B 993 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8442 (tp) REVERT: B 1038 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8266 (mtpp) REVERT: B 1073 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8244 (mtpp) REVERT: B 1086 LYS cc_start: 0.8256 (ptmt) cc_final: 0.7996 (mtpt) REVERT: B 1097 SER cc_start: 0.8761 (t) cc_final: 0.8141 (p) REVERT: C 41 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7869 (pttt) REVERT: C 105 ILE cc_start: 0.7765 (mm) cc_final: 0.7389 (mm) REVERT: C 106 PHE cc_start: 0.7685 (m-80) cc_final: 0.7377 (m-10) REVERT: C 188 ARG cc_start: 0.6994 (ptp-170) cc_final: 0.6662 (ptp-170) REVERT: C 204 LYS cc_start: 0.8510 (tttt) cc_final: 0.7991 (tttp) REVERT: C 224 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: C 269 TYR cc_start: 0.8553 (m-80) cc_final: 0.7954 (m-80) REVERT: C 307 THR cc_start: 0.7457 (m) cc_final: 0.7126 (p) REVERT: C 353 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.5864 (m-10) REVERT: C 414 GLN cc_start: 0.7932 (mp10) cc_final: 0.7486 (mp10) REVERT: C 454 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7342 (ttt180) REVERT: C 465 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 509 ARG cc_start: 0.6440 (mtm110) cc_final: 0.6076 (mtm110) REVERT: C 588 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8067 (p) REVERT: C 655 TYR cc_start: 0.7855 (t80) cc_final: 0.7654 (t80) REVERT: C 707 TYR cc_start: 0.7899 (t80) cc_final: 0.7066 (t80) REVERT: C 711 SER cc_start: 0.8670 (m) cc_final: 0.8355 (p) REVERT: C 724 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (p) REVERT: C 752 LEU cc_start: 0.8858 (mm) cc_final: 0.8420 (mt) REVERT: C 755 GLN cc_start: 0.7686 (pp30) cc_final: 0.7328 (pp30) REVERT: C 776 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8146 (tttp) REVERT: C 825 LYS cc_start: 0.8312 (tppt) cc_final: 0.7992 (tppt) REVERT: C 868 GLU cc_start: 0.7247 (tp30) cc_final: 0.6970 (tp30) REVERT: C 869 MET cc_start: 0.7708 (mmm) cc_final: 0.7471 (mmm) REVERT: C 921 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8056 (mmmm) REVERT: C 927 PHE cc_start: 0.8673 (t80) cc_final: 0.8183 (t80) REVERT: C 1014 ARG cc_start: 0.7391 (tpp80) cc_final: 0.7080 (ttm170) REVERT: C 1038 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (mmtt) REVERT: C 1073 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7849 (mtpp) REVERT: C 1107 ARG cc_start: 0.7225 (mmm-85) cc_final: 0.6758 (mmm-85) REVERT: C 1123 SER cc_start: 0.8207 (t) cc_final: 0.7997 (t) REVERT: C 1144 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7545 (mm-30) outliers start: 140 outliers final: 105 residues processed: 730 average time/residue: 0.3664 time to fit residues: 413.3147 Evaluate side-chains 752 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 629 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 0.0050 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 644 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 907 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 388 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 957 GLN B1011 GLN C 30 ASN C 52 GLN C 81 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 613 GLN C1101 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25040 Z= 0.209 Angle : 0.618 10.265 34095 Z= 0.315 Chirality : 0.047 0.338 3957 Planarity : 0.004 0.068 4379 Dihedral : 6.979 96.500 3983 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.92 % Favored : 90.05 % Rotamer: Outliers : 5.29 % Allowed : 23.25 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 3044 helix: 1.01 (0.21), residues: 649 sheet: -1.58 (0.20), residues: 574 loop : -2.61 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.010 0.001 HIS C1048 PHE 0.047 0.002 PHE A 347 TYR 0.025 0.001 TYR C 904 ARG 0.008 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 649 time to evaluate : 2.882 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: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6477 (tm-30) REVERT: A 88 ASP cc_start: 0.8109 (m-30) cc_final: 0.7637 (m-30) REVERT: A 102 ARG cc_start: 0.6677 (mtm-85) cc_final: 0.6415 (mtm-85) REVERT: A 188 ARG cc_start: 0.7848 (ptp-110) cc_final: 0.7496 (ptp90) REVERT: A 203 SER cc_start: 0.8480 (p) cc_final: 0.8107 (m) REVERT: A 224 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 307 THR cc_start: 0.8371 (m) cc_final: 0.8041 (p) REVERT: A 328 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7683 (mtp180) REVERT: A 356 LYS cc_start: 0.7782 (ptmm) cc_final: 0.7507 (ptmm) REVERT: A 358 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7125 (pt) REVERT: A 360 ASN cc_start: 0.8192 (m110) cc_final: 0.7977 (m110) REVERT: A 380 TYR cc_start: 0.6933 (m-80) cc_final: 0.6560 (m-10) REVERT: A 386 LYS cc_start: 0.8473 (mttp) cc_final: 0.7894 (mtmm) REVERT: A 537 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7695 (mtpp) REVERT: A 542 ASN cc_start: 0.8851 (t0) cc_final: 0.8592 (t0) REVERT: A 544 ASN cc_start: 0.7859 (m110) cc_final: 0.7447 (m-40) REVERT: A 558 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7959 (mtpp) REVERT: A 564 GLN cc_start: 0.7634 (tm-30) cc_final: 0.6886 (tm-30) REVERT: A 619 GLU cc_start: 0.6512 (tt0) cc_final: 0.6157 (tt0) REVERT: A 675 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6861 (mm-40) REVERT: A 698 SER cc_start: 0.8496 (t) cc_final: 0.7985 (p) REVERT: A 803 SER cc_start: 0.8416 (t) cc_final: 0.8016 (t) REVERT: A 855 PHE cc_start: 0.8174 (m-80) cc_final: 0.7954 (m-80) REVERT: A 918 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 949 GLN cc_start: 0.7882 (mm110) cc_final: 0.7489 (mm-40) REVERT: A 992 GLN cc_start: 0.7933 (mm110) cc_final: 0.7515 (mt0) REVERT: A 997 ILE cc_start: 0.8696 (mm) cc_final: 0.8481 (mt) REVERT: A 998 THR cc_start: 0.8119 (t) cc_final: 0.7785 (p) REVERT: A 1097 SER cc_start: 0.8396 (t) cc_final: 0.7550 (p) REVERT: A 1139 ASP cc_start: 0.7785 (t70) cc_final: 0.7458 (t70) REVERT: B 52 GLN cc_start: 0.7738 (tp40) cc_final: 0.7418 (tp40) REVERT: B 82 PRO cc_start: 0.8636 (Cg_endo) cc_final: 0.8259 (Cg_exo) REVERT: B 119 ILE cc_start: 0.8322 (mt) cc_final: 0.8116 (mm) REVERT: B 129 LYS cc_start: 0.7824 (tppt) cc_final: 0.7380 (tppt) REVERT: B 169 GLU cc_start: 0.7490 (pm20) cc_final: 0.6946 (pm20) REVERT: B 177 MET cc_start: 0.6592 (tmt) cc_final: 0.6190 (tmt) REVERT: B 190 PHE cc_start: 0.8096 (m-10) cc_final: 0.7719 (m-10) REVERT: B 201 ILE cc_start: 0.8366 (mt) cc_final: 0.7777 (tt) REVERT: B 224 GLU cc_start: 0.6594 (pm20) cc_final: 0.6257 (pm20) REVERT: B 237 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6191 (mtp180) REVERT: B 239 GLN cc_start: 0.7017 (tp40) cc_final: 0.6655 (mm110) REVERT: B 279 TYR cc_start: 0.8098 (m-10) cc_final: 0.7849 (m-10) REVERT: B 406 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6609 (tt0) REVERT: B 537 LYS cc_start: 0.8211 (tttp) cc_final: 0.7824 (tttm) REVERT: B 551 VAL cc_start: 0.8889 (t) cc_final: 0.8551 (p) REVERT: B 556 ASN cc_start: 0.8299 (p0) cc_final: 0.7966 (p0) REVERT: B 558 LYS cc_start: 0.8388 (mppt) cc_final: 0.7976 (mppt) REVERT: B 563 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: B 571 ASP cc_start: 0.7380 (t70) cc_final: 0.7076 (t70) REVERT: B 645 THR cc_start: 0.7791 (t) cc_final: 0.6733 (m) REVERT: B 711 SER cc_start: 0.8509 (t) cc_final: 0.8264 (t) REVERT: B 719 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 752 LEU cc_start: 0.8617 (mt) cc_final: 0.8334 (mp) REVERT: B 773 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6117 (tm-30) REVERT: B 774 GLN cc_start: 0.8040 (mm-40) cc_final: 0.6982 (mm110) REVERT: B 777 ASN cc_start: 0.7840 (m-40) cc_final: 0.7204 (m110) REVERT: B 821 LEU cc_start: 0.8459 (tp) cc_final: 0.8084 (tt) REVERT: B 904 TYR cc_start: 0.7144 (m-80) cc_final: 0.6754 (m-80) REVERT: B 918 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6971 (mt-10) REVERT: B 935 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7301 (tp-100) REVERT: B 950 ASP cc_start: 0.7143 (t70) cc_final: 0.6817 (t70) REVERT: B 975 SER cc_start: 0.8629 (m) cc_final: 0.8232 (p) REVERT: B 984 LEU cc_start: 0.7966 (tp) cc_final: 0.7720 (tp) REVERT: B 990 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: B 993 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8444 (tp) REVERT: B 1038 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8257 (mtpp) REVERT: B 1073 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8247 (mtpp) REVERT: B 1086 LYS cc_start: 0.8244 (ptmt) cc_final: 0.8003 (mtpt) REVERT: B 1097 SER cc_start: 0.8681 (t) cc_final: 0.8088 (p) REVERT: C 41 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7893 (pttt) REVERT: C 105 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7387 (mm) REVERT: C 106 PHE cc_start: 0.7673 (m-80) cc_final: 0.7379 (m-10) REVERT: C 119 ILE cc_start: 0.8488 (mm) cc_final: 0.8188 (mt) REVERT: C 188 ARG cc_start: 0.6966 (ptp-170) cc_final: 0.6605 (ptp-170) REVERT: C 204 LYS cc_start: 0.8517 (tttt) cc_final: 0.7843 (tttm) REVERT: C 224 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: C 242 LEU cc_start: 0.7120 (pt) cc_final: 0.6636 (pt) REVERT: C 327 VAL cc_start: 0.8436 (m) cc_final: 0.7959 (t) REVERT: C 349 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.7923 (t) REVERT: C 353 TRP cc_start: 0.6984 (OUTLIER) cc_final: 0.5909 (m-10) REVERT: C 364 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.6487 (p0) REVERT: C 414 GLN cc_start: 0.8082 (mp10) cc_final: 0.7771 (mp10) REVERT: C 454 ARG cc_start: 0.7610 (ttt180) cc_final: 0.7349 (ttt180) REVERT: C 461 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7541 (mt) REVERT: C 465 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7226 (tm-30) REVERT: C 588 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8021 (p) REVERT: C 707 TYR cc_start: 0.7929 (t80) cc_final: 0.7058 (t80) REVERT: C 711 SER cc_start: 0.8648 (m) cc_final: 0.8344 (p) REVERT: C 724 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8434 (p) REVERT: C 742 ILE cc_start: 0.8046 (tt) cc_final: 0.7812 (pt) REVERT: C 776 LYS cc_start: 0.8421 (ttpt) cc_final: 0.8161 (tttp) REVERT: C 825 LYS cc_start: 0.8278 (tppt) cc_final: 0.7978 (tppt) REVERT: C 868 GLU cc_start: 0.7251 (tp30) cc_final: 0.6985 (tp30) REVERT: C 869 MET cc_start: 0.7698 (mmm) cc_final: 0.7441 (mmm) REVERT: C 907 ASN cc_start: 0.8295 (t0) cc_final: 0.8036 (t0) REVERT: C 921 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8062 (mmmm) REVERT: C 927 PHE cc_start: 0.8655 (t80) cc_final: 0.8203 (t80) REVERT: C 1005 GLN cc_start: 0.7721 (tp40) cc_final: 0.7310 (tp40) REVERT: C 1014 ARG cc_start: 0.7429 (tpp80) cc_final: 0.7161 (ttm170) REVERT: C 1038 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8281 (mmtt) REVERT: C 1073 LYS cc_start: 0.8362 (mtpt) cc_final: 0.7856 (mtpp) REVERT: C 1123 SER cc_start: 0.8195 (t) cc_final: 0.7981 (t) outliers start: 141 outliers final: 100 residues processed: 737 average time/residue: 0.3586 time to fit residues: 409.1310 Evaluate side-chains 745 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 628 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 3.9990 chunk 284 optimal weight: 0.3980 chunk 259 optimal weight: 0.7980 chunk 276 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 261 optimal weight: 0.0270 chunk 275 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 774 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 81 ASN B 121 ASN B 218 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 957 GLN C 52 GLN C 81 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 926 GLN C1101 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25040 Z= 0.195 Angle : 0.621 10.353 34095 Z= 0.317 Chirality : 0.047 0.360 3957 Planarity : 0.004 0.068 4379 Dihedral : 6.916 96.806 3981 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 4.91 % Allowed : 23.85 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 3044 helix: 1.09 (0.21), residues: 650 sheet: -1.45 (0.21), residues: 557 loop : -2.53 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.011 0.001 HIS A 49 PHE 0.041 0.002 PHE A 347 TYR 0.039 0.001 TYR B 91 ARG 0.009 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 631 time to evaluate : 2.789 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7694 (t70) cc_final: 0.7461 (t-170) REVERT: A 52 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6441 (tm-30) REVERT: A 88 ASP cc_start: 0.8117 (m-30) cc_final: 0.7630 (m-30) REVERT: A 102 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.6397 (mtm-85) REVERT: A 169 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: A 188 ARG cc_start: 0.7902 (ptp-110) cc_final: 0.7583 (ptp90) REVERT: A 203 SER cc_start: 0.8470 (p) cc_final: 0.8069 (m) REVERT: A 224 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6617 (mm-30) REVERT: A 275 PHE cc_start: 0.8307 (m-80) cc_final: 0.8037 (m-10) REVERT: A 307 THR cc_start: 0.8394 (m) cc_final: 0.8048 (p) REVERT: A 328 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7633 (mtp85) REVERT: A 356 LYS cc_start: 0.7777 (ptmm) cc_final: 0.7513 (ptmm) REVERT: A 359 SER cc_start: 0.7880 (p) cc_final: 0.7447 (t) REVERT: A 360 ASN cc_start: 0.8107 (m110) cc_final: 0.7794 (m110) REVERT: A 380 TYR cc_start: 0.6923 (m-80) cc_final: 0.6583 (m-10) REVERT: A 386 LYS cc_start: 0.8467 (mttp) cc_final: 0.7890 (mtmm) REVERT: A 537 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7768 (mtpp) REVERT: A 542 ASN cc_start: 0.8848 (t0) cc_final: 0.8587 (t0) REVERT: A 544 ASN cc_start: 0.7850 (m110) cc_final: 0.7436 (m-40) REVERT: A 564 GLN cc_start: 0.7635 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 619 GLU cc_start: 0.6405 (tt0) cc_final: 0.6077 (tt0) REVERT: A 675 GLN cc_start: 0.7116 (mm-40) cc_final: 0.6845 (mm-40) REVERT: A 698 SER cc_start: 0.8472 (t) cc_final: 0.7973 (p) REVERT: A 773 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6885 (tm-30) REVERT: A 855 PHE cc_start: 0.8155 (m-80) cc_final: 0.7944 (m-80) REVERT: A 918 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 949 GLN cc_start: 0.7839 (mm110) cc_final: 0.7446 (mm-40) REVERT: A 992 GLN cc_start: 0.7923 (mm110) cc_final: 0.7489 (mt0) REVERT: A 997 ILE cc_start: 0.8671 (mm) cc_final: 0.8465 (mt) REVERT: A 998 THR cc_start: 0.8101 (t) cc_final: 0.7770 (p) REVERT: A 1029 MET cc_start: 0.8468 (tpp) cc_final: 0.8114 (ttm) REVERT: A 1139 ASP cc_start: 0.7766 (t70) cc_final: 0.7453 (t70) REVERT: B 52 GLN cc_start: 0.7776 (tp40) cc_final: 0.7416 (tp40) REVERT: B 82 PRO cc_start: 0.8558 (Cg_endo) cc_final: 0.8150 (Cg_exo) REVERT: B 102 ARG cc_start: 0.6972 (mmt90) cc_final: 0.6730 (mmt90) REVERT: B 119 ILE cc_start: 0.8339 (mt) cc_final: 0.8132 (mm) REVERT: B 129 LYS cc_start: 0.7739 (tppt) cc_final: 0.7249 (tppt) REVERT: B 169 GLU cc_start: 0.7449 (pm20) cc_final: 0.6958 (pm20) REVERT: B 177 MET cc_start: 0.6605 (tmt) cc_final: 0.6196 (tmt) REVERT: B 190 PHE cc_start: 0.8097 (m-10) cc_final: 0.7779 (m-10) REVERT: B 201 ILE cc_start: 0.8377 (mt) cc_final: 0.7780 (tt) REVERT: B 224 GLU cc_start: 0.6563 (pm20) cc_final: 0.6224 (pm20) REVERT: B 237 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6217 (mtp180) REVERT: B 239 GLN cc_start: 0.6964 (tp40) cc_final: 0.6613 (mm110) REVERT: B 279 TYR cc_start: 0.8149 (m-10) cc_final: 0.7911 (m-10) REVERT: B 324 GLU cc_start: 0.7640 (pm20) cc_final: 0.7080 (pm20) REVERT: B 406 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6665 (tt0) REVERT: B 537 LYS cc_start: 0.8193 (tttp) cc_final: 0.7734 (tttm) REVERT: B 551 VAL cc_start: 0.8891 (t) cc_final: 0.8549 (p) REVERT: B 556 ASN cc_start: 0.8300 (p0) cc_final: 0.7979 (p0) REVERT: B 558 LYS cc_start: 0.8397 (mppt) cc_final: 0.7974 (mppt) REVERT: B 563 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: B 571 ASP cc_start: 0.7370 (t70) cc_final: 0.7078 (t70) REVERT: B 711 SER cc_start: 0.8504 (t) cc_final: 0.8234 (t) REVERT: B 719 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8168 (p) REVERT: B 746 SER cc_start: 0.7917 (t) cc_final: 0.7580 (t) REVERT: B 752 LEU cc_start: 0.8646 (mt) cc_final: 0.8355 (mp) REVERT: B 773 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6124 (tm-30) REVERT: B 774 GLN cc_start: 0.8048 (mm-40) cc_final: 0.6932 (mm110) REVERT: B 777 ASN cc_start: 0.7806 (m-40) cc_final: 0.7224 (m110) REVERT: B 821 LEU cc_start: 0.8626 (tp) cc_final: 0.8157 (tt) REVERT: B 904 TYR cc_start: 0.7123 (m-80) cc_final: 0.6740 (m-80) REVERT: B 918 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6947 (mt-10) REVERT: B 950 ASP cc_start: 0.7136 (t70) cc_final: 0.6819 (t70) REVERT: B 975 SER cc_start: 0.8627 (m) cc_final: 0.8241 (p) REVERT: B 984 LEU cc_start: 0.7950 (tp) cc_final: 0.7695 (tp) REVERT: B 990 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: B 993 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8452 (tp) REVERT: B 1038 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8265 (mtpp) REVERT: B 1073 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8241 (mtpp) REVERT: B 1086 LYS cc_start: 0.8249 (ptmt) cc_final: 0.7974 (mtpt) REVERT: B 1097 SER cc_start: 0.8668 (t) cc_final: 0.8079 (p) REVERT: C 41 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7931 (pttt) REVERT: C 105 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7341 (mm) REVERT: C 106 PHE cc_start: 0.7634 (m-80) cc_final: 0.7342 (m-10) REVERT: C 188 ARG cc_start: 0.6914 (ptp-170) cc_final: 0.6597 (ptp-170) REVERT: C 204 LYS cc_start: 0.8528 (tttt) cc_final: 0.7851 (tttm) REVERT: C 349 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.7973 (t) REVERT: C 353 TRP cc_start: 0.6945 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: C 364 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.6863 (p0) REVERT: C 414 GLN cc_start: 0.8080 (mp10) cc_final: 0.7847 (mp10) REVERT: C 454 ARG cc_start: 0.7426 (ttt180) cc_final: 0.7165 (ttt180) REVERT: C 465 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 543 PHE cc_start: 0.7448 (m-10) cc_final: 0.7171 (m-10) REVERT: C 588 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8004 (p) REVERT: C 707 TYR cc_start: 0.7914 (t80) cc_final: 0.6986 (t80) REVERT: C 711 SER cc_start: 0.8649 (m) cc_final: 0.8334 (p) REVERT: C 724 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8440 (p) REVERT: C 742 ILE cc_start: 0.7963 (tt) cc_final: 0.7737 (pt) REVERT: C 776 LYS cc_start: 0.8439 (ttpt) cc_final: 0.8166 (tttp) REVERT: C 825 LYS cc_start: 0.8262 (tppt) cc_final: 0.7971 (tppt) REVERT: C 868 GLU cc_start: 0.7248 (tp30) cc_final: 0.6971 (tp30) REVERT: C 869 MET cc_start: 0.7681 (mmm) cc_final: 0.7427 (mmm) REVERT: C 900 MET cc_start: 0.7817 (mtp) cc_final: 0.7489 (ttm) REVERT: C 921 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8054 (mmmm) REVERT: C 927 PHE cc_start: 0.8634 (t80) cc_final: 0.8166 (t80) REVERT: C 1005 GLN cc_start: 0.7733 (tp40) cc_final: 0.7304 (tp40) REVERT: C 1014 ARG cc_start: 0.7422 (tpp80) cc_final: 0.7151 (ttm170) REVERT: C 1038 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8267 (mmtt) REVERT: C 1073 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7838 (mtpp) REVERT: C 1123 SER cc_start: 0.8194 (t) cc_final: 0.7982 (t) outliers start: 131 outliers final: 100 residues processed: 711 average time/residue: 0.3864 time to fit residues: 430.2093 Evaluate side-chains 729 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 615 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 282 optimal weight: 0.0030 chunk 244 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1108 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 935 GLN B 957 GLN C 81 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25040 Z= 0.197 Angle : 0.626 9.770 34095 Z= 0.319 Chirality : 0.047 0.333 3957 Planarity : 0.004 0.067 4379 Dihedral : 6.816 97.109 3976 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 4.61 % Allowed : 24.41 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 3044 helix: 1.16 (0.21), residues: 649 sheet: -1.34 (0.21), residues: 540 loop : -2.48 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.011 0.001 HIS C1048 PHE 0.036 0.002 PHE A 643 TYR 0.035 0.001 TYR B 91 ARG 0.008 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 618 time to evaluate : 2.680 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7720 (t70) cc_final: 0.7477 (t-170) REVERT: A 52 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6482 (tm-30) REVERT: A 102 ARG cc_start: 0.6681 (mtm-85) cc_final: 0.6381 (mtm-85) REVERT: A 169 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: A 188 ARG cc_start: 0.7891 (ptp-110) cc_final: 0.7538 (ptp90) REVERT: A 203 SER cc_start: 0.8441 (p) cc_final: 0.8075 (m) REVERT: A 224 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6597 (mm-30) REVERT: A 275 PHE cc_start: 0.8295 (m-80) cc_final: 0.8021 (m-10) REVERT: A 307 THR cc_start: 0.8326 (m) cc_final: 0.7994 (p) REVERT: A 356 LYS cc_start: 0.7750 (ptmm) cc_final: 0.7529 (ptmm) REVERT: A 359 SER cc_start: 0.7952 (p) cc_final: 0.7570 (t) REVERT: A 360 ASN cc_start: 0.8114 (m110) cc_final: 0.7829 (m110) REVERT: A 380 TYR cc_start: 0.6934 (m-80) cc_final: 0.6570 (m-10) REVERT: A 386 LYS cc_start: 0.8468 (mttp) cc_final: 0.7895 (mtmm) REVERT: A 537 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7734 (mtpp) REVERT: A 542 ASN cc_start: 0.8841 (t0) cc_final: 0.8581 (t0) REVERT: A 564 GLN cc_start: 0.7630 (mm-40) cc_final: 0.6912 (tm-30) REVERT: A 619 GLU cc_start: 0.6279 (tt0) cc_final: 0.5950 (tt0) REVERT: A 675 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6805 (mm-40) REVERT: A 698 SER cc_start: 0.8429 (t) cc_final: 0.7953 (p) REVERT: A 855 PHE cc_start: 0.8184 (m-80) cc_final: 0.7941 (m-80) REVERT: A 918 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 949 GLN cc_start: 0.7844 (mm110) cc_final: 0.7449 (mm-40) REVERT: A 997 ILE cc_start: 0.8670 (mm) cc_final: 0.8462 (mt) REVERT: A 998 THR cc_start: 0.8105 (t) cc_final: 0.7767 (p) REVERT: A 1108 ASN cc_start: 0.8330 (m110) cc_final: 0.8088 (m-40) REVERT: A 1139 ASP cc_start: 0.7768 (t70) cc_final: 0.7457 (t70) REVERT: A 1141 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 52 GLN cc_start: 0.7771 (tp40) cc_final: 0.7371 (tp40) REVERT: B 82 PRO cc_start: 0.8568 (Cg_endo) cc_final: 0.8168 (Cg_exo) REVERT: B 129 LYS cc_start: 0.7763 (tppt) cc_final: 0.7251 (tppt) REVERT: B 169 GLU cc_start: 0.7486 (pm20) cc_final: 0.6953 (pm20) REVERT: B 177 MET cc_start: 0.6596 (tmt) cc_final: 0.6201 (tmt) REVERT: B 190 PHE cc_start: 0.8093 (m-10) cc_final: 0.7796 (m-10) REVERT: B 201 ILE cc_start: 0.8372 (mt) cc_final: 0.7773 (tt) REVERT: B 224 GLU cc_start: 0.6546 (pm20) cc_final: 0.6199 (pm20) REVERT: B 237 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6292 (mtp180) REVERT: B 239 GLN cc_start: 0.7072 (tp40) cc_final: 0.6716 (mm110) REVERT: B 279 TYR cc_start: 0.8146 (m-10) cc_final: 0.7922 (m-10) REVERT: B 324 GLU cc_start: 0.7641 (pm20) cc_final: 0.7074 (pm20) REVERT: B 406 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6671 (tt0) REVERT: B 537 LYS cc_start: 0.8191 (tttp) cc_final: 0.7716 (tttm) REVERT: B 551 VAL cc_start: 0.8867 (t) cc_final: 0.8535 (p) REVERT: B 556 ASN cc_start: 0.8311 (p0) cc_final: 0.8048 (p0) REVERT: B 558 LYS cc_start: 0.8385 (mppt) cc_final: 0.7978 (mppt) REVERT: B 563 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: B 571 ASP cc_start: 0.7382 (t70) cc_final: 0.7087 (t70) REVERT: B 711 SER cc_start: 0.8481 (t) cc_final: 0.8224 (t) REVERT: B 719 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8192 (p) REVERT: B 742 ILE cc_start: 0.8586 (mm) cc_final: 0.8350 (mt) REVERT: B 746 SER cc_start: 0.7910 (t) cc_final: 0.7593 (t) REVERT: B 752 LEU cc_start: 0.8621 (mt) cc_final: 0.8340 (mp) REVERT: B 773 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6140 (tm-30) REVERT: B 774 GLN cc_start: 0.8042 (mm-40) cc_final: 0.6875 (mm110) REVERT: B 777 ASN cc_start: 0.7825 (m-40) cc_final: 0.7242 (m110) REVERT: B 821 LEU cc_start: 0.8600 (tp) cc_final: 0.8147 (tt) REVERT: B 869 MET cc_start: 0.7999 (mtt) cc_final: 0.7747 (mtp) REVERT: B 904 TYR cc_start: 0.7144 (m-80) cc_final: 0.6765 (m-80) REVERT: B 918 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6935 (mt-10) REVERT: B 950 ASP cc_start: 0.7147 (t70) cc_final: 0.6825 (t70) REVERT: B 975 SER cc_start: 0.8620 (m) cc_final: 0.8149 (t) REVERT: B 977 LEU cc_start: 0.8438 (mm) cc_final: 0.8180 (mt) REVERT: B 984 LEU cc_start: 0.7970 (tp) cc_final: 0.7514 (tp) REVERT: B 988 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6588 (tp30) REVERT: B 990 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: B 993 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8450 (tp) REVERT: B 1038 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8263 (mtpp) REVERT: B 1073 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8285 (mtpp) REVERT: B 1086 LYS cc_start: 0.8239 (ptmt) cc_final: 0.8005 (mtpt) REVERT: B 1097 SER cc_start: 0.8655 (t) cc_final: 0.8078 (p) REVERT: C 41 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7924 (pttt) REVERT: C 53 ASP cc_start: 0.6652 (t0) cc_final: 0.6253 (t0) REVERT: C 105 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7318 (mm) REVERT: C 106 PHE cc_start: 0.7619 (m-80) cc_final: 0.7340 (m-10) REVERT: C 119 ILE cc_start: 0.8495 (mm) cc_final: 0.8140 (mt) REVERT: C 204 LYS cc_start: 0.8542 (tttt) cc_final: 0.7868 (tttm) REVERT: C 224 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6759 (pm20) REVERT: C 327 VAL cc_start: 0.8399 (m) cc_final: 0.7933 (t) REVERT: C 349 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7940 (t) REVERT: C 353 TRP cc_start: 0.6988 (OUTLIER) cc_final: 0.5902 (m-10) REVERT: C 364 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.6527 (p0) REVERT: C 414 GLN cc_start: 0.8066 (mp10) cc_final: 0.7798 (mp10) REVERT: C 454 ARG cc_start: 0.7448 (ttt180) cc_final: 0.7247 (ttt180) REVERT: C 465 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7245 (tm-30) REVERT: C 495 TYR cc_start: 0.7522 (m-10) cc_final: 0.7318 (m-10) REVERT: C 565 PHE cc_start: 0.6842 (m-10) cc_final: 0.6479 (m-10) REVERT: C 588 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.7979 (p) REVERT: C 707 TYR cc_start: 0.7923 (t80) cc_final: 0.6988 (t80) REVERT: C 711 SER cc_start: 0.8607 (m) cc_final: 0.8290 (p) REVERT: C 724 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (p) REVERT: C 776 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8171 (tttp) REVERT: C 825 LYS cc_start: 0.8262 (tppt) cc_final: 0.7968 (tppt) REVERT: C 868 GLU cc_start: 0.7258 (tp30) cc_final: 0.6934 (tp30) REVERT: C 869 MET cc_start: 0.7655 (mmm) cc_final: 0.7409 (mmm) REVERT: C 900 MET cc_start: 0.7804 (mtp) cc_final: 0.7499 (ttm) REVERT: C 921 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8069 (mmmm) REVERT: C 927 PHE cc_start: 0.8613 (t80) cc_final: 0.8191 (t80) REVERT: C 1005 GLN cc_start: 0.7729 (tp40) cc_final: 0.7270 (tp40) REVERT: C 1014 ARG cc_start: 0.7412 (tpp80) cc_final: 0.7174 (ttm170) REVERT: C 1038 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8294 (mmtt) REVERT: C 1073 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7853 (mtpp) REVERT: C 1123 SER cc_start: 0.8195 (t) cc_final: 0.7983 (t) outliers start: 123 outliers final: 99 residues processed: 698 average time/residue: 0.3570 time to fit residues: 384.7447 Evaluate side-chains 716 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 601 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 225 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 251 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 957 GLN C 52 GLN C 81 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113654 restraints weight = 40557.951| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.75 r_work: 0.3342 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25040 Z= 0.220 Angle : 0.634 14.024 34095 Z= 0.322 Chirality : 0.048 0.336 3957 Planarity : 0.004 0.067 4379 Dihedral : 6.870 97.595 3976 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.28 % Favored : 89.68 % Rotamer: Outliers : 4.87 % Allowed : 24.18 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 3044 helix: 1.17 (0.21), residues: 649 sheet: -1.29 (0.21), residues: 549 loop : -2.46 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.013 0.001 HIS C1048 PHE 0.036 0.002 PHE A 643 TYR 0.044 0.001 TYR C 904 ARG 0.010 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7628.95 seconds wall clock time: 136 minutes 21.37 seconds (8181.37 seconds total)