Starting phenix.real_space_refine on Fri Apr 12 16:16:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woq_32655/04_2024/7woq_32655.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woq_32655/04_2024/7woq_32655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woq_32655/04_2024/7woq_32655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woq_32655/04_2024/7woq_32655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woq_32655/04_2024/7woq_32655.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woq_32655/04_2024/7woq_32655.pdb" } resolution = 3.47 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= 0.026 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 119 5.16 5 C 16756 2.51 5 N 4322 2.21 5 O 5024 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 "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 "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 223": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26221 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" 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: "B" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} 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: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 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: 14.13, per 1000 atoms: 0.54 Number of scatterers: 26221 At special positions: 0 Unit cell: (137.256, 134.064, 200.032, 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 119 16.00 O 5024 8.00 N 4322 7.00 C 16756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.04 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " 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: 10.20 Conformation dependent library (CDL) restraints added in 5.1 seconds 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6220 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 52 sheets defined 20.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.214A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.157A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 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 756 Processing helix chain 'A' and resid 761 through 782 removed outlier: 3.772A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.894A 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: 4.029A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 939 removed outlier: 4.422A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.530A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.836A 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 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.177A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1001 " --> pdb=" O ILE A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1147 removed outlier: 3.838A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1143 through 1147' Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.137A pdb=" N ASP B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.862A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.606A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.694A 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 747 through 755 removed outlier: 3.582A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 778 removed outlier: 3.836A 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: 3.608A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.591A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.533A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.571A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 4.327A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 981' Processing helix chain 'B' and resid 985 through 993 removed outlier: 4.259A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1033 removed outlier: 3.606A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.905A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.075A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.504A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.855A pdb=" N GLY C 447 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.693A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.581A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.933A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.502A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.052A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.487A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.993A 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 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: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.365A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 201 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 229 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.748A 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: 7.184A 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: 7.773A 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: 5.762A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 718 removed outlier: 6.877A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 728 removed outlier: 7.156A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.503A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.267A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 224 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.516A pdb=" N ARG C 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.672A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 93 through 96 removed outlier: 3.925A pdb=" N SER B 94 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.989A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.564A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.709A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 728 removed outlier: 3.767A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.533A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.694A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.876A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.524A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.921A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 90 through 93 removed outlier: 7.614A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 203 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.979A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.863A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.323A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.791A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.294A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.165A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 64 through 69 removed outlier: 5.425A pdb=" N SER D 65 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 172 through 176 removed outlier: 6.127A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2004 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: 10.24 Time building geometry restraints manager: 11.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7262 1.33 - 1.45: 4990 1.45 - 1.57: 14433 1.57 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 26835 Sorted by residual: bond pdb=" CA ASN A 30 " pdb=" C ASN A 30 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.28e-02 6.10e+03 6.37e+01 bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.14e-02 7.69e+03 2.24e+01 bond pdb=" CA ALA B 27 " pdb=" C ALA B 27 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.36e+01 bond pdb=" CA ASN A 331 " pdb=" C ASN A 331 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.28e-02 6.10e+03 1.32e+01 bond pdb=" N TYR B 28 " pdb=" CA TYR B 28 " ideal model delta sigma weight residual 1.458 1.416 0.042 1.16e-02 7.43e+03 1.28e+01 ... (remaining 26830 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 860 107.15 - 113.85: 14889 113.85 - 120.56: 9876 120.56 - 127.27: 10673 127.27 - 133.97: 235 Bond angle restraints: 36533 Sorted by residual: angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 120.82 129.70 -8.88 1.47e+00 4.63e-01 3.65e+01 angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 120.21 114.92 5.29 9.60e-01 1.09e+00 3.04e+01 angle pdb=" C ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta sigma weight residual 110.92 103.52 7.40 1.59e+00 3.96e-01 2.16e+01 angle pdb=" N ASN B 30 " pdb=" CA ASN B 30 " pdb=" C ASN B 30 " ideal model delta sigma weight residual 109.94 117.04 -7.10 1.57e+00 4.06e-01 2.04e+01 angle pdb=" C ASN B 30 " pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " ideal model delta sigma weight residual 112.63 103.66 8.97 2.16e+00 2.14e-01 1.73e+01 ... (remaining 36528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 15553 17.27 - 34.54: 655 34.54 - 51.82: 110 51.82 - 69.09: 21 69.09 - 86.36: 2 Dihedral angle restraints: 16341 sinusoidal: 6664 harmonic: 9677 Sorted by residual: dihedral pdb=" CA ASN C1135 " pdb=" CB ASN C1135 " pdb=" CG ASN C1135 " pdb=" OD1 ASN C1135 " ideal model delta sinusoidal sigma weight residual 120.00 -173.94 -66.06 2 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" C ASN A 331 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta harmonic sigma weight residual -122.60 -114.69 -7.91 0 2.50e+00 1.60e-01 1.00e+01 dihedral pdb=" CA ALA B 570 " pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta harmonic sigma weight residual 180.00 164.23 15.77 0 5.00e+00 4.00e-02 9.95e+00 ... (remaining 16338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4195 0.136 - 0.272: 16 0.272 - 0.408: 3 0.408 - 0.544: 1 0.544 - 0.680: 1 Chirality restraints: 4216 Sorted by residual: 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 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 4213 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG A1308 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.092 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1305 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG C1305 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C1305 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG C1305 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG C1305 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG B1310 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " 0.146 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2830 2.75 - 3.29: 26309 3.29 - 3.83: 42867 3.83 - 4.36: 49414 4.36 - 4.90: 85041 Nonbonded interactions: 206461 Sorted by model distance: nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.216 2.440 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.217 2.440 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.229 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR B 719 " pdb=" O VAL B1068 " model vdw 2.236 2.440 ... (remaining 206456 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 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 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: 1.800 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: 8.310 Check model and map are aligned: 0.380 Set scattering table: 0.260 Process input model: 70.260 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 0.102 26835 Z= 0.209 Angle : 0.563 8.975 36533 Z= 0.321 Chirality : 0.046 0.680 4216 Planarity : 0.016 0.306 4697 Dihedral : 9.328 86.360 9998 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.75 % Favored : 91.94 % Rotamer: Outliers : 5.15 % Allowed : 8.37 % Favored : 86.49 % 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: -4.15 (0.12), residues: 3276 helix: -0.87 (0.19), residues: 639 sheet: -2.88 (0.18), residues: 595 loop : -3.56 (0.11), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 162 HIS 0.002 0.000 HIS C 519 PHE 0.010 0.001 PHE C 375 TYR 0.011 0.001 TYR C1067 ARG 0.001 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 737 time to evaluate : 3.163 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7624 (p0) cc_final: 0.7316 (p0) REVERT: A 43 PHE cc_start: 0.8230 (t80) cc_final: 0.8005 (t80) REVERT: A 46 SER cc_start: 0.8974 (m) cc_final: 0.8726 (p) REVERT: A 118 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7278 (pp) REVERT: A 186 ASN cc_start: 0.7068 (p0) cc_final: 0.6674 (p0) REVERT: A 208 ILE cc_start: 0.8579 (pp) cc_final: 0.8376 (pt) REVERT: A 239 GLN cc_start: 0.7272 (tp40) cc_final: 0.6972 (tp40) REVERT: A 241 LEU cc_start: 0.7851 (pt) cc_final: 0.7389 (pp) REVERT: A 307 THR cc_start: 0.8400 (m) cc_final: 0.7929 (p) REVERT: A 528 LYS cc_start: 0.7364 (tptp) cc_final: 0.7158 (tptp) REVERT: A 558 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8273 (mmmm) REVERT: A 563 GLN cc_start: 0.6738 (mt0) cc_final: 0.6380 (mt0) REVERT: A 574 ASP cc_start: 0.6988 (t70) cc_final: 0.6608 (t0) REVERT: A 581 THR cc_start: 0.8154 (t) cc_final: 0.7950 (t) REVERT: A 602 THR cc_start: 0.8516 (m) cc_final: 0.8245 (p) REVERT: A 615 VAL cc_start: 0.8521 (t) cc_final: 0.8118 (m) REVERT: A 655 TYR cc_start: 0.8202 (t80) cc_final: 0.7935 (t80) REVERT: A 663 ASP cc_start: 0.7739 (t70) cc_final: 0.7354 (t0) REVERT: A 664 ILE cc_start: 0.8743 (mt) cc_final: 0.8256 (mm) REVERT: A 675 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6750 (mm-40) REVERT: A 703 ASN cc_start: 0.7907 (t0) cc_final: 0.7623 (t0) REVERT: A 803 SER cc_start: 0.8156 (m) cc_final: 0.7936 (p) REVERT: A 819 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 820 ASP cc_start: 0.7516 (m-30) cc_final: 0.7259 (m-30) REVERT: A 851 CYS cc_start: 0.8033 (t) cc_final: 0.7679 (t) REVERT: A 854 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7966 (tttm) REVERT: A 868 GLU cc_start: 0.7530 (tp30) cc_final: 0.7242 (tp30) REVERT: A 933 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8142 (mttp) REVERT: A 985 ASP cc_start: 0.7337 (p0) cc_final: 0.7031 (p0) REVERT: A 1017 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 1048 HIS cc_start: 0.8225 (t70) cc_final: 0.7886 (t-170) REVERT: A 1050 MET cc_start: 0.7243 (mtm) cc_final: 0.6902 (mtm) REVERT: A 1072 GLU cc_start: 0.8390 (pm20) cc_final: 0.7927 (pm20) REVERT: A 1135 ASN cc_start: 0.8183 (t0) cc_final: 0.7936 (t0) REVERT: A 1144 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 129 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7603 (tppt) REVERT: B 187 LEU cc_start: 0.7933 (tp) cc_final: 0.7598 (mt) REVERT: B 204 LYS cc_start: 0.7539 (tptp) cc_final: 0.7176 (tptp) REVERT: B 280 ASN cc_start: 0.8334 (t0) cc_final: 0.8122 (t0) REVERT: B 281 GLU cc_start: 0.7201 (pp20) cc_final: 0.6956 (pp20) REVERT: B 297 SER cc_start: 0.8216 (m) cc_final: 0.7926 (p) REVERT: B 307 THR cc_start: 0.8753 (m) cc_final: 0.8369 (p) REVERT: B 319 ARG cc_start: 0.7390 (ttm110) cc_final: 0.6871 (ptp-110) REVERT: B 362 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7786 (m) REVERT: B 406 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7342 (mt-10) REVERT: B 542 ASN cc_start: 0.8120 (t0) cc_final: 0.7899 (t0) REVERT: B 557 LYS cc_start: 0.8340 (mttm) cc_final: 0.8105 (mttm) REVERT: B 580 GLN cc_start: 0.8198 (mm110) cc_final: 0.7947 (mm-40) REVERT: B 586 ASP cc_start: 0.7483 (t0) cc_final: 0.7266 (t0) REVERT: B 674 TYR cc_start: 0.8018 (t80) cc_final: 0.7639 (t80) REVERT: B 747 THR cc_start: 0.8276 (p) cc_final: 0.7566 (p) REVERT: B 754 LEU cc_start: 0.8895 (mt) cc_final: 0.8670 (mm) REVERT: B 773 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6436 (tm-30) REVERT: B 776 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8218 (tptm) REVERT: B 780 GLU cc_start: 0.7006 (pt0) cc_final: 0.6737 (pt0) REVERT: B 795 LYS cc_start: 0.8590 (mttt) cc_final: 0.8384 (mttm) REVERT: B 821 LEU cc_start: 0.8647 (tp) cc_final: 0.8204 (tp) REVERT: B 851 CYS cc_start: 0.7665 (t) cc_final: 0.7365 (t) REVERT: B 856 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8667 (mmtm) REVERT: B 914 ASN cc_start: 0.7937 (p0) cc_final: 0.7267 (p0) REVERT: B 949 GLN cc_start: 0.8216 (mm110) cc_final: 0.7673 (mm-40) REVERT: B 953 ASN cc_start: 0.8268 (m-40) cc_final: 0.7775 (m-40) REVERT: B 960 ASN cc_start: 0.7724 (m110) cc_final: 0.7434 (t0) REVERT: B 964 LYS cc_start: 0.8180 (mtmp) cc_final: 0.7836 (mtmm) REVERT: B 979 ASP cc_start: 0.7866 (m-30) cc_final: 0.7425 (m-30) REVERT: B 991 VAL cc_start: 0.8878 (t) cc_final: 0.8098 (p) REVERT: B 1097 SER cc_start: 0.9232 (t) cc_final: 0.9018 (p) REVERT: B 1123 SER cc_start: 0.7890 (t) cc_final: 0.7575 (p) REVERT: C 54 LEU cc_start: 0.8543 (mt) cc_final: 0.8076 (mt) REVERT: C 91 TYR cc_start: 0.7331 (t80) cc_final: 0.6335 (t80) REVERT: C 92 PHE cc_start: 0.7558 (t80) cc_final: 0.7011 (t80) REVERT: C 120 VAL cc_start: 0.8099 (m) cc_final: 0.7871 (p) REVERT: C 133 PHE cc_start: 0.7496 (p90) cc_final: 0.7159 (p90) REVERT: C 224 GLU cc_start: 0.8272 (pm20) cc_final: 0.7832 (pm20) REVERT: C 235 ILE cc_start: 0.8243 (mt) cc_final: 0.7853 (mm) REVERT: C 237 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7268 (ptt180) REVERT: C 265 TYR cc_start: 0.7049 (p90) cc_final: 0.6826 (p90) REVERT: C 355 ARG cc_start: 0.8292 (ttt90) cc_final: 0.7842 (ttt-90) REVERT: C 378 LYS cc_start: 0.7449 (mmmm) cc_final: 0.7173 (mmmm) REVERT: C 546 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7508 (tp) REVERT: C 560 LEU cc_start: 0.8183 (mt) cc_final: 0.7506 (mp) REVERT: C 562 PHE cc_start: 0.7728 (p90) cc_final: 0.7390 (p90) REVERT: C 564 GLN cc_start: 0.6365 (mp-120) cc_final: 0.6093 (mp10) REVERT: C 574 ASP cc_start: 0.6799 (t70) cc_final: 0.6220 (t0) REVERT: C 615 VAL cc_start: 0.8413 (t) cc_final: 0.8178 (m) REVERT: C 663 ASP cc_start: 0.7719 (t70) cc_final: 0.7478 (t0) REVERT: C 693 ILE cc_start: 0.8725 (pt) cc_final: 0.8495 (pt) REVERT: C 732 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8527 (p) REVERT: C 772 VAL cc_start: 0.8603 (t) cc_final: 0.8287 (m) REVERT: C 773 GLU cc_start: 0.7246 (tt0) cc_final: 0.6777 (tt0) REVERT: C 776 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8135 (ttmm) REVERT: C 777 ASN cc_start: 0.7871 (m-40) cc_final: 0.7574 (m110) REVERT: C 797 PHE cc_start: 0.8037 (m-10) cc_final: 0.7826 (m-80) REVERT: C 803 SER cc_start: 0.8725 (m) cc_final: 0.8392 (p) REVERT: C 821 LEU cc_start: 0.8418 (tp) cc_final: 0.7947 (tt) REVERT: C 949 GLN cc_start: 0.7888 (mm110) cc_final: 0.7438 (mm-40) REVERT: C 953 ASN cc_start: 0.7906 (m-40) cc_final: 0.7594 (m110) REVERT: C 964 LYS cc_start: 0.8404 (tmtm) cc_final: 0.8121 (ttmm) REVERT: C 965 GLN cc_start: 0.7809 (mt0) cc_final: 0.7586 (tt0) REVERT: C 970 PHE cc_start: 0.8406 (m-10) cc_final: 0.8185 (m-10) REVERT: C 976 VAL cc_start: 0.8791 (t) cc_final: 0.8462 (t) REVERT: C 979 ASP cc_start: 0.7692 (m-30) cc_final: 0.7408 (m-30) REVERT: C 1072 GLU cc_start: 0.8150 (pm20) cc_final: 0.7936 (pm20) REVERT: C 1111 GLU cc_start: 0.7411 (tt0) cc_final: 0.7168 (tt0) REVERT: C 1118 ASP cc_start: 0.7428 (t70) cc_final: 0.7012 (t0) REVERT: C 1136 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8140 (p) REVERT: C 1138 TYR cc_start: 0.7143 (t80) cc_final: 0.6899 (t80) outliers start: 147 outliers final: 60 residues processed: 855 average time/residue: 0.4272 time to fit residues: 557.2653 Evaluate side-chains 621 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 554 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN 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 386 LYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 358 ILE 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 546 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 100 optimal weight: 0.0670 chunk 157 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 173 GLN A 181 GLN A 245 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 853 GLN A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1010 GLN A1048 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 205 HIS B 354 ASN B 370 ASN B 409 GLN B 540 ASN B 580 GLN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 853 GLN B 872 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 913 GLN B 914 ASN B 935 GLN B 957 GLN B 960 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 360 ASN C 394 ASN C 409 GLN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 564 GLN C 784 GLN C 853 GLN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1002 GLN C1005 GLN C1011 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 165 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26835 Z= 0.235 Angle : 0.598 9.581 36533 Z= 0.300 Chirality : 0.046 0.337 4216 Planarity : 0.004 0.049 4697 Dihedral : 7.082 59.535 4312 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.43 % Allowed : 14.98 % Favored : 79.59 % 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: -3.24 (0.13), residues: 3276 helix: 0.26 (0.21), residues: 658 sheet: -2.28 (0.19), residues: 621 loop : -3.14 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 104 HIS 0.007 0.001 HIS C1048 PHE 0.029 0.001 PHE C 375 TYR 0.022 0.001 TYR A 28 ARG 0.007 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 575 time to evaluate : 2.753 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.9053 (m) cc_final: 0.8847 (p) REVERT: A 104 TRP cc_start: 0.8300 (m-90) cc_final: 0.8058 (m-90) REVERT: A 109 THR cc_start: 0.8519 (p) cc_final: 0.8315 (t) REVERT: A 132 GLU cc_start: 0.6680 (pm20) cc_final: 0.5539 (pm20) REVERT: A 185 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7604 (mmmt) REVERT: A 188 ARG cc_start: 0.7047 (mtt-85) cc_final: 0.6555 (mtp85) REVERT: A 208 ILE cc_start: 0.8606 (pp) cc_final: 0.8371 (pt) REVERT: A 215 ASP cc_start: 0.7533 (m-30) cc_final: 0.7251 (m-30) REVERT: A 239 GLN cc_start: 0.7318 (tp40) cc_final: 0.6870 (tp40) REVERT: A 269 TYR cc_start: 0.8093 (m-80) cc_final: 0.7769 (m-80) REVERT: A 275 PHE cc_start: 0.8406 (m-80) cc_final: 0.8118 (m-10) REVERT: A 297 SER cc_start: 0.8381 (m) cc_final: 0.7760 (p) REVERT: A 306 PHE cc_start: 0.8455 (m-10) cc_final: 0.8184 (m-80) REVERT: A 307 THR cc_start: 0.8585 (m) cc_final: 0.8306 (p) REVERT: A 528 LYS cc_start: 0.7825 (tptp) cc_final: 0.7552 (tptp) REVERT: A 574 ASP cc_start: 0.7333 (t70) cc_final: 0.6853 (t0) REVERT: A 615 VAL cc_start: 0.8101 (t) cc_final: 0.7838 (t) REVERT: A 655 TYR cc_start: 0.8310 (t80) cc_final: 0.7964 (t80) REVERT: A 663 ASP cc_start: 0.7555 (t70) cc_final: 0.7101 (t0) REVERT: A 664 ILE cc_start: 0.8786 (mt) cc_final: 0.8312 (mm) REVERT: A 675 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6821 (mm-40) REVERT: A 780 GLU cc_start: 0.7705 (pt0) cc_final: 0.7330 (tm-30) REVERT: A 851 CYS cc_start: 0.8243 (t) cc_final: 0.7951 (t) REVERT: A 855 PHE cc_start: 0.8032 (m-80) cc_final: 0.7814 (m-80) REVERT: A 894 LEU cc_start: 0.8575 (mp) cc_final: 0.8324 (mm) REVERT: A 933 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8230 (mttp) REVERT: A 1002 GLN cc_start: 0.7588 (tp40) cc_final: 0.7193 (tp40) REVERT: A 1017 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7430 (tp30) REVERT: A 1050 MET cc_start: 0.7626 (mtm) cc_final: 0.7294 (mtp) REVERT: A 1072 GLU cc_start: 0.8321 (pm20) cc_final: 0.7729 (pm20) REVERT: A 1107 ARG cc_start: 0.7414 (mtt90) cc_final: 0.7071 (mtt90) REVERT: A 1112 PRO cc_start: 0.8833 (Cg_exo) cc_final: 0.8503 (Cg_endo) REVERT: B 92 PHE cc_start: 0.7483 (t80) cc_final: 0.7223 (t80) REVERT: B 121 ASN cc_start: 0.6868 (p0) cc_final: 0.6474 (p0) REVERT: B 190 PHE cc_start: 0.8008 (m-10) cc_final: 0.7617 (m-10) REVERT: B 199 PHE cc_start: 0.8558 (t80) cc_final: 0.8135 (t80) REVERT: B 204 LYS cc_start: 0.7805 (tptp) cc_final: 0.7453 (tptp) REVERT: B 229 LEU cc_start: 0.8238 (pp) cc_final: 0.8025 (pp) REVERT: B 271 GLN cc_start: 0.8033 (mt0) cc_final: 0.7767 (mt0) REVERT: B 307 THR cc_start: 0.8769 (m) cc_final: 0.8376 (p) REVERT: B 361 CYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6379 (t) REVERT: B 406 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7727 (mt-10) REVERT: B 542 ASN cc_start: 0.8132 (t0) cc_final: 0.7781 (t0) REVERT: B 552 LEU cc_start: 0.9159 (mm) cc_final: 0.8951 (mp) REVERT: B 558 LYS cc_start: 0.8395 (mmmt) cc_final: 0.7990 (mmmt) REVERT: B 580 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 586 ASP cc_start: 0.7513 (t0) cc_final: 0.7234 (t0) REVERT: B 764 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8116 (ttmm) REVERT: B 773 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6604 (tm-30) REVERT: B 776 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8342 (tptm) REVERT: B 795 LYS cc_start: 0.8654 (mttt) cc_final: 0.8400 (mttm) REVERT: B 821 LEU cc_start: 0.8674 (tp) cc_final: 0.8410 (tp) REVERT: B 851 CYS cc_start: 0.7925 (t) cc_final: 0.7556 (t) REVERT: B 855 PHE cc_start: 0.8228 (m-80) cc_final: 0.7991 (m-80) REVERT: B 856 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8769 (tppt) REVERT: B 904 TYR cc_start: 0.7951 (m-10) cc_final: 0.6943 (m-10) REVERT: B 914 ASN cc_start: 0.7610 (p0) cc_final: 0.7315 (p0) REVERT: B 949 GLN cc_start: 0.8410 (mm110) cc_final: 0.8129 (mm-40) REVERT: B 964 LYS cc_start: 0.8317 (mtmp) cc_final: 0.7993 (ttmm) REVERT: B 978 ASN cc_start: 0.8675 (m-40) cc_final: 0.8313 (m110) REVERT: B 979 ASP cc_start: 0.7985 (m-30) cc_final: 0.7395 (m-30) REVERT: B 1097 SER cc_start: 0.9237 (t) cc_final: 0.9028 (p) REVERT: B 1118 ASP cc_start: 0.7074 (t70) cc_final: 0.6646 (t0) REVERT: C 40 ASP cc_start: 0.7602 (t70) cc_final: 0.7260 (t70) REVERT: C 120 VAL cc_start: 0.8324 (m) cc_final: 0.8033 (p) REVERT: C 224 GLU cc_start: 0.8297 (pm20) cc_final: 0.7545 (pt0) REVERT: C 235 ILE cc_start: 0.8393 (mt) cc_final: 0.8062 (mm) REVERT: C 269 TYR cc_start: 0.8160 (m-80) cc_final: 0.7855 (m-80) REVERT: C 280 ASN cc_start: 0.7757 (t0) cc_final: 0.7377 (t0) REVERT: C 281 GLU cc_start: 0.7508 (pp20) cc_final: 0.7300 (pp20) REVERT: C 293 LEU cc_start: 0.8446 (mp) cc_final: 0.8202 (mt) REVERT: C 378 LYS cc_start: 0.7573 (mmmm) cc_final: 0.7247 (mmmm) REVERT: C 386 LYS cc_start: 0.8154 (mttp) cc_final: 0.7654 (mtpp) REVERT: C 392 PHE cc_start: 0.6396 (m-80) cc_final: 0.5982 (m-80) REVERT: C 462 LYS cc_start: 0.8228 (tptt) cc_final: 0.7755 (ttmm) REVERT: C 528 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8152 (mmmm) REVERT: C 537 LYS cc_start: 0.8521 (tttp) cc_final: 0.7982 (mtpp) REVERT: C 558 LYS cc_start: 0.7840 (mmtp) cc_final: 0.7603 (mmtm) REVERT: C 562 PHE cc_start: 0.7803 (p90) cc_final: 0.7437 (p90) REVERT: C 563 GLN cc_start: 0.7284 (pt0) cc_final: 0.7023 (pt0) REVERT: C 564 GLN cc_start: 0.6701 (mp10) cc_final: 0.6449 (mp10) REVERT: C 574 ASP cc_start: 0.7260 (t70) cc_final: 0.6837 (t0) REVERT: C 615 VAL cc_start: 0.8269 (t) cc_final: 0.7690 (m) REVERT: C 693 ILE cc_start: 0.8814 (pt) cc_final: 0.8540 (pt) REVERT: C 732 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8844 (p) REVERT: C 773 GLU cc_start: 0.7620 (tt0) cc_final: 0.6994 (tp30) REVERT: C 776 LYS cc_start: 0.8465 (tmmt) cc_final: 0.8127 (ttmm) REVERT: C 777 ASN cc_start: 0.8156 (m-40) cc_final: 0.7361 (m110) REVERT: C 779 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 792 PRO cc_start: 0.8188 (Cg_exo) cc_final: 0.7969 (Cg_endo) REVERT: C 803 SER cc_start: 0.8824 (m) cc_final: 0.8548 (p) REVERT: C 821 LEU cc_start: 0.8409 (tp) cc_final: 0.8205 (tt) REVERT: C 851 CYS cc_start: 0.8036 (t) cc_final: 0.7461 (t) REVERT: C 949 GLN cc_start: 0.8075 (mm110) cc_final: 0.7855 (mm-40) REVERT: C 964 LYS cc_start: 0.8512 (tmtm) cc_final: 0.8197 (ttmm) REVERT: C 965 GLN cc_start: 0.8104 (mt0) cc_final: 0.7831 (tt0) REVERT: C 978 ASN cc_start: 0.8230 (m-40) cc_final: 0.8024 (m-40) REVERT: C 983 ARG cc_start: 0.8640 (ptt90) cc_final: 0.8374 (ptt90) REVERT: C 990 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7639 (tm-30) REVERT: C 1002 GLN cc_start: 0.7663 (tp40) cc_final: 0.7007 (tp-100) REVERT: C 1072 GLU cc_start: 0.8141 (pm20) cc_final: 0.7790 (pm20) REVERT: C 1107 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6936 (mtt180) REVERT: C 1118 ASP cc_start: 0.7582 (t70) cc_final: 0.7215 (t0) outliers start: 155 outliers final: 94 residues processed: 695 average time/residue: 0.4098 time to fit residues: 440.3449 Evaluate side-chains 625 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 528 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN 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 386 LYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 325 optimal weight: 50.0000 chunk 268 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 321 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1011 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 30 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1058 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 26835 Z= 0.356 Angle : 0.661 14.351 36533 Z= 0.336 Chirality : 0.048 0.353 4216 Planarity : 0.004 0.049 4697 Dihedral : 7.072 59.729 4289 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 5.85 % Allowed : 16.63 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.80 (0.14), residues: 3276 helix: 0.56 (0.21), residues: 660 sheet: -1.79 (0.20), residues: 607 loop : -2.90 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 64 HIS 0.007 0.001 HIS A 205 PHE 0.025 0.002 PHE C 759 TYR 0.024 0.001 TYR C1067 ARG 0.007 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 548 time to evaluate : 2.761 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 45 SER cc_start: 0.8803 (t) cc_final: 0.8594 (t) REVERT: A 46 SER cc_start: 0.9087 (m) cc_final: 0.8854 (p) REVERT: A 64 TRP cc_start: 0.8042 (t60) cc_final: 0.7676 (t-100) REVERT: A 97 LYS cc_start: 0.8474 (tppt) cc_final: 0.8066 (tppt) REVERT: A 102 ARG cc_start: 0.8406 (ptp-170) cc_final: 0.8101 (ptp-170) REVERT: A 104 TRP cc_start: 0.8574 (m-90) cc_final: 0.7829 (m-90) REVERT: A 109 THR cc_start: 0.8549 (p) cc_final: 0.8311 (t) REVERT: A 132 GLU cc_start: 0.6321 (pm20) cc_final: 0.5602 (pm20) REVERT: A 164 ASN cc_start: 0.7457 (p0) cc_final: 0.7053 (p0) REVERT: A 215 ASP cc_start: 0.7531 (m-30) cc_final: 0.7302 (m-30) REVERT: A 269 TYR cc_start: 0.8235 (m-80) cc_final: 0.7254 (m-80) REVERT: A 282 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8098 (m-40) REVERT: A 297 SER cc_start: 0.8464 (m) cc_final: 0.7982 (p) REVERT: A 307 THR cc_start: 0.8654 (m) cc_final: 0.8361 (p) REVERT: A 386 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7285 (mttp) REVERT: A 390 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7079 (tt) REVERT: A 542 ASN cc_start: 0.8499 (t0) cc_final: 0.8112 (t0) REVERT: A 544 ASN cc_start: 0.8420 (m110) cc_final: 0.8143 (t0) REVERT: A 569 ILE cc_start: 0.8568 (pt) cc_final: 0.8230 (mp) REVERT: A 602 THR cc_start: 0.8617 (m) cc_final: 0.8242 (p) REVERT: A 663 ASP cc_start: 0.7520 (t70) cc_final: 0.7213 (t0) REVERT: A 664 ILE cc_start: 0.8770 (mt) cc_final: 0.8333 (mm) REVERT: A 675 GLN cc_start: 0.7130 (mm-40) cc_final: 0.6827 (mm-40) REVERT: A 707 TYR cc_start: 0.8182 (t80) cc_final: 0.7965 (t80) REVERT: A 708 SER cc_start: 0.8622 (t) cc_final: 0.8174 (m) REVERT: A 725 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7004 (tm-30) REVERT: A 780 GLU cc_start: 0.7768 (pt0) cc_final: 0.7392 (tm-30) REVERT: A 790 LYS cc_start: 0.7944 (mppt) cc_final: 0.7558 (mppt) REVERT: A 851 CYS cc_start: 0.8153 (t) cc_final: 0.7731 (t) REVERT: A 855 PHE cc_start: 0.8276 (m-80) cc_final: 0.7916 (m-80) REVERT: A 933 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8197 (mttp) REVERT: A 994 ASP cc_start: 0.7466 (t70) cc_final: 0.7178 (t70) REVERT: A 1001 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8737 (tp) REVERT: A 1006 THR cc_start: 0.8663 (p) cc_final: 0.8380 (t) REVERT: A 1017 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7430 (tp30) REVERT: A 1038 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8458 (mttp) REVERT: A 1050 MET cc_start: 0.7650 (mtm) cc_final: 0.7434 (mtp) REVERT: A 1107 ARG cc_start: 0.7401 (mtt90) cc_final: 0.7134 (mtt90) REVERT: B 52 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 95 ILE cc_start: 0.8864 (mm) cc_final: 0.8295 (tt) REVERT: B 120 VAL cc_start: 0.8182 (t) cc_final: 0.7927 (p) REVERT: B 121 ASN cc_start: 0.7263 (p0) cc_final: 0.6835 (p0) REVERT: B 129 LYS cc_start: 0.8396 (ttmt) cc_final: 0.7812 (tmtt) REVERT: B 190 PHE cc_start: 0.8052 (m-10) cc_final: 0.7838 (m-10) REVERT: B 199 PHE cc_start: 0.8713 (t80) cc_final: 0.8475 (t80) REVERT: B 224 GLU cc_start: 0.7716 (pm20) cc_final: 0.7303 (pt0) REVERT: B 271 GLN cc_start: 0.8063 (mt0) cc_final: 0.7761 (mt0) REVERT: B 299 THR cc_start: 0.8654 (m) cc_final: 0.8329 (p) REVERT: B 307 THR cc_start: 0.8779 (m) cc_final: 0.8380 (p) REVERT: B 324 GLU cc_start: 0.8289 (pm20) cc_final: 0.7780 (pp20) REVERT: B 347 PHE cc_start: 0.4370 (OUTLIER) cc_final: 0.3637 (t80) REVERT: B 406 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 542 ASN cc_start: 0.8258 (t0) cc_final: 0.8018 (t0) REVERT: B 558 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8116 (mmmt) REVERT: B 580 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8069 (mm-40) REVERT: B 586 ASP cc_start: 0.7542 (t0) cc_final: 0.7291 (t0) REVERT: B 764 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8203 (ttpp) REVERT: B 773 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6681 (tm-30) REVERT: B 850 ILE cc_start: 0.9038 (mm) cc_final: 0.8755 (tp) REVERT: B 851 CYS cc_start: 0.8036 (t) cc_final: 0.7463 (p) REVERT: B 904 TYR cc_start: 0.7967 (m-10) cc_final: 0.7681 (m-10) REVERT: B 949 GLN cc_start: 0.8509 (mm110) cc_final: 0.8256 (mm-40) REVERT: B 950 ASP cc_start: 0.7498 (t70) cc_final: 0.7167 (t70) REVERT: B 964 LYS cc_start: 0.8369 (mtmp) cc_final: 0.8098 (ttmm) REVERT: B 978 ASN cc_start: 0.8785 (m-40) cc_final: 0.8561 (m110) REVERT: B 979 ASP cc_start: 0.7933 (m-30) cc_final: 0.7572 (m-30) REVERT: B 1041 ASP cc_start: 0.8221 (m-30) cc_final: 0.7806 (t0) REVERT: B 1118 ASP cc_start: 0.7418 (t70) cc_final: 0.7044 (t0) REVERT: C 40 ASP cc_start: 0.7544 (t70) cc_final: 0.7173 (t70) REVERT: C 104 TRP cc_start: 0.8272 (m-90) cc_final: 0.8040 (m-10) REVERT: C 120 VAL cc_start: 0.8323 (m) cc_final: 0.8037 (p) REVERT: C 235 ILE cc_start: 0.8562 (mt) cc_final: 0.8060 (mm) REVERT: C 280 ASN cc_start: 0.7641 (t0) cc_final: 0.7332 (t0) REVERT: C 281 GLU cc_start: 0.7688 (pp20) cc_final: 0.7431 (pp20) REVERT: C 293 LEU cc_start: 0.8659 (mp) cc_final: 0.8408 (tp) REVERT: C 355 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7890 (ttm-80) REVERT: C 357 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7183 (ttm110) REVERT: C 378 LYS cc_start: 0.7680 (mmmm) cc_final: 0.7319 (mmmm) REVERT: C 386 LYS cc_start: 0.8349 (mttp) cc_final: 0.7802 (tttt) REVERT: C 392 PHE cc_start: 0.6657 (m-80) cc_final: 0.6368 (m-80) REVERT: C 398 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7083 (p0) REVERT: C 409 GLN cc_start: 0.8443 (mt0) cc_final: 0.8103 (tt0) REVERT: C 420 ASP cc_start: 0.8418 (t0) cc_final: 0.7923 (t0) REVERT: C 462 LYS cc_start: 0.8146 (tptt) cc_final: 0.7738 (ttmm) REVERT: C 528 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8286 (mmmt) REVERT: C 537 LYS cc_start: 0.8526 (tttp) cc_final: 0.8261 (mtpp) REVERT: C 551 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (p) REVERT: C 562 PHE cc_start: 0.7868 (p90) cc_final: 0.7556 (p90) REVERT: C 569 ILE cc_start: 0.7855 (mm) cc_final: 0.7554 (mm) REVERT: C 574 ASP cc_start: 0.7452 (t70) cc_final: 0.7101 (t0) REVERT: C 655 TYR cc_start: 0.8016 (t80) cc_final: 0.7754 (t80) REVERT: C 671 CYS cc_start: 0.5235 (m) cc_final: 0.4813 (m) REVERT: C 725 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7133 (tm-30) REVERT: C 773 GLU cc_start: 0.7660 (tt0) cc_final: 0.7034 (tp30) REVERT: C 776 LYS cc_start: 0.8470 (tmmt) cc_final: 0.8188 (ttmm) REVERT: C 777 ASN cc_start: 0.8309 (m-40) cc_final: 0.7274 (m110) REVERT: C 779 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 851 CYS cc_start: 0.7995 (t) cc_final: 0.7433 (t) REVERT: C 949 GLN cc_start: 0.8263 (mm110) cc_final: 0.7831 (mm-40) REVERT: C 964 LYS cc_start: 0.8601 (tmtm) cc_final: 0.8314 (ttmm) REVERT: C 965 GLN cc_start: 0.8150 (mt0) cc_final: 0.7929 (tt0) REVERT: C 1002 GLN cc_start: 0.7905 (tp40) cc_final: 0.7516 (tp40) REVERT: C 1072 GLU cc_start: 0.8155 (pm20) cc_final: 0.7806 (pm20) REVERT: C 1107 ARG cc_start: 0.7381 (mtt180) cc_final: 0.7119 (mpt-90) REVERT: C 1118 ASP cc_start: 0.7683 (t70) cc_final: 0.7322 (t0) outliers start: 167 outliers final: 118 residues processed: 670 average time/residue: 0.4061 time to fit residues: 418.4869 Evaluate side-chains 642 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 516 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 343 ASN 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 143 optimal weight: 40.0000 chunk 202 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 chunk 319 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 186 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 542 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 955 ASN C1058 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26835 Z= 0.286 Angle : 0.635 16.924 36533 Z= 0.318 Chirality : 0.047 0.337 4216 Planarity : 0.004 0.049 4697 Dihedral : 6.789 59.842 4275 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 5.53 % Allowed : 17.92 % Favored : 76.55 % 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: -2.60 (0.14), residues: 3276 helix: 0.78 (0.21), residues: 663 sheet: -1.72 (0.20), residues: 603 loop : -2.78 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.013 0.001 HIS A 205 PHE 0.024 0.002 PHE A 168 TYR 0.026 0.001 TYR C 707 ARG 0.007 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 545 time to evaluate : 3.275 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 45 SER cc_start: 0.8822 (t) cc_final: 0.8616 (t) REVERT: A 46 SER cc_start: 0.9082 (m) cc_final: 0.8855 (p) REVERT: A 64 TRP cc_start: 0.7775 (t60) cc_final: 0.7520 (t-100) REVERT: A 66 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7350 (m90) REVERT: A 97 LYS cc_start: 0.8519 (tppt) cc_final: 0.8248 (tppt) REVERT: A 102 ARG cc_start: 0.8577 (ptp-170) cc_final: 0.8144 (ptm160) REVERT: A 109 THR cc_start: 0.8537 (p) cc_final: 0.8298 (t) REVERT: A 132 GLU cc_start: 0.6589 (pm20) cc_final: 0.5901 (pm20) REVERT: A 164 ASN cc_start: 0.7532 (p0) cc_final: 0.7208 (p0) REVERT: A 186 ASN cc_start: 0.7210 (p0) cc_final: 0.6816 (p0) REVERT: A 282 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: A 297 SER cc_start: 0.8427 (m) cc_final: 0.7932 (p) REVERT: A 298 GLU cc_start: 0.7770 (tt0) cc_final: 0.7501 (tp30) REVERT: A 307 THR cc_start: 0.8691 (m) cc_final: 0.8353 (p) REVERT: A 356 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7340 (tmmm) REVERT: A 390 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7080 (tt) REVERT: A 519 HIS cc_start: 0.3634 (OUTLIER) cc_final: 0.3421 (p90) REVERT: A 537 LYS cc_start: 0.8482 (ttmt) cc_final: 0.7989 (ttmm) REVERT: A 542 ASN cc_start: 0.8525 (t0) cc_final: 0.8268 (t0) REVERT: A 544 ASN cc_start: 0.8460 (m110) cc_final: 0.8087 (t0) REVERT: A 602 THR cc_start: 0.8501 (m) cc_final: 0.8122 (p) REVERT: A 708 SER cc_start: 0.8633 (t) cc_final: 0.8253 (m) REVERT: A 725 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6994 (tm-30) REVERT: A 726 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8418 (mm) REVERT: A 773 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6624 (tm-30) REVERT: A 780 GLU cc_start: 0.7763 (pt0) cc_final: 0.7428 (tm-30) REVERT: A 788 ILE cc_start: 0.8862 (mm) cc_final: 0.8560 (mm) REVERT: A 790 LYS cc_start: 0.7955 (mppt) cc_final: 0.7565 (mppt) REVERT: A 851 CYS cc_start: 0.8218 (t) cc_final: 0.7903 (t) REVERT: A 869 MET cc_start: 0.8345 (mtt) cc_final: 0.8083 (mtm) REVERT: A 933 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8143 (mttp) REVERT: A 955 ASN cc_start: 0.8091 (t0) cc_final: 0.7866 (t0) REVERT: A 957 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7160 (tm130) REVERT: A 994 ASP cc_start: 0.7402 (t70) cc_final: 0.6921 (t0) REVERT: A 1006 THR cc_start: 0.8621 (p) cc_final: 0.8385 (t) REVERT: A 1017 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7488 (tp30) REVERT: A 1038 LYS cc_start: 0.8694 (mttm) cc_final: 0.8467 (mttp) REVERT: A 1050 MET cc_start: 0.7600 (mtm) cc_final: 0.7391 (mtp) REVERT: A 1135 ASN cc_start: 0.8489 (t0) cc_final: 0.8226 (t0) REVERT: B 52 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 95 ILE cc_start: 0.8752 (mm) cc_final: 0.8163 (tp) REVERT: B 120 VAL cc_start: 0.8303 (t) cc_final: 0.7966 (p) REVERT: B 121 ASN cc_start: 0.7169 (p0) cc_final: 0.6698 (p0) REVERT: B 189 GLU cc_start: 0.7841 (mp0) cc_final: 0.7524 (mp0) REVERT: B 190 PHE cc_start: 0.8079 (m-10) cc_final: 0.7689 (m-10) REVERT: B 199 PHE cc_start: 0.8770 (t80) cc_final: 0.8551 (t80) REVERT: B 224 GLU cc_start: 0.7728 (pm20) cc_final: 0.7245 (pt0) REVERT: B 271 GLN cc_start: 0.8055 (mt0) cc_final: 0.7814 (mt0) REVERT: B 299 THR cc_start: 0.8617 (m) cc_final: 0.8312 (p) REVERT: B 307 THR cc_start: 0.8775 (m) cc_final: 0.8350 (p) REVERT: B 347 PHE cc_start: 0.4433 (OUTLIER) cc_final: 0.3714 (t80) REVERT: B 406 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7853 (mt-10) REVERT: B 558 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8083 (mmmt) REVERT: B 568 ASP cc_start: 0.7684 (p0) cc_final: 0.7363 (p0) REVERT: B 580 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8067 (mm-40) REVERT: B 726 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 764 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8117 (ttpp) REVERT: B 773 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6661 (tm-30) REVERT: B 776 LYS cc_start: 0.8712 (tptm) cc_final: 0.8463 (tptm) REVERT: B 796 TYR cc_start: 0.8590 (t80) cc_final: 0.8202 (t80) REVERT: B 821 LEU cc_start: 0.8985 (tp) cc_final: 0.8627 (tt) REVERT: B 850 ILE cc_start: 0.9034 (mm) cc_final: 0.8766 (tp) REVERT: B 851 CYS cc_start: 0.8027 (t) cc_final: 0.7677 (t) REVERT: B 904 TYR cc_start: 0.7963 (m-10) cc_final: 0.6593 (m-10) REVERT: B 947 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8015 (mtmm) REVERT: B 949 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8246 (mm-40) REVERT: B 950 ASP cc_start: 0.7567 (t70) cc_final: 0.7269 (t70) REVERT: B 964 LYS cc_start: 0.8377 (mtmp) cc_final: 0.8062 (ttmm) REVERT: B 979 ASP cc_start: 0.7936 (m-30) cc_final: 0.7574 (m-30) REVERT: B 1041 ASP cc_start: 0.8156 (m-30) cc_final: 0.7765 (t0) REVERT: B 1118 ASP cc_start: 0.7519 (t70) cc_final: 0.7063 (t0) REVERT: C 40 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7378 (t0) REVERT: C 81 ASN cc_start: 0.7254 (p0) cc_final: 0.7009 (t0) REVERT: C 135 PHE cc_start: 0.6254 (p90) cc_final: 0.5771 (p90) REVERT: C 188 ARG cc_start: 0.7362 (ptp-170) cc_final: 0.6905 (ptp-170) REVERT: C 190 PHE cc_start: 0.7575 (m-80) cc_final: 0.7341 (m-80) REVERT: C 226 LEU cc_start: 0.8545 (mt) cc_final: 0.8334 (mp) REVERT: C 237 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7423 (mtp180) REVERT: C 280 ASN cc_start: 0.7600 (t0) cc_final: 0.7287 (t0) REVERT: C 281 GLU cc_start: 0.7766 (pp20) cc_final: 0.7565 (pp20) REVERT: C 323 THR cc_start: 0.8257 (p) cc_final: 0.7092 (m) REVERT: C 355 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8089 (ttm-80) REVERT: C 357 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7011 (ttm110) REVERT: C 378 LYS cc_start: 0.7694 (mmmm) cc_final: 0.7310 (mmmm) REVERT: C 386 LYS cc_start: 0.8296 (mttp) cc_final: 0.7768 (tttt) REVERT: C 392 PHE cc_start: 0.6711 (m-80) cc_final: 0.6350 (m-80) REVERT: C 409 GLN cc_start: 0.8452 (mt0) cc_final: 0.7943 (tt0) REVERT: C 420 ASP cc_start: 0.8423 (t0) cc_final: 0.7902 (t0) REVERT: C 462 LYS cc_start: 0.8126 (tptt) cc_final: 0.7725 (ttmm) REVERT: C 511 VAL cc_start: 0.7671 (t) cc_final: 0.7466 (p) REVERT: C 528 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8270 (mmmm) REVERT: C 537 LYS cc_start: 0.8508 (tttp) cc_final: 0.8272 (mtpp) REVERT: C 551 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 557 LYS cc_start: 0.7778 (mttt) cc_final: 0.7509 (mtmt) REVERT: C 558 LYS cc_start: 0.8339 (mptt) cc_final: 0.7677 (mppt) REVERT: C 563 GLN cc_start: 0.7005 (pt0) cc_final: 0.6752 (pt0) REVERT: C 569 ILE cc_start: 0.7860 (mm) cc_final: 0.7596 (mm) REVERT: C 574 ASP cc_start: 0.7525 (t70) cc_final: 0.7081 (t0) REVERT: C 602 THR cc_start: 0.8601 (m) cc_final: 0.8189 (p) REVERT: C 671 CYS cc_start: 0.5236 (m) cc_final: 0.4811 (m) REVERT: C 675 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6835 (tm-30) REVERT: C 707 TYR cc_start: 0.8048 (t80) cc_final: 0.7761 (t80) REVERT: C 725 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6932 (tm-30) REVERT: C 773 GLU cc_start: 0.7622 (tt0) cc_final: 0.7131 (tp30) REVERT: C 776 LYS cc_start: 0.8508 (tmmt) cc_final: 0.8166 (ttmm) REVERT: C 777 ASN cc_start: 0.8302 (m-40) cc_final: 0.7464 (m110) REVERT: C 779 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 821 LEU cc_start: 0.8367 (tp) cc_final: 0.8081 (tt) REVERT: C 851 CYS cc_start: 0.7968 (t) cc_final: 0.7424 (t) REVERT: C 868 GLU cc_start: 0.7898 (mp0) cc_final: 0.7691 (mp0) REVERT: C 933 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8232 (mtmm) REVERT: C 964 LYS cc_start: 0.8590 (tmtm) cc_final: 0.8265 (ttmm) REVERT: C 991 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8601 (p) REVERT: C 1002 GLN cc_start: 0.7888 (tp40) cc_final: 0.7435 (tp40) REVERT: C 1010 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: C 1072 GLU cc_start: 0.8108 (pm20) cc_final: 0.7760 (pm20) REVERT: C 1107 ARG cc_start: 0.7377 (mtt180) cc_final: 0.7102 (mtt180) REVERT: C 1118 ASP cc_start: 0.7735 (t70) cc_final: 0.7306 (t0) REVERT: C 1144 GLU cc_start: 0.7694 (pp20) cc_final: 0.7404 (pp20) outliers start: 158 outliers final: 107 residues processed: 653 average time/residue: 0.4100 time to fit residues: 412.5382 Evaluate side-chains 648 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 528 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 356 LYS 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 221 optimal weight: 0.0010 chunk 0 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1106 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C1058 HIS C1064 HIS ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26835 Z= 0.221 Angle : 0.610 17.546 36533 Z= 0.303 Chirality : 0.045 0.333 4216 Planarity : 0.004 0.061 4697 Dihedral : 6.498 59.837 4266 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 5.50 % Allowed : 18.66 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3276 helix: 0.91 (0.22), residues: 661 sheet: -1.75 (0.20), residues: 614 loop : -2.57 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 104 HIS 0.005 0.001 HIS C1083 PHE 0.022 0.001 PHE C 759 TYR 0.025 0.001 TYR C 707 ARG 0.005 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 540 time to evaluate : 2.938 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 46 SER cc_start: 0.9036 (m) cc_final: 0.8803 (p) REVERT: A 97 LYS cc_start: 0.8530 (tppt) cc_final: 0.8255 (tppt) REVERT: A 102 ARG cc_start: 0.8480 (ptp-170) cc_final: 0.8197 (ptp-170) REVERT: A 132 GLU cc_start: 0.6571 (pm20) cc_final: 0.5853 (pm20) REVERT: A 164 ASN cc_start: 0.7433 (p0) cc_final: 0.7056 (p0) REVERT: A 186 ASN cc_start: 0.7484 (p0) cc_final: 0.7086 (p0) REVERT: A 239 GLN cc_start: 0.7290 (tp-100) cc_final: 0.7070 (tp-100) REVERT: A 282 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8147 (m-40) REVERT: A 297 SER cc_start: 0.8410 (m) cc_final: 0.7949 (p) REVERT: A 307 THR cc_start: 0.8700 (m) cc_final: 0.8377 (p) REVERT: A 356 LYS cc_start: 0.7816 (tmmm) cc_final: 0.7392 (tmmm) REVERT: A 390 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6955 (tt) REVERT: A 392 PHE cc_start: 0.7177 (m-80) cc_final: 0.6916 (m-80) REVERT: A 542 ASN cc_start: 0.8516 (t0) cc_final: 0.8201 (t0) REVERT: A 602 THR cc_start: 0.8449 (m) cc_final: 0.8066 (p) REVERT: A 664 ILE cc_start: 0.8798 (mt) cc_final: 0.8512 (mp) REVERT: A 708 SER cc_start: 0.8453 (t) cc_final: 0.8047 (m) REVERT: A 725 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7018 (tm-30) REVERT: A 773 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6604 (tm-30) REVERT: A 780 GLU cc_start: 0.7751 (pt0) cc_final: 0.7435 (tm-30) REVERT: A 788 ILE cc_start: 0.8865 (mm) cc_final: 0.8577 (mm) REVERT: A 790 LYS cc_start: 0.7963 (mppt) cc_final: 0.7610 (mppt) REVERT: A 851 CYS cc_start: 0.8244 (t) cc_final: 0.7873 (t) REVERT: A 933 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8126 (mttp) REVERT: A 957 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7206 (tm130) REVERT: A 990 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 994 ASP cc_start: 0.7350 (t70) cc_final: 0.7066 (t70) REVERT: A 995 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7801 (ttp-110) REVERT: A 1017 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7455 (tp30) REVERT: A 1038 LYS cc_start: 0.8676 (mttm) cc_final: 0.8456 (mttm) REVERT: A 1050 MET cc_start: 0.7572 (mtm) cc_final: 0.7360 (mtp) REVERT: A 1135 ASN cc_start: 0.8527 (t0) cc_final: 0.8278 (t0) REVERT: B 52 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 120 VAL cc_start: 0.8417 (t) cc_final: 0.8191 (p) REVERT: B 121 ASN cc_start: 0.7334 (p0) cc_final: 0.6394 (t0) REVERT: B 127 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7442 (t) REVERT: B 129 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7766 (tmtt) REVERT: B 190 PHE cc_start: 0.8001 (m-80) cc_final: 0.7774 (m-10) REVERT: B 199 PHE cc_start: 0.8613 (t80) cc_final: 0.8395 (t80) REVERT: B 228 ASP cc_start: 0.7675 (m-30) cc_final: 0.7411 (t70) REVERT: B 299 THR cc_start: 0.8590 (m) cc_final: 0.8303 (p) REVERT: B 307 THR cc_start: 0.8757 (m) cc_final: 0.8333 (p) REVERT: B 347 PHE cc_start: 0.4383 (OUTLIER) cc_final: 0.3668 (t80) REVERT: B 406 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 558 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8012 (mmmt) REVERT: B 568 ASP cc_start: 0.7687 (p0) cc_final: 0.7485 (p0) REVERT: B 580 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8068 (mm-40) REVERT: B 707 TYR cc_start: 0.8403 (t80) cc_final: 0.8100 (t80) REVERT: B 726 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8543 (mm) REVERT: B 740 MET cc_start: 0.7933 (ttm) cc_final: 0.7608 (mtt) REVERT: B 764 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8076 (ttpp) REVERT: B 773 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6569 (tm-30) REVERT: B 776 LYS cc_start: 0.8714 (tptm) cc_final: 0.8473 (tptm) REVERT: B 796 TYR cc_start: 0.8583 (t80) cc_final: 0.8314 (t80) REVERT: B 851 CYS cc_start: 0.8069 (t) cc_final: 0.7696 (t) REVERT: B 904 TYR cc_start: 0.7913 (m-10) cc_final: 0.6571 (m-10) REVERT: B 947 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8012 (mtmm) REVERT: B 949 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8232 (mm-40) REVERT: B 950 ASP cc_start: 0.7511 (t70) cc_final: 0.7209 (t70) REVERT: B 964 LYS cc_start: 0.8386 (mtmp) cc_final: 0.8060 (ttmm) REVERT: B 979 ASP cc_start: 0.7933 (m-30) cc_final: 0.7560 (m-30) REVERT: B 1017 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 1019 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7334 (ttp80) REVERT: B 1041 ASP cc_start: 0.8108 (m-30) cc_final: 0.7768 (t0) REVERT: B 1118 ASP cc_start: 0.7518 (t70) cc_final: 0.7048 (t0) REVERT: C 130 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7930 (p) REVERT: C 135 PHE cc_start: 0.6397 (p90) cc_final: 0.6148 (p90) REVERT: C 188 ARG cc_start: 0.7540 (ptp-170) cc_final: 0.7013 (ptp-110) REVERT: C 190 PHE cc_start: 0.7594 (m-80) cc_final: 0.7327 (m-80) REVERT: C 199 PHE cc_start: 0.7749 (t80) cc_final: 0.7288 (t80) REVERT: C 237 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7349 (mtm180) REVERT: C 269 TYR cc_start: 0.8270 (m-80) cc_final: 0.7877 (m-80) REVERT: C 280 ASN cc_start: 0.7626 (t0) cc_final: 0.7297 (t0) REVERT: C 319 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: C 323 THR cc_start: 0.8363 (p) cc_final: 0.7338 (m) REVERT: C 357 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.6944 (ttm110) REVERT: C 378 LYS cc_start: 0.7668 (mmmm) cc_final: 0.7288 (mmmm) REVERT: C 386 LYS cc_start: 0.8274 (mttp) cc_final: 0.7715 (mtpt) REVERT: C 388 ASN cc_start: 0.8003 (p0) cc_final: 0.7523 (p0) REVERT: C 392 PHE cc_start: 0.6768 (m-80) cc_final: 0.6374 (m-80) REVERT: C 409 GLN cc_start: 0.8462 (mt0) cc_final: 0.8062 (tt0) REVERT: C 420 ASP cc_start: 0.8419 (t0) cc_final: 0.7886 (t0) REVERT: C 462 LYS cc_start: 0.8098 (tptt) cc_final: 0.7701 (ttmm) REVERT: C 528 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8464 (mmtm) REVERT: C 537 LYS cc_start: 0.8470 (tttp) cc_final: 0.8113 (mtpp) REVERT: C 551 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8225 (p) REVERT: C 558 LYS cc_start: 0.8318 (mptt) cc_final: 0.7664 (mppt) REVERT: C 569 ILE cc_start: 0.7822 (mm) cc_final: 0.7553 (mm) REVERT: C 574 ASP cc_start: 0.7401 (t70) cc_final: 0.6969 (t0) REVERT: C 592 PHE cc_start: 0.8440 (p90) cc_final: 0.8170 (p90) REVERT: C 602 THR cc_start: 0.8586 (m) cc_final: 0.8175 (p) REVERT: C 671 CYS cc_start: 0.5203 (m) cc_final: 0.4745 (m) REVERT: C 675 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 725 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6917 (tm-30) REVERT: C 737 ASP cc_start: 0.7639 (t0) cc_final: 0.7356 (t0) REVERT: C 745 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5631 (p0) REVERT: C 773 GLU cc_start: 0.7629 (tt0) cc_final: 0.6906 (tp30) REVERT: C 776 LYS cc_start: 0.8511 (tmmt) cc_final: 0.8235 (ttmm) REVERT: C 777 ASN cc_start: 0.8263 (m-40) cc_final: 0.7391 (m110) REVERT: C 779 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 821 LEU cc_start: 0.8364 (tp) cc_final: 0.8061 (tt) REVERT: C 851 CYS cc_start: 0.7971 (t) cc_final: 0.7383 (t) REVERT: C 868 GLU cc_start: 0.7901 (mp0) cc_final: 0.7682 (mp0) REVERT: C 933 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8242 (mtmm) REVERT: C 964 LYS cc_start: 0.8614 (tmtm) cc_final: 0.8358 (ttmm) REVERT: C 991 VAL cc_start: 0.8787 (m) cc_final: 0.8587 (p) REVERT: C 1002 GLN cc_start: 0.7900 (tp40) cc_final: 0.7335 (tp-100) REVERT: C 1072 GLU cc_start: 0.8085 (pm20) cc_final: 0.7739 (pm20) REVERT: C 1107 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6961 (mtt180) REVERT: C 1118 ASP cc_start: 0.7679 (t70) cc_final: 0.7328 (t0) REVERT: C 1144 GLU cc_start: 0.7626 (pp20) cc_final: 0.7394 (pp20) outliers start: 157 outliers final: 115 residues processed: 650 average time/residue: 0.4169 time to fit residues: 417.4068 Evaluate side-chains 635 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 511 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 343 ASN 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 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 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 320 optimal weight: 0.0170 chunk 265 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 26 optimal weight: 0.0070 chunk 105 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 901 GLN C 955 ASN C1101 HIS C1119 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26835 Z= 0.164 Angle : 0.600 16.681 36533 Z= 0.295 Chirality : 0.045 0.326 4216 Planarity : 0.004 0.049 4697 Dihedral : 6.234 59.194 4265 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.80 % Allowed : 20.06 % Favored : 75.15 % 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: -2.22 (0.14), residues: 3276 helix: 1.16 (0.22), residues: 661 sheet: -1.75 (0.20), residues: 613 loop : -2.45 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.005 0.001 HIS A1048 PHE 0.028 0.001 PHE A 168 TYR 0.019 0.001 TYR A 170 ARG 0.007 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 528 time to evaluate : 2.686 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 66 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7652 (m90) REVERT: A 97 LYS cc_start: 0.8452 (tppt) cc_final: 0.8207 (tppt) REVERT: A 102 ARG cc_start: 0.8426 (ptp-170) cc_final: 0.8207 (ptp-170) REVERT: A 104 TRP cc_start: 0.8423 (m-90) cc_final: 0.7752 (m-90) REVERT: A 132 GLU cc_start: 0.6501 (pm20) cc_final: 0.5800 (pm20) REVERT: A 164 ASN cc_start: 0.7360 (p0) cc_final: 0.6991 (p0) REVERT: A 186 ASN cc_start: 0.7374 (p0) cc_final: 0.6979 (p0) REVERT: A 198 TYR cc_start: 0.7991 (m-10) cc_final: 0.7667 (m-80) REVERT: A 214 GLU cc_start: 0.7614 (pm20) cc_final: 0.7224 (pm20) REVERT: A 239 GLN cc_start: 0.7306 (tp-100) cc_final: 0.7064 (tp-100) REVERT: A 269 TYR cc_start: 0.8260 (m-80) cc_final: 0.7105 (m-80) REVERT: A 282 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: A 297 SER cc_start: 0.8245 (m) cc_final: 0.7808 (p) REVERT: A 298 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 307 THR cc_start: 0.8672 (m) cc_final: 0.8361 (p) REVERT: A 356 LYS cc_start: 0.7793 (tmmm) cc_final: 0.7382 (tmmm) REVERT: A 390 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.6974 (tt) REVERT: A 392 PHE cc_start: 0.7281 (m-80) cc_final: 0.6962 (m-80) REVERT: A 602 THR cc_start: 0.8368 (m) cc_final: 0.7889 (p) REVERT: A 675 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6729 (mm-40) REVERT: A 708 SER cc_start: 0.8258 (t) cc_final: 0.7890 (m) REVERT: A 725 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7069 (tm-30) REVERT: A 726 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8141 (mm) REVERT: A 773 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6530 (tm-30) REVERT: A 780 GLU cc_start: 0.7741 (pt0) cc_final: 0.7451 (tm-30) REVERT: A 788 ILE cc_start: 0.8816 (mm) cc_final: 0.8545 (mm) REVERT: A 790 LYS cc_start: 0.7977 (mppt) cc_final: 0.7665 (mppt) REVERT: A 796 TYR cc_start: 0.8353 (t80) cc_final: 0.8120 (t80) REVERT: A 851 CYS cc_start: 0.8279 (t) cc_final: 0.7892 (t) REVERT: A 933 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8102 (mttp) REVERT: A 957 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7156 (tm130) REVERT: A 990 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 994 ASP cc_start: 0.7309 (t70) cc_final: 0.7048 (t70) REVERT: A 995 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7737 (ttp-110) REVERT: A 996 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8223 (tt) REVERT: A 1017 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7450 (tp30) REVERT: A 1038 LYS cc_start: 0.8656 (mttm) cc_final: 0.8446 (mttm) REVERT: A 1135 ASN cc_start: 0.8539 (t0) cc_final: 0.8260 (t0) REVERT: B 52 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 92 PHE cc_start: 0.7813 (t80) cc_final: 0.7034 (t80) REVERT: B 120 VAL cc_start: 0.8442 (t) cc_final: 0.8214 (p) REVERT: B 121 ASN cc_start: 0.7277 (p0) cc_final: 0.6267 (t0) REVERT: B 127 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7418 (t) REVERT: B 199 PHE cc_start: 0.8596 (t80) cc_final: 0.8379 (t80) REVERT: B 224 GLU cc_start: 0.7657 (pm20) cc_final: 0.7402 (pm20) REVERT: B 298 GLU cc_start: 0.7872 (tt0) cc_final: 0.7632 (tt0) REVERT: B 307 THR cc_start: 0.8762 (m) cc_final: 0.8314 (p) REVERT: B 327 VAL cc_start: 0.8564 (t) cc_final: 0.8227 (m) REVERT: B 406 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7759 (mt-10) REVERT: B 558 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8105 (mmmt) REVERT: B 580 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8069 (mm-40) REVERT: B 707 TYR cc_start: 0.8384 (t80) cc_final: 0.8102 (t80) REVERT: B 726 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8495 (mm) REVERT: B 764 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8055 (ttpp) REVERT: B 773 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6548 (tm-30) REVERT: B 776 LYS cc_start: 0.8683 (tptm) cc_final: 0.8435 (tptm) REVERT: B 796 TYR cc_start: 0.8584 (t80) cc_final: 0.8324 (t80) REVERT: B 851 CYS cc_start: 0.8077 (t) cc_final: 0.7714 (t) REVERT: B 904 TYR cc_start: 0.7858 (m-10) cc_final: 0.6448 (m-10) REVERT: B 914 ASN cc_start: 0.7984 (p0) cc_final: 0.7670 (p0) REVERT: B 947 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8017 (mtmm) REVERT: B 949 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8208 (mm-40) REVERT: B 950 ASP cc_start: 0.7518 (t70) cc_final: 0.7236 (t70) REVERT: B 964 LYS cc_start: 0.8352 (mtmp) cc_final: 0.8042 (ttmm) REVERT: B 979 ASP cc_start: 0.7924 (m-30) cc_final: 0.7610 (m-30) REVERT: B 1017 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 1019 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7057 (ttp80) REVERT: B 1041 ASP cc_start: 0.8075 (m-30) cc_final: 0.7788 (t0) REVERT: B 1118 ASP cc_start: 0.7457 (t70) cc_final: 0.7008 (t0) REVERT: C 41 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8328 (mtpp) REVERT: C 135 PHE cc_start: 0.5907 (p90) cc_final: 0.5485 (p90) REVERT: C 188 ARG cc_start: 0.7532 (ptp-170) cc_final: 0.7032 (ptp-170) REVERT: C 237 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7377 (mtm180) REVERT: C 269 TYR cc_start: 0.8219 (m-80) cc_final: 0.7940 (m-80) REVERT: C 280 ASN cc_start: 0.7728 (t0) cc_final: 0.7462 (t0) REVERT: C 319 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: C 323 THR cc_start: 0.8362 (p) cc_final: 0.8148 (p) REVERT: C 335 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6914 (tt) REVERT: C 347 PHE cc_start: 0.8674 (t80) cc_final: 0.7767 (t80) REVERT: C 357 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7074 (ttm110) REVERT: C 378 LYS cc_start: 0.7638 (mmmm) cc_final: 0.7262 (mmmm) REVERT: C 386 LYS cc_start: 0.8164 (mttp) cc_final: 0.7749 (mtpt) REVERT: C 388 ASN cc_start: 0.7948 (p0) cc_final: 0.7506 (p0) REVERT: C 409 GLN cc_start: 0.8443 (mt0) cc_final: 0.8121 (tt0) REVERT: C 420 ASP cc_start: 0.8405 (t0) cc_final: 0.7854 (t0) REVERT: C 462 LYS cc_start: 0.8085 (tptt) cc_final: 0.7687 (ttmm) REVERT: C 528 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8489 (mmtm) REVERT: C 537 LYS cc_start: 0.8453 (tttp) cc_final: 0.8167 (mtpp) REVERT: C 558 LYS cc_start: 0.8276 (mptt) cc_final: 0.7671 (mppt) REVERT: C 569 ILE cc_start: 0.7814 (mm) cc_final: 0.7569 (mm) REVERT: C 574 ASP cc_start: 0.7251 (t70) cc_final: 0.6838 (t0) REVERT: C 577 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8037 (ttm-80) REVERT: C 602 THR cc_start: 0.8537 (m) cc_final: 0.8065 (p) REVERT: C 655 TYR cc_start: 0.8005 (t80) cc_final: 0.7778 (t80) REVERT: C 671 CYS cc_start: 0.5139 (m) cc_final: 0.4742 (m) REVERT: C 675 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6866 (tm-30) REVERT: C 725 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6806 (tm-30) REVERT: C 737 ASP cc_start: 0.7579 (t0) cc_final: 0.7356 (t0) REVERT: C 745 ASP cc_start: 0.5868 (OUTLIER) cc_final: 0.5389 (p0) REVERT: C 773 GLU cc_start: 0.7540 (tt0) cc_final: 0.6670 (tp30) REVERT: C 776 LYS cc_start: 0.8533 (tmmt) cc_final: 0.8237 (ttmm) REVERT: C 777 ASN cc_start: 0.8180 (m-40) cc_final: 0.7369 (m110) REVERT: C 779 GLN cc_start: 0.8220 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 821 LEU cc_start: 0.8357 (tp) cc_final: 0.8051 (tt) REVERT: C 851 CYS cc_start: 0.7976 (t) cc_final: 0.7417 (t) REVERT: C 933 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8252 (mtmm) REVERT: C 949 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7851 (mm-40) REVERT: C 964 LYS cc_start: 0.8588 (tmtm) cc_final: 0.8344 (ttmm) REVERT: C 1002 GLN cc_start: 0.7822 (tp40) cc_final: 0.7256 (tp-100) REVERT: C 1017 GLU cc_start: 0.7608 (tp30) cc_final: 0.7064 (tp30) REVERT: C 1072 GLU cc_start: 0.8079 (pm20) cc_final: 0.7717 (pm20) REVERT: C 1107 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6928 (mtt180) REVERT: C 1118 ASP cc_start: 0.7701 (t70) cc_final: 0.7275 (t0) REVERT: C 1144 GLU cc_start: 0.7569 (pp20) cc_final: 0.7329 (pp20) outliers start: 137 outliers final: 101 residues processed: 633 average time/residue: 0.4143 time to fit residues: 403.4578 Evaluate side-chains 613 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 502 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 343 ASN 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU 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 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 50.0000 chunk 36 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 319 optimal weight: 0.0970 chunk 199 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 448 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1119 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 26835 Z= 0.323 Angle : 0.656 17.411 36533 Z= 0.326 Chirality : 0.047 0.337 4216 Planarity : 0.004 0.048 4697 Dihedral : 6.459 58.238 4263 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 4.97 % Allowed : 20.86 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.25 (0.14), residues: 3276 helix: 1.02 (0.21), residues: 665 sheet: -1.59 (0.20), residues: 590 loop : -2.48 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 64 HIS 0.007 0.001 HIS B1064 PHE 0.025 0.002 PHE B 855 TYR 0.020 0.001 TYR C1067 ARG 0.008 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 524 time to evaluate : 3.288 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 64 TRP cc_start: 0.7695 (t60) cc_final: 0.7329 (t-100) REVERT: A 66 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7509 (m90) REVERT: A 97 LYS cc_start: 0.8499 (tppt) cc_final: 0.8237 (tppt) REVERT: A 132 GLU cc_start: 0.6470 (pm20) cc_final: 0.5599 (pm20) REVERT: A 164 ASN cc_start: 0.7418 (p0) cc_final: 0.6986 (p0) REVERT: A 186 ASN cc_start: 0.7349 (p0) cc_final: 0.6835 (p0) REVERT: A 239 GLN cc_start: 0.7221 (tp-100) cc_final: 0.6934 (tp-100) REVERT: A 269 TYR cc_start: 0.8407 (m-80) cc_final: 0.7228 (m-80) REVERT: A 282 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: A 297 SER cc_start: 0.8331 (m) cc_final: 0.7907 (p) REVERT: A 307 THR cc_start: 0.8736 (m) cc_final: 0.8436 (p) REVERT: A 356 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7518 (tmmm) REVERT: A 386 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7155 (mttp) REVERT: A 390 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7053 (tt) REVERT: A 392 PHE cc_start: 0.7451 (m-80) cc_final: 0.7089 (m-80) REVERT: A 544 ASN cc_start: 0.8385 (m-40) cc_final: 0.8132 (t0) REVERT: A 565 PHE cc_start: 0.7448 (m-10) cc_final: 0.7216 (m-10) REVERT: A 569 ILE cc_start: 0.8497 (pt) cc_final: 0.8272 (mp) REVERT: A 602 THR cc_start: 0.8412 (m) cc_final: 0.8036 (p) REVERT: A 615 VAL cc_start: 0.8426 (t) cc_final: 0.8199 (t) REVERT: A 664 ILE cc_start: 0.8771 (mt) cc_final: 0.8461 (mm) REVERT: A 708 SER cc_start: 0.8357 (t) cc_final: 0.7965 (m) REVERT: A 725 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7053 (tm-30) REVERT: A 726 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8139 (mm) REVERT: A 765 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7800 (mtm-85) REVERT: A 773 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 780 GLU cc_start: 0.7797 (pt0) cc_final: 0.7459 (tm-30) REVERT: A 788 ILE cc_start: 0.8840 (mm) cc_final: 0.8565 (mm) REVERT: A 790 LYS cc_start: 0.8014 (mppt) cc_final: 0.7736 (mppt) REVERT: A 851 CYS cc_start: 0.8265 (t) cc_final: 0.7765 (t) REVERT: A 900 MET cc_start: 0.7929 (mtp) cc_final: 0.7600 (mtp) REVERT: A 933 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8143 (mttp) REVERT: A 955 ASN cc_start: 0.8066 (t0) cc_final: 0.7844 (t0) REVERT: A 990 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 994 ASP cc_start: 0.7448 (t70) cc_final: 0.7167 (t70) REVERT: A 996 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 1005 GLN cc_start: 0.8470 (tp40) cc_final: 0.8189 (tp-100) REVERT: A 1017 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7449 (tp30) REVERT: A 1038 LYS cc_start: 0.8667 (mttm) cc_final: 0.8459 (mttm) REVERT: A 1107 ARG cc_start: 0.7426 (mtt90) cc_final: 0.5215 (mtt90) REVERT: B 52 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7721 (tm-30) REVERT: B 95 ILE cc_start: 0.8571 (mm) cc_final: 0.7988 (tt) REVERT: B 120 VAL cc_start: 0.8546 (t) cc_final: 0.8265 (p) REVERT: B 121 ASN cc_start: 0.7401 (p0) cc_final: 0.6462 (t0) REVERT: B 127 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7594 (t) REVERT: B 129 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7770 (tmtt) REVERT: B 190 PHE cc_start: 0.8100 (m-10) cc_final: 0.7844 (m-10) REVERT: B 224 GLU cc_start: 0.7820 (pm20) cc_final: 0.6892 (mp0) REVERT: B 307 THR cc_start: 0.8772 (m) cc_final: 0.8344 (p) REVERT: B 347 PHE cc_start: 0.4746 (OUTLIER) cc_final: 0.4083 (t80) REVERT: B 380 TYR cc_start: 0.7215 (m-80) cc_final: 0.6912 (m-80) REVERT: B 406 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 534 VAL cc_start: 0.8645 (t) cc_final: 0.8427 (m) REVERT: B 558 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8151 (mmmt) REVERT: B 568 ASP cc_start: 0.7823 (p0) cc_final: 0.7539 (p0) REVERT: B 580 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8068 (mm-40) REVERT: B 740 MET cc_start: 0.7984 (mtt) cc_final: 0.7722 (mtt) REVERT: B 764 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8193 (ttpp) REVERT: B 773 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 796 TYR cc_start: 0.8676 (t80) cc_final: 0.8397 (t80) REVERT: B 851 CYS cc_start: 0.8114 (t) cc_final: 0.7711 (t) REVERT: B 902 MET cc_start: 0.8660 (tpp) cc_final: 0.8286 (tpt) REVERT: B 914 ASN cc_start: 0.7980 (p0) cc_final: 0.7736 (p0) REVERT: B 949 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8263 (mm-40) REVERT: B 950 ASP cc_start: 0.7594 (t70) cc_final: 0.7295 (t70) REVERT: B 964 LYS cc_start: 0.8423 (mtmp) cc_final: 0.8087 (ttmm) REVERT: B 979 ASP cc_start: 0.7991 (m-30) cc_final: 0.7649 (m-30) REVERT: B 990 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: B 1017 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 1041 ASP cc_start: 0.8096 (m-30) cc_final: 0.7781 (t0) REVERT: B 1118 ASP cc_start: 0.7571 (t70) cc_final: 0.7127 (t0) REVERT: C 41 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8365 (mtpp) REVERT: C 86 PHE cc_start: 0.8287 (t80) cc_final: 0.7918 (t80) REVERT: C 135 PHE cc_start: 0.6237 (p90) cc_final: 0.5673 (p90) REVERT: C 188 ARG cc_start: 0.7596 (ptp-170) cc_final: 0.7143 (ptp-170) REVERT: C 199 PHE cc_start: 0.7927 (t80) cc_final: 0.7500 (t80) REVERT: C 237 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7373 (mtm180) REVERT: C 280 ASN cc_start: 0.7814 (t0) cc_final: 0.7558 (t0) REVERT: C 335 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6845 (tt) REVERT: C 347 PHE cc_start: 0.8658 (t80) cc_final: 0.7792 (t80) REVERT: C 357 ARG cc_start: 0.7985 (ttp-110) cc_final: 0.7453 (ttm110) REVERT: C 378 LYS cc_start: 0.7681 (mmmm) cc_final: 0.7240 (mmmm) REVERT: C 386 LYS cc_start: 0.8327 (mttp) cc_final: 0.7692 (ttmt) REVERT: C 409 GLN cc_start: 0.8381 (mt0) cc_final: 0.7990 (tt0) REVERT: C 420 ASP cc_start: 0.8425 (t0) cc_final: 0.7862 (t0) REVERT: C 462 LYS cc_start: 0.8059 (tptt) cc_final: 0.7701 (ttmm) REVERT: C 464 PHE cc_start: 0.8797 (m-10) cc_final: 0.8374 (m-80) REVERT: C 528 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8520 (mmmm) REVERT: C 537 LYS cc_start: 0.8487 (tttp) cc_final: 0.8282 (mtpp) REVERT: C 558 LYS cc_start: 0.8316 (mptt) cc_final: 0.7712 (mppt) REVERT: C 569 ILE cc_start: 0.7925 (mm) cc_final: 0.7724 (mm) REVERT: C 592 PHE cc_start: 0.8497 (p90) cc_final: 0.8292 (p90) REVERT: C 602 THR cc_start: 0.8588 (m) cc_final: 0.8197 (p) REVERT: C 671 CYS cc_start: 0.5235 (m) cc_final: 0.4815 (m) REVERT: C 675 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6812 (tm-30) REVERT: C 725 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6796 (tm-30) REVERT: C 745 ASP cc_start: 0.6262 (p0) cc_final: 0.5753 (p0) REVERT: C 773 GLU cc_start: 0.7620 (tt0) cc_final: 0.6921 (tp30) REVERT: C 776 LYS cc_start: 0.8527 (tmmt) cc_final: 0.8249 (ttmm) REVERT: C 777 ASN cc_start: 0.8243 (m-40) cc_final: 0.7416 (m110) REVERT: C 779 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 851 CYS cc_start: 0.7971 (t) cc_final: 0.7426 (t) REVERT: C 900 MET cc_start: 0.7882 (mtp) cc_final: 0.7555 (mtp) REVERT: C 904 TYR cc_start: 0.7714 (m-10) cc_final: 0.7430 (m-10) REVERT: C 964 LYS cc_start: 0.8603 (tmtm) cc_final: 0.8343 (ttmm) REVERT: C 1002 GLN cc_start: 0.7946 (tp40) cc_final: 0.7360 (tp-100) REVERT: C 1072 GLU cc_start: 0.8076 (pm20) cc_final: 0.7752 (pm20) REVERT: C 1118 ASP cc_start: 0.7725 (t70) cc_final: 0.7362 (t0) REVERT: D 208 MET cc_start: 0.0253 (tpp) cc_final: 0.0025 (tpp) outliers start: 142 outliers final: 112 residues processed: 623 average time/residue: 0.4293 time to fit residues: 408.7302 Evaluate side-chains 634 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 511 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 356 LYS 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU 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 B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 250 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1101 HIS C1119 ASN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26835 Z= 0.191 Angle : 0.626 16.187 36533 Z= 0.310 Chirality : 0.046 0.353 4216 Planarity : 0.004 0.048 4697 Dihedral : 6.284 59.910 4261 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.66 % Allowed : 21.67 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.12 (0.14), residues: 3276 helix: 1.20 (0.21), residues: 671 sheet: -1.63 (0.20), residues: 607 loop : -2.40 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.013 0.001 HIS A 205 PHE 0.034 0.001 PHE B 199 TYR 0.025 0.001 TYR A 170 ARG 0.007 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 505 time to evaluate : 2.899 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 66 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7538 (m90) REVERT: A 97 LYS cc_start: 0.8516 (tppt) cc_final: 0.8286 (tppt) REVERT: A 104 TRP cc_start: 0.8468 (m-90) cc_final: 0.7740 (m-90) REVERT: A 132 GLU cc_start: 0.6468 (pm20) cc_final: 0.5648 (pm20) REVERT: A 164 ASN cc_start: 0.7316 (p0) cc_final: 0.6985 (p0) REVERT: A 186 ASN cc_start: 0.7307 (p0) cc_final: 0.6774 (p0) REVERT: A 227 VAL cc_start: 0.8865 (p) cc_final: 0.8593 (m) REVERT: A 239 GLN cc_start: 0.7320 (tp-100) cc_final: 0.7039 (tp-100) REVERT: A 269 TYR cc_start: 0.8336 (m-80) cc_final: 0.7231 (m-80) REVERT: A 282 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8187 (m-40) REVERT: A 297 SER cc_start: 0.8268 (m) cc_final: 0.7840 (p) REVERT: A 307 THR cc_start: 0.8713 (m) cc_final: 0.8408 (p) REVERT: A 356 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7525 (tmmm) REVERT: A 390 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7117 (tt) REVERT: A 392 PHE cc_start: 0.7527 (m-80) cc_final: 0.7139 (m-80) REVERT: A 544 ASN cc_start: 0.8375 (m-40) cc_final: 0.8126 (t0) REVERT: A 565 PHE cc_start: 0.7325 (m-10) cc_final: 0.7079 (m-10) REVERT: A 602 THR cc_start: 0.8363 (m) cc_final: 0.7954 (p) REVERT: A 708 SER cc_start: 0.8250 (t) cc_final: 0.7860 (m) REVERT: A 725 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 726 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8145 (mm) REVERT: A 773 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 780 GLU cc_start: 0.7760 (pt0) cc_final: 0.7460 (tm-30) REVERT: A 788 ILE cc_start: 0.8829 (mm) cc_final: 0.8546 (mm) REVERT: A 790 LYS cc_start: 0.7991 (mppt) cc_final: 0.7721 (mppt) REVERT: A 851 CYS cc_start: 0.8303 (t) cc_final: 0.7935 (t) REVERT: A 869 MET cc_start: 0.8292 (mtt) cc_final: 0.8056 (mtm) REVERT: A 900 MET cc_start: 0.7952 (mtp) cc_final: 0.7613 (mtp) REVERT: A 933 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8087 (mttp) REVERT: A 955 ASN cc_start: 0.8035 (t0) cc_final: 0.7795 (t0) REVERT: A 957 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7210 (tm130) REVERT: A 964 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8366 (ttpp) REVERT: A 994 ASP cc_start: 0.7365 (t70) cc_final: 0.7095 (t70) REVERT: A 996 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 1005 GLN cc_start: 0.8412 (tp40) cc_final: 0.8156 (tp-100) REVERT: A 1017 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7466 (tp30) REVERT: A 1107 ARG cc_start: 0.7396 (mtt90) cc_final: 0.7130 (mtt90) REVERT: B 52 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 120 VAL cc_start: 0.8482 (t) cc_final: 0.8178 (p) REVERT: B 121 ASN cc_start: 0.7368 (p0) cc_final: 0.6421 (t0) REVERT: B 127 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7481 (t) REVERT: B 169 GLU cc_start: 0.7952 (mp0) cc_final: 0.7702 (mp0) REVERT: B 224 GLU cc_start: 0.7699 (pm20) cc_final: 0.6995 (pm20) REVERT: B 307 THR cc_start: 0.8770 (m) cc_final: 0.8319 (p) REVERT: B 327 VAL cc_start: 0.8613 (t) cc_final: 0.8279 (m) REVERT: B 347 PHE cc_start: 0.4486 (OUTLIER) cc_final: 0.3753 (t80) REVERT: B 406 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 558 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8109 (mmmt) REVERT: B 568 ASP cc_start: 0.7700 (p0) cc_final: 0.7455 (p0) REVERT: B 580 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8045 (mm-40) REVERT: B 707 TYR cc_start: 0.8426 (t80) cc_final: 0.8073 (t80) REVERT: B 764 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8075 (ttpp) REVERT: B 773 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6577 (tm-30) REVERT: B 796 TYR cc_start: 0.8654 (t80) cc_final: 0.8370 (t80) REVERT: B 850 ILE cc_start: 0.9006 (mm) cc_final: 0.8691 (tp) REVERT: B 851 CYS cc_start: 0.8085 (t) cc_final: 0.7632 (t) REVERT: B 914 ASN cc_start: 0.7848 (p0) cc_final: 0.7514 (p0) REVERT: B 949 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8172 (mm-40) REVERT: B 950 ASP cc_start: 0.7529 (t70) cc_final: 0.7246 (t70) REVERT: B 964 LYS cc_start: 0.8374 (mtmp) cc_final: 0.8072 (ttmm) REVERT: B 979 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: B 990 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: B 1017 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7375 (tm-30) REVERT: B 1019 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7086 (ttp80) REVERT: B 1041 ASP cc_start: 0.8068 (m-30) cc_final: 0.7758 (t0) REVERT: B 1118 ASP cc_start: 0.7512 (t70) cc_final: 0.7061 (t0) REVERT: C 40 ASP cc_start: 0.7521 (t0) cc_final: 0.7299 (t0) REVERT: C 41 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8266 (mtpp) REVERT: C 86 PHE cc_start: 0.8195 (t80) cc_final: 0.7862 (t80) REVERT: C 130 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8009 (p) REVERT: C 135 PHE cc_start: 0.6119 (p90) cc_final: 0.5610 (p90) REVERT: C 188 ARG cc_start: 0.7564 (ptp-170) cc_final: 0.7043 (ptp-170) REVERT: C 199 PHE cc_start: 0.7849 (t80) cc_final: 0.7416 (t80) REVERT: C 237 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7294 (mtm180) REVERT: C 269 TYR cc_start: 0.8235 (m-80) cc_final: 0.7953 (m-80) REVERT: C 280 ASN cc_start: 0.7921 (t0) cc_final: 0.7662 (t0) REVERT: C 335 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6732 (tt) REVERT: C 347 PHE cc_start: 0.8653 (t80) cc_final: 0.7802 (t80) REVERT: C 357 ARG cc_start: 0.7898 (ttp-110) cc_final: 0.7158 (ttm110) REVERT: C 378 LYS cc_start: 0.7580 (mmmm) cc_final: 0.7198 (mmmm) REVERT: C 386 LYS cc_start: 0.8259 (mttp) cc_final: 0.7645 (tttt) REVERT: C 409 GLN cc_start: 0.8401 (mt0) cc_final: 0.8117 (tt0) REVERT: C 420 ASP cc_start: 0.8403 (t0) cc_final: 0.7831 (t0) REVERT: C 462 LYS cc_start: 0.8038 (tptt) cc_final: 0.7672 (ttmm) REVERT: C 464 PHE cc_start: 0.8789 (m-10) cc_final: 0.8367 (m-80) REVERT: C 528 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8449 (mmmm) REVERT: C 537 LYS cc_start: 0.8468 (tttp) cc_final: 0.8096 (mtpp) REVERT: C 577 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8072 (ttm-80) REVERT: C 602 THR cc_start: 0.8537 (m) cc_final: 0.8128 (p) REVERT: C 671 CYS cc_start: 0.5190 (m) cc_final: 0.4766 (m) REVERT: C 675 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6864 (tm-30) REVERT: C 725 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6837 (tm-30) REVERT: C 745 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5662 (p0) REVERT: C 773 GLU cc_start: 0.7526 (tt0) cc_final: 0.6688 (tp30) REVERT: C 774 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7282 (mm110) REVERT: C 776 LYS cc_start: 0.8552 (tmmt) cc_final: 0.8280 (ttmm) REVERT: C 777 ASN cc_start: 0.8137 (m-40) cc_final: 0.7320 (m110) REVERT: C 779 GLN cc_start: 0.8272 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 851 CYS cc_start: 0.7967 (t) cc_final: 0.7419 (t) REVERT: C 964 LYS cc_start: 0.8588 (tmtm) cc_final: 0.8317 (ttmm) REVERT: C 1002 GLN cc_start: 0.7874 (tp40) cc_final: 0.7355 (tp-100) REVERT: C 1010 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: C 1072 GLU cc_start: 0.8040 (pm20) cc_final: 0.7699 (pm20) REVERT: C 1107 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6963 (mtt180) REVERT: C 1118 ASP cc_start: 0.7715 (t70) cc_final: 0.7298 (t0) REVERT: D 208 MET cc_start: 0.0763 (tpp) cc_final: 0.0422 (tpp) outliers start: 133 outliers final: 105 residues processed: 597 average time/residue: 0.4205 time to fit residues: 385.8027 Evaluate side-chains 612 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 492 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 356 LYS 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 268 optimal weight: 0.5980 chunk 281 optimal weight: 0.9990 chunk 296 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1101 HIS C1119 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26835 Z= 0.247 Angle : 0.654 16.492 36533 Z= 0.323 Chirality : 0.046 0.336 4216 Planarity : 0.004 0.048 4697 Dihedral : 6.366 58.342 4261 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 4.59 % Allowed : 22.26 % Favored : 73.15 % 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: -2.09 (0.14), residues: 3276 helix: 1.34 (0.21), residues: 650 sheet: -1.58 (0.20), residues: 602 loop : -2.39 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 64 HIS 0.008 0.001 HIS C1083 PHE 0.037 0.002 PHE A 168 TYR 0.021 0.001 TYR A 170 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 507 time to evaluate : 2.715 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 102 ARG cc_start: 0.8544 (ptp-170) cc_final: 0.7883 (mtt-85) REVERT: A 132 GLU cc_start: 0.6446 (pm20) cc_final: 0.5592 (pm20) REVERT: A 164 ASN cc_start: 0.7225 (p0) cc_final: 0.6895 (p0) REVERT: A 186 ASN cc_start: 0.7296 (p0) cc_final: 0.6532 (p0) REVERT: A 239 GLN cc_start: 0.7238 (tp-100) cc_final: 0.6924 (tp-100) REVERT: A 269 TYR cc_start: 0.8363 (m-80) cc_final: 0.7216 (m-80) REVERT: A 282 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8154 (m-40) REVERT: A 297 SER cc_start: 0.8325 (m) cc_final: 0.7861 (p) REVERT: A 307 THR cc_start: 0.8742 (m) cc_final: 0.8408 (p) REVERT: A 356 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7556 (tmmm) REVERT: A 386 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7152 (mttp) REVERT: A 390 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7049 (tt) REVERT: A 392 PHE cc_start: 0.7551 (m-80) cc_final: 0.7162 (m-80) REVERT: A 708 SER cc_start: 0.8290 (t) cc_final: 0.7933 (m) REVERT: A 725 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7058 (tm-30) REVERT: A 726 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 765 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7729 (mtm-85) REVERT: A 773 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6631 (tm-30) REVERT: A 780 GLU cc_start: 0.7799 (pt0) cc_final: 0.7457 (tm-30) REVERT: A 788 ILE cc_start: 0.8833 (mm) cc_final: 0.8567 (mm) REVERT: A 790 LYS cc_start: 0.8002 (mppt) cc_final: 0.7731 (mppt) REVERT: A 851 CYS cc_start: 0.8333 (t) cc_final: 0.7851 (t) REVERT: A 933 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8121 (mttp) REVERT: A 955 ASN cc_start: 0.8049 (t0) cc_final: 0.7830 (t0) REVERT: A 957 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7305 (tm130) REVERT: A 964 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8346 (ttpp) REVERT: A 994 ASP cc_start: 0.7435 (t70) cc_final: 0.7168 (t70) REVERT: A 996 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 1017 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7449 (tp30) REVERT: A 1050 MET cc_start: 0.7224 (mtm) cc_final: 0.6961 (mtm) REVERT: A 1107 ARG cc_start: 0.7429 (mtt90) cc_final: 0.5243 (mtt90) REVERT: B 52 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 95 ILE cc_start: 0.8551 (mm) cc_final: 0.8002 (tt) REVERT: B 120 VAL cc_start: 0.8489 (t) cc_final: 0.8158 (p) REVERT: B 121 ASN cc_start: 0.7383 (p0) cc_final: 0.6522 (t0) REVERT: B 127 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7528 (t) REVERT: B 169 GLU cc_start: 0.8142 (mp0) cc_final: 0.7801 (mp0) REVERT: B 201 ILE cc_start: 0.8539 (mt) cc_final: 0.8285 (mp) REVERT: B 224 GLU cc_start: 0.7770 (pm20) cc_final: 0.7093 (pm20) REVERT: B 307 THR cc_start: 0.8749 (m) cc_final: 0.8304 (p) REVERT: B 327 VAL cc_start: 0.8619 (t) cc_final: 0.8274 (m) REVERT: B 347 PHE cc_start: 0.4669 (OUTLIER) cc_final: 0.3992 (t80) REVERT: B 392 PHE cc_start: 0.7698 (m-10) cc_final: 0.7360 (m-10) REVERT: B 406 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7304 (mp0) REVERT: B 534 VAL cc_start: 0.8616 (t) cc_final: 0.8392 (m) REVERT: B 558 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8129 (mmmt) REVERT: B 580 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8052 (mm-40) REVERT: B 764 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8115 (ttpp) REVERT: B 773 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6610 (tm-30) REVERT: B 796 TYR cc_start: 0.8694 (t80) cc_final: 0.8412 (t80) REVERT: B 850 ILE cc_start: 0.8980 (mm) cc_final: 0.8698 (tp) REVERT: B 851 CYS cc_start: 0.7978 (t) cc_final: 0.7643 (t) REVERT: B 949 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8213 (mm-40) REVERT: B 950 ASP cc_start: 0.7573 (t70) cc_final: 0.7279 (t70) REVERT: B 964 LYS cc_start: 0.8398 (mtmp) cc_final: 0.8088 (ttmm) REVERT: B 979 ASP cc_start: 0.7985 (m-30) cc_final: 0.7677 (m-30) REVERT: B 990 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: B 1017 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7378 (tm-30) REVERT: B 1019 ARG cc_start: 0.7467 (ttp80) cc_final: 0.7082 (ttp80) REVERT: B 1041 ASP cc_start: 0.8056 (m-30) cc_final: 0.7757 (t0) REVERT: B 1118 ASP cc_start: 0.7521 (t70) cc_final: 0.7068 (t0) REVERT: C 40 ASP cc_start: 0.7500 (t0) cc_final: 0.7272 (t0) REVERT: C 41 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8263 (mtpp) REVERT: C 86 PHE cc_start: 0.8212 (t80) cc_final: 0.7940 (t80) REVERT: C 135 PHE cc_start: 0.6191 (p90) cc_final: 0.5611 (p90) REVERT: C 188 ARG cc_start: 0.7570 (ptp-170) cc_final: 0.7055 (ptp-170) REVERT: C 199 PHE cc_start: 0.7913 (t80) cc_final: 0.7449 (t80) REVERT: C 237 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7337 (mtm180) REVERT: C 269 TYR cc_start: 0.8298 (m-80) cc_final: 0.7915 (m-80) REVERT: C 280 ASN cc_start: 0.7978 (t0) cc_final: 0.7724 (t0) REVERT: C 335 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6691 (tt) REVERT: C 347 PHE cc_start: 0.8631 (t80) cc_final: 0.7747 (t80) REVERT: C 357 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7607 (ttm110) REVERT: C 378 LYS cc_start: 0.7588 (mmmm) cc_final: 0.7164 (mmmm) REVERT: C 386 LYS cc_start: 0.8297 (mttp) cc_final: 0.7611 (ttmt) REVERT: C 392 PHE cc_start: 0.6694 (m-80) cc_final: 0.6455 (m-80) REVERT: C 409 GLN cc_start: 0.8393 (mt0) cc_final: 0.8121 (tt0) REVERT: C 462 LYS cc_start: 0.8042 (tptt) cc_final: 0.7668 (ttmm) REVERT: C 464 PHE cc_start: 0.8802 (m-10) cc_final: 0.8598 (m-80) REVERT: C 528 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8503 (mmmm) REVERT: C 537 LYS cc_start: 0.8490 (tttp) cc_final: 0.8115 (mtpp) REVERT: C 577 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8092 (ttm-80) REVERT: C 602 THR cc_start: 0.8558 (m) cc_final: 0.8163 (p) REVERT: C 671 CYS cc_start: 0.5226 (m) cc_final: 0.4808 (m) REVERT: C 675 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6858 (tm-30) REVERT: C 725 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6835 (tm-30) REVERT: C 745 ASP cc_start: 0.6394 (p0) cc_final: 0.6096 (p0) REVERT: C 773 GLU cc_start: 0.7598 (tt0) cc_final: 0.6883 (tp30) REVERT: C 774 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7303 (mm110) REVERT: C 776 LYS cc_start: 0.8554 (tmmt) cc_final: 0.8289 (ttmm) REVERT: C 777 ASN cc_start: 0.8209 (m-40) cc_final: 0.7405 (m110) REVERT: C 779 GLN cc_start: 0.8327 (tm-30) cc_final: 0.8092 (tm-30) REVERT: C 851 CYS cc_start: 0.7978 (t) cc_final: 0.7425 (t) REVERT: C 900 MET cc_start: 0.7832 (mtp) cc_final: 0.7501 (mtp) REVERT: C 904 TYR cc_start: 0.7685 (m-10) cc_final: 0.7369 (m-10) REVERT: C 949 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7891 (mm-40) REVERT: C 964 LYS cc_start: 0.8610 (tmtm) cc_final: 0.8349 (ttmm) REVERT: C 1002 GLN cc_start: 0.7936 (tp40) cc_final: 0.7393 (tp-100) REVERT: C 1072 GLU cc_start: 0.8021 (pm20) cc_final: 0.7698 (pm20) REVERT: C 1118 ASP cc_start: 0.7710 (t70) cc_final: 0.7348 (t0) REVERT: D 208 MET cc_start: 0.0878 (tpp) cc_final: 0.0626 (tpp) outliers start: 131 outliers final: 111 residues processed: 600 average time/residue: 0.4225 time to fit residues: 389.5138 Evaluate side-chains 620 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 498 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 356 LYS 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 0.8980 chunk 314 optimal weight: 20.0000 chunk 191 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 202 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 751 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26835 Z= 0.202 Angle : 0.647 15.954 36533 Z= 0.319 Chirality : 0.046 0.397 4216 Planarity : 0.004 0.048 4697 Dihedral : 6.270 59.334 4261 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 4.38 % Allowed : 22.93 % Favored : 72.70 % 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: -2.01 (0.14), residues: 3276 helix: 1.35 (0.21), residues: 659 sheet: -1.58 (0.20), residues: 620 loop : -2.33 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 64 HIS 0.008 0.001 HIS B1064 PHE 0.046 0.001 PHE B 190 TYR 0.022 0.001 TYR A 170 ARG 0.006 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 497 time to evaluate : 3.185 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: A 102 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.8071 (mtt180) REVERT: A 132 GLU cc_start: 0.6457 (pm20) cc_final: 0.5597 (pm20) REVERT: A 164 ASN cc_start: 0.7254 (p0) cc_final: 0.6952 (p0) REVERT: A 186 ASN cc_start: 0.7290 (p0) cc_final: 0.6798 (p0) REVERT: A 239 GLN cc_start: 0.7306 (tp-100) cc_final: 0.7023 (tp-100) REVERT: A 269 TYR cc_start: 0.8327 (m-80) cc_final: 0.7228 (m-80) REVERT: A 282 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8173 (m-40) REVERT: A 294 ASP cc_start: 0.7581 (t70) cc_final: 0.7265 (t0) REVERT: A 297 SER cc_start: 0.8356 (m) cc_final: 0.7756 (p) REVERT: A 356 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7551 (tmmm) REVERT: A 386 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7145 (mttp) REVERT: A 390 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7015 (tt) REVERT: A 392 PHE cc_start: 0.7544 (m-80) cc_final: 0.7135 (m-80) REVERT: A 664 ILE cc_start: 0.8774 (mt) cc_final: 0.8509 (mm) REVERT: A 725 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 726 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8102 (mm) REVERT: A 773 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6548 (tm-30) REVERT: A 780 GLU cc_start: 0.7766 (pt0) cc_final: 0.7457 (tm-30) REVERT: A 788 ILE cc_start: 0.8820 (mm) cc_final: 0.8560 (mm) REVERT: A 790 LYS cc_start: 0.8000 (mppt) cc_final: 0.7721 (mppt) REVERT: A 851 CYS cc_start: 0.8340 (t) cc_final: 0.7810 (t) REVERT: A 933 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8058 (mttp) REVERT: A 955 ASN cc_start: 0.8041 (t0) cc_final: 0.7799 (t0) REVERT: A 957 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7253 (tm130) REVERT: A 964 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8356 (ttpp) REVERT: A 994 ASP cc_start: 0.7394 (t70) cc_final: 0.7117 (t70) REVERT: A 995 ARG cc_start: 0.7990 (ttp-110) cc_final: 0.7657 (ttp-110) REVERT: A 996 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8308 (tp) REVERT: A 1005 GLN cc_start: 0.8401 (tp40) cc_final: 0.8153 (tp-100) REVERT: A 1017 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7464 (tp30) REVERT: A 1107 ARG cc_start: 0.7397 (mtt90) cc_final: 0.7131 (mtt90) REVERT: B 52 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 95 ILE cc_start: 0.8633 (mm) cc_final: 0.8021 (tt) REVERT: B 120 VAL cc_start: 0.8472 (t) cc_final: 0.8130 (p) REVERT: B 121 ASN cc_start: 0.7357 (p0) cc_final: 0.6465 (t0) REVERT: B 127 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7581 (t) REVERT: B 169 GLU cc_start: 0.7960 (mp0) cc_final: 0.7704 (mp0) REVERT: B 201 ILE cc_start: 0.8483 (mt) cc_final: 0.8236 (mp) REVERT: B 224 GLU cc_start: 0.7735 (pm20) cc_final: 0.7041 (pm20) REVERT: B 307 THR cc_start: 0.8757 (m) cc_final: 0.8311 (p) REVERT: B 327 VAL cc_start: 0.8593 (t) cc_final: 0.8256 (m) REVERT: B 347 PHE cc_start: 0.4572 (OUTLIER) cc_final: 0.3875 (t80) REVERT: B 406 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7305 (mp0) REVERT: B 515 PHE cc_start: 0.7632 (m-10) cc_final: 0.7381 (m-10) REVERT: B 558 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8143 (mmmt) REVERT: B 580 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 707 TYR cc_start: 0.8445 (t80) cc_final: 0.8137 (t80) REVERT: B 764 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8089 (ttpp) REVERT: B 773 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 796 TYR cc_start: 0.8628 (t80) cc_final: 0.8360 (t80) REVERT: B 850 ILE cc_start: 0.8967 (mm) cc_final: 0.8684 (tp) REVERT: B 851 CYS cc_start: 0.7962 (t) cc_final: 0.7637 (t) REVERT: B 949 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8180 (mm-40) REVERT: B 950 ASP cc_start: 0.7559 (t70) cc_final: 0.7269 (t70) REVERT: B 964 LYS cc_start: 0.8423 (mtmp) cc_final: 0.8127 (ttmm) REVERT: B 979 ASP cc_start: 0.7978 (m-30) cc_final: 0.7665 (m-30) REVERT: B 1017 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 1019 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7068 (ttp80) REVERT: B 1041 ASP cc_start: 0.8033 (m-30) cc_final: 0.7729 (t0) REVERT: B 1118 ASP cc_start: 0.7489 (t70) cc_final: 0.7031 (t0) REVERT: C 40 ASP cc_start: 0.7509 (t0) cc_final: 0.7300 (t0) REVERT: C 41 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8236 (mtpp) REVERT: C 86 PHE cc_start: 0.8151 (t80) cc_final: 0.7941 (t80) REVERT: C 135 PHE cc_start: 0.6188 (p90) cc_final: 0.5605 (p90) REVERT: C 188 ARG cc_start: 0.7599 (ptp-170) cc_final: 0.7082 (ptp-170) REVERT: C 199 PHE cc_start: 0.7878 (t80) cc_final: 0.7434 (t80) REVERT: C 237 ARG cc_start: 0.7825 (mtm180) cc_final: 0.7269 (mtm180) REVERT: C 269 TYR cc_start: 0.8245 (m-80) cc_final: 0.7958 (m-80) REVERT: C 280 ASN cc_start: 0.8111 (t0) cc_final: 0.7855 (t0) REVERT: C 319 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7672 (ttm-80) REVERT: C 335 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6656 (tt) REVERT: C 347 PHE cc_start: 0.8593 (t80) cc_final: 0.7699 (t80) REVERT: C 357 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7561 (ttm110) REVERT: C 378 LYS cc_start: 0.7568 (mmmm) cc_final: 0.7186 (mmmm) REVERT: C 386 LYS cc_start: 0.8252 (mttp) cc_final: 0.7568 (tttt) REVERT: C 392 PHE cc_start: 0.6676 (m-80) cc_final: 0.6426 (m-80) REVERT: C 398 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7230 (p0) REVERT: C 409 GLN cc_start: 0.8354 (mt0) cc_final: 0.8101 (tt0) REVERT: C 462 LYS cc_start: 0.8065 (tptt) cc_final: 0.7698 (ttmm) REVERT: C 464 PHE cc_start: 0.8797 (m-10) cc_final: 0.8587 (m-80) REVERT: C 528 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8506 (mmmm) REVERT: C 537 LYS cc_start: 0.8465 (tttp) cc_final: 0.8184 (mtpp) REVERT: C 577 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8084 (ttm-80) REVERT: C 602 THR cc_start: 0.8525 (m) cc_final: 0.8119 (p) REVERT: C 671 CYS cc_start: 0.5205 (m) cc_final: 0.4793 (m) REVERT: C 675 GLN cc_start: 0.7130 (tm-30) cc_final: 0.6807 (tm-30) REVERT: C 725 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6846 (tm-30) REVERT: C 745 ASP cc_start: 0.6290 (p0) cc_final: 0.5844 (p0) REVERT: C 773 GLU cc_start: 0.7474 (tt0) cc_final: 0.6594 (tp30) REVERT: C 774 GLN cc_start: 0.7600 (mm-40) cc_final: 0.6790 (mm110) REVERT: C 776 LYS cc_start: 0.8562 (tmmt) cc_final: 0.8272 (ttmm) REVERT: C 777 ASN cc_start: 0.8152 (m-40) cc_final: 0.7299 (m110) REVERT: C 779 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7923 (tm-30) REVERT: C 851 CYS cc_start: 0.7990 (t) cc_final: 0.7438 (t) REVERT: C 900 MET cc_start: 0.7766 (mtp) cc_final: 0.7498 (mtp) REVERT: C 964 LYS cc_start: 0.8594 (tmtm) cc_final: 0.8336 (ttmm) REVERT: C 1002 GLN cc_start: 0.7914 (tp40) cc_final: 0.7519 (tp40) REVERT: C 1107 ARG cc_start: 0.7360 (mtt180) cc_final: 0.7034 (mtt-85) REVERT: C 1118 ASP cc_start: 0.7723 (t70) cc_final: 0.7275 (t0) REVERT: D 208 MET cc_start: 0.0838 (tpp) cc_final: 0.0594 (tpp) outliers start: 125 outliers final: 105 residues processed: 586 average time/residue: 0.4599 time to fit residues: 419.2777 Evaluate side-chains 607 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 491 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 356 LYS 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 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 1.9990 chunk 279 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 242 optimal weight: 0.0370 chunk 38 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1002 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116332 restraints weight = 46847.637| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.85 r_work: 0.3325 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 26835 Z= 0.299 Angle : 0.825 59.199 36533 Z= 0.469 Chirality : 0.048 0.592 4216 Planarity : 0.006 0.210 4697 Dihedral : 6.307 59.323 4261 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.83 % Favored : 90.14 % Rotamer: Outliers : 4.38 % Allowed : 22.82 % Favored : 72.80 % Cbeta Deviations : 0.10 % 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: -2.03 (0.14), residues: 3276 helix: 1.30 (0.21), residues: 659 sheet: -1.57 (0.20), residues: 620 loop : -2.32 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 64 HIS 0.222 0.004 HIS A 205 PHE 0.037 0.001 PHE B 190 TYR 0.020 0.001 TYR B 707 ARG 0.023 0.000 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7622.84 seconds wall clock time: 138 minutes 50.75 seconds (8330.75 seconds total)