Starting phenix.real_space_refine on Tue Feb 20 15:50:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whi_32500/02_2024/7whi_32500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whi_32500/02_2024/7whi_32500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whi_32500/02_2024/7whi_32500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whi_32500/02_2024/7whi_32500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whi_32500/02_2024/7whi_32500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whi_32500/02_2024/7whi_32500.pdb" } resolution = 2.93 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= 0.001 sd= 0.021 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 138 5.16 5 C 18093 2.51 5 N 4666 2.21 5 O 5453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28350 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8122 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 58, 'TRANS': 983} Chain breaks: 7 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 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: 7984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7984 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 7 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 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: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8133 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 58, 'TRANS': 984} Chain breaks: 7 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 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: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.84, per 1000 atoms: 0.52 Number of scatterers: 28350 At special positions: 0 Unit cell: (147.896, 153.216, 197.904, 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 138 16.00 O 5453 8.00 N 4666 7.00 C 18093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " 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 234 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 717 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 122 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 343 " " NAG A1313 " - " ASN A 709 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 282 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 122 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 616 " Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 5.1 seconds 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 63 sheets defined 20.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.614A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.733A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.504A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 removed outlier: 4.154A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.630A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 853 removed outlier: 3.964A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 853' Processing helix chain 'A' and resid 854 through 857 removed outlier: 3.532A pdb=" N GLY A 857 " --> pdb=" O LYS A 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 857' Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.861A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.569A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.024A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.808A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.856A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.611A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.718A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.522A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.724A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.553A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.797A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.632A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.839A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.532A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.666A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.917A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.738A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 826 removed outlier: 3.547A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 852 removed outlier: 3.502A pdb=" N ALA C 852 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.625A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.149A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.753A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.878A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.723A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.784A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.778A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.080A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.351A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.059A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 227 removed outlier: 6.779A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.884A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 403 removed outlier: 3.561A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.609A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.804A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.595A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.770A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.238A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.765A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.981A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.637A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.945A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 230 removed outlier: 6.036A pdb=" N SER B 203 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.010A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.131A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.568A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.816A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.848A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.740A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.740A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.392A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.503A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.808A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.657A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.689A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 65 through 67 Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.031A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 224 through 229 removed outlier: 6.097A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 229 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE C 199 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.643A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.552A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF2, first strand: chain 'C' and resid 539 through 542 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.964A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.694A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.813A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'D' and resid 17 through 20 Processing sheet with id=AG2, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.720A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR D 93 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR D 112 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'E' and resid 47 through 51 removed outlier: 7.150A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'F' and resid 57 through 58 removed outlier: 3.617A pdb=" N TYR F 58 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER F 50 " --> pdb=" O TYR F 58 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.599A pdb=" N VAL G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU G 18 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 69 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.524A pdb=" N VAL G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 114 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR G 94 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 116 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA G 92 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.524A pdb=" N VAL G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 114 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR G 94 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 116 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA G 92 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR G 98 " --> pdb=" O TYR G 109 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2409 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: 13.43 Time building geometry restraints manager: 11.75 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: 5619 1.33 - 1.45: 7401 1.45 - 1.57: 15808 1.57 - 1.70: 0 1.70 - 1.82: 182 Bond restraints: 29010 Sorted by residual: bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.23e-02 6.61e+03 2.12e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.28e-02 6.10e+03 1.76e+01 bond pdb=" CA ASN A 717 " pdb=" C ASN A 717 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.25e-02 6.40e+03 1.65e+01 bond pdb=" CA ALA B 123 " pdb=" C ALA B 123 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.34e-02 5.57e+03 1.61e+01 bond pdb=" CA ASN B 717 " pdb=" C ASN B 717 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.25e-02 6.40e+03 1.49e+01 ... (remaining 29005 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.04: 932 107.04 - 113.80: 15962 113.80 - 120.57: 10912 120.57 - 127.33: 11420 127.33 - 134.10: 263 Bond angle restraints: 39489 Sorted by residual: angle pdb=" N ALA A 163 " pdb=" CA ALA A 163 " pdb=" C ALA A 163 " ideal model delta sigma weight residual 109.96 121.40 -11.44 1.58e+00 4.01e-01 5.24e+01 angle pdb=" N TYR A 160 " pdb=" CA TYR A 160 " pdb=" C TYR A 160 " ideal model delta sigma weight residual 109.81 118.79 -8.98 1.53e+00 4.27e-01 3.44e+01 angle pdb=" C ALA B 123 " pdb=" N THR B 124 " pdb=" CA THR B 124 " ideal model delta sigma weight residual 122.65 113.37 9.28 1.60e+00 3.91e-01 3.36e+01 angle pdb=" N ALA B 852 " pdb=" CA ALA B 852 " pdb=" C ALA B 852 " ideal model delta sigma weight residual 114.75 107.56 7.19 1.26e+00 6.30e-01 3.25e+01 angle pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" C SER A 161 " ideal model delta sigma weight residual 112.57 106.70 5.87 1.13e+00 7.83e-01 2.70e+01 ... (remaining 39484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 16736 17.38 - 34.76: 766 34.76 - 52.14: 184 52.14 - 69.53: 36 69.53 - 86.91: 20 Dihedral angle restraints: 17742 sinusoidal: 7330 harmonic: 10412 Sorted by residual: dihedral pdb=" CA TYR A 160 " pdb=" C TYR A 160 " pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO C 213 " pdb=" C PRO C 213 " pdb=" N GLU C 214 " pdb=" CA GLU C 214 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C TYR A 160 " pdb=" N TYR A 160 " pdb=" CA TYR A 160 " pdb=" CB TYR A 160 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 17739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4360 0.102 - 0.204: 175 0.204 - 0.306: 18 0.306 - 0.408: 5 0.408 - 0.509: 4 Chirality restraints: 4562 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 4559 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG C1309 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " -0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1311 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.349 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B1305 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.098 2.00e-02 2.50e+03 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2809 2.75 - 3.29: 27495 3.29 - 3.83: 46371 3.83 - 4.36: 53603 4.36 - 4.90: 93195 Nonbonded interactions: 223473 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.213 2.440 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.217 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.244 2.440 nonbonded pdb=" OG1 THR A 961 " pdb=" OE1 GLN C 762 " model vdw 2.268 2.440 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.271 2.440 ... (remaining 223468 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 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 849 through 1147 or resid 1301 through 1311)) selection = (chain 'B' and (resid 26 through 1147 or resid 1301 through 1311)) selection = (chain 'C' and (resid 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 849 through 1147 or resid 1301 through 1311)) } ncs_group { reference = (chain 'D' and resid 1 through 116) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 8.350 Check model and map are aligned: 0.400 Set scattering table: 0.300 Process input model: 76.750 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 : 0.004 0.057 29010 Z= 0.232 Angle : 0.642 11.440 39489 Z= 0.377 Chirality : 0.050 0.509 4562 Planarity : 0.016 0.305 5055 Dihedral : 10.721 86.907 10917 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 5.48 % Allowed : 9.18 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.55 (0.12), residues: 3522 helix: -0.48 (0.19), residues: 629 sheet: -2.05 (0.17), residues: 736 loop : -3.25 (0.11), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 36 HIS 0.002 0.000 HIS C 205 PHE 0.012 0.001 PHE B 175 TYR 0.015 0.001 TYR C 265 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 682 time to evaluate : 3.100 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6459 (m) REVERT: A 126 VAL cc_start: 0.8044 (t) cc_final: 0.7823 (m) REVERT: A 127 VAL cc_start: 0.8248 (t) cc_final: 0.7890 (m) REVERT: A 129 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7314 (tppp) REVERT: A 173 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.4383 (tm130) REVERT: A 189 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6915 (mt-10) REVERT: A 235 ILE cc_start: 0.3149 (OUTLIER) cc_final: 0.2924 (mp) REVERT: A 281 GLU cc_start: 0.6762 (pm20) cc_final: 0.6520 (pm20) REVERT: A 434 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7524 (tp) REVERT: A 516 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5783 (tm-30) REVERT: A 517 LEU cc_start: 0.7487 (tm) cc_final: 0.7198 (pp) REVERT: A 539 VAL cc_start: 0.8337 (t) cc_final: 0.8065 (m) REVERT: A 776 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8186 (ttpp) REVERT: A 821 LEU cc_start: 0.7505 (mt) cc_final: 0.7053 (mp) REVERT: A 943 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7683 (t) REVERT: A 1118 ASP cc_start: 0.6901 (t0) cc_final: 0.6659 (t0) REVERT: B 52 GLN cc_start: 0.7316 (tm-30) cc_final: 0.6610 (tm-30) REVERT: B 340 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6612 (tm-30) REVERT: B 449 TYR cc_start: 0.6601 (m-80) cc_final: 0.6167 (m-80) REVERT: B 586 ASP cc_start: 0.6809 (t0) cc_final: 0.6539 (t0) REVERT: B 773 GLU cc_start: 0.7101 (tt0) cc_final: 0.6405 (tt0) REVERT: B 933 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7795 (mtmm) REVERT: C 81 ASN cc_start: 0.7547 (t0) cc_final: 0.7189 (t0) REVERT: C 96 GLU cc_start: 0.5650 (mt-10) cc_final: 0.5232 (mt-10) REVERT: C 297 SER cc_start: 0.8080 (p) cc_final: 0.7846 (m) REVERT: C 317 ASN cc_start: 0.7947 (m110) cc_final: 0.7711 (m-40) REVERT: C 407 VAL cc_start: 0.6467 (OUTLIER) cc_final: 0.6228 (t) REVERT: C 425 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5707 (pp) REVERT: C 551 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7654 (p) REVERT: C 654 GLU cc_start: 0.6864 (mp0) cc_final: 0.6661 (pm20) REVERT: C 675 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6881 (mp10) REVERT: C 772 VAL cc_start: 0.8669 (t) cc_final: 0.8440 (m) REVERT: C 814 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7605 (mppt) REVERT: C 869 MET cc_start: 0.8291 (mtt) cc_final: 0.8047 (mtm) REVERT: D 18 LEU cc_start: 0.7832 (mm) cc_final: 0.7004 (mm) REVERT: D 34 MET cc_start: 0.6870 (ttm) cc_final: 0.6539 (ttp) REVERT: D 35 SER cc_start: 0.7290 (m) cc_final: 0.6935 (t) REVERT: D 54 SER cc_start: 0.8296 (t) cc_final: 0.8066 (t) REVERT: D 82 MET cc_start: 0.6351 (ppp) cc_final: 0.5915 (ppp) REVERT: E 3 GLN cc_start: 0.3907 (OUTLIER) cc_final: 0.3614 (tm-30) REVERT: E 4 LEU cc_start: -0.5314 (OUTLIER) cc_final: -0.5517 (tt) REVERT: E 31 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5431 (p0) REVERT: E 99 TRP cc_start: 0.4310 (OUTLIER) cc_final: 0.2987 (t60) REVERT: F 110 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.2948 (pm20) REVERT: G 28 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.5885 (p90) REVERT: G 34 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6603 (tpt) outliers start: 169 outliers final: 56 residues processed: 824 average time/residue: 1.1673 time to fit residues: 1146.6603 Evaluate side-chains 563 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 491 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 206 optimal weight: 30.0000 chunk 321 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 173 GLN A 218 GLN A 334 ASN A 388 ASN A 409 GLN A 422 ASN A 448 ASN A 506 GLN A 540 ASN A 641 ASN A 658 ASN A 779 GLN A 895 GLN A 901 GLN A 907 ASN A 957 GLN A 978 ASN A1002 GLN A1011 GLN A1048 HIS A1083 HIS A1106 GLN B 49 HIS B 121 ASN B 354 ASN B 437 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 540 ASN B 580 GLN B 784 GLN B 895 GLN B 901 GLN B 907 ASN B 957 GLN B 965 GLN B1010 GLN B1048 HIS B1058 HIS B1106 GLN C 30 ASN C 49 HIS C 66 HIS C 271 GLN C 334 ASN C 354 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 540 ASN C 564 GLN C 613 GLN C 751 ASN C 895 GLN C 957 GLN C 960 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN C1048 HIS C1074 ASN C1106 GLN C1119 ASN D 13 GLN E 60 ASN E 76 ASN F 3 GLN G 3 GLN G 39 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29010 Z= 0.264 Angle : 0.639 10.916 39489 Z= 0.318 Chirality : 0.047 0.312 4562 Planarity : 0.005 0.042 5055 Dihedral : 7.349 80.554 4743 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 6.10 % Allowed : 16.80 % Favored : 77.11 % 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: -2.62 (0.13), residues: 3522 helix: 0.60 (0.21), residues: 636 sheet: -1.59 (0.17), residues: 780 loop : -2.70 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 436 HIS 0.005 0.001 HIS A1064 PHE 0.030 0.002 PHE C 541 TYR 0.026 0.002 TYR B 660 ARG 0.008 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 515 time to evaluate : 3.213 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: A 127 VAL cc_start: 0.8372 (t) cc_final: 0.8019 (m) REVERT: A 129 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7811 (tppp) REVERT: A 184 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.5444 (m-10) REVERT: A 204 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7916 (tmtm) REVERT: A 224 GLU cc_start: 0.7270 (tt0) cc_final: 0.7054 (mt-10) REVERT: A 235 ILE cc_start: 0.3794 (OUTLIER) cc_final: 0.3330 (mp) REVERT: A 277 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 281 GLU cc_start: 0.7028 (pm20) cc_final: 0.6811 (pm20) REVERT: A 393 THR cc_start: 0.8751 (t) cc_final: 0.7784 (t) REVERT: A 394 ASN cc_start: 0.6956 (t0) cc_final: 0.6506 (m-40) REVERT: A 516 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.5735 (tm-30) REVERT: A 517 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7135 (OUTLIER) REVERT: A 776 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8163 (ttpp) REVERT: A 796 TYR cc_start: 0.8298 (t80) cc_final: 0.7918 (t80) REVERT: A 902 MET cc_start: 0.8467 (mmm) cc_final: 0.8259 (tpt) REVERT: B 52 GLN cc_start: 0.7492 (tm-30) cc_final: 0.6826 (tm-30) REVERT: B 80 ASP cc_start: 0.6798 (t0) cc_final: 0.6550 (p0) REVERT: B 186 ASN cc_start: 0.7784 (p0) cc_final: 0.7028 (p0) REVERT: B 237 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7741 (mtp-110) REVERT: B 340 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6687 (tm-30) REVERT: B 449 TYR cc_start: 0.7006 (m-80) cc_final: 0.6474 (m-80) REVERT: B 762 GLN cc_start: 0.7246 (pp30) cc_final: 0.6899 (pp30) REVERT: B 765 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.6312 (mtm-85) REVERT: B 1141 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7833 (tm) REVERT: C 81 ASN cc_start: 0.7552 (t0) cc_final: 0.6473 (t0) REVERT: C 88 ASP cc_start: 0.6708 (m-30) cc_final: 0.6497 (m-30) REVERT: C 101 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8136 (pp) REVERT: C 102 ARG cc_start: 0.7327 (mtp85) cc_final: 0.7025 (mmm-85) REVERT: C 118 LEU cc_start: 0.8120 (tp) cc_final: 0.7902 (tt) REVERT: C 129 LYS cc_start: 0.7338 (mmtt) cc_final: 0.7006 (mmtm) REVERT: C 188 ARG cc_start: 0.7477 (ptp-170) cc_final: 0.6780 (mtp180) REVERT: C 239 GLN cc_start: 0.7290 (pt0) cc_final: 0.6875 (tt0) REVERT: C 317 ASN cc_start: 0.7977 (m110) cc_final: 0.7776 (m-40) REVERT: C 321 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7918 (mm110) REVERT: C 407 VAL cc_start: 0.6463 (OUTLIER) cc_final: 0.6214 (t) REVERT: C 549 THR cc_start: 0.8211 (t) cc_final: 0.7901 (m) REVERT: C 779 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7765 (tm-30) REVERT: C 814 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7551 (mppt) REVERT: C 859 THR cc_start: 0.8445 (m) cc_final: 0.8157 (p) REVERT: C 957 GLN cc_start: 0.7432 (tt0) cc_final: 0.7036 (tt0) REVERT: D 33 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7128 (tm-30) REVERT: D 82 MET cc_start: 0.6365 (ppp) cc_final: 0.5817 (ppp) REVERT: E 3 GLN cc_start: 0.4015 (OUTLIER) cc_final: 0.3690 (tm-30) REVERT: E 4 LEU cc_start: -0.5031 (OUTLIER) cc_final: -0.5310 (tt) REVERT: E 31 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.5487 (p0) REVERT: E 92 MET cc_start: 0.4237 (tpp) cc_final: 0.3682 (tpp) REVERT: E 99 TRP cc_start: 0.4416 (OUTLIER) cc_final: 0.3083 (t60) REVERT: F 110 GLN cc_start: 0.3406 (OUTLIER) cc_final: 0.3016 (pm20) REVERT: G 28 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.3949 (p90) REVERT: G 32 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: G 34 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6517 (tpt) REVERT: G 83 MET cc_start: 0.6607 (ptp) cc_final: 0.6176 (ptp) outliers start: 188 outliers final: 76 residues processed: 655 average time/residue: 1.2567 time to fit residues: 975.9226 Evaluate side-chains 574 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 482 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 322 optimal weight: 50.0000 chunk 347 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 658 ASN A 895 GLN B 30 ASN B 49 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 448 ASN B 450 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 935 GLN B 955 ASN B 957 GLN B1010 GLN C 30 ASN C 66 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 564 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 960 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29010 Z= 0.389 Angle : 0.670 9.506 39489 Z= 0.339 Chirality : 0.048 0.277 4562 Planarity : 0.005 0.057 5055 Dihedral : 7.045 81.042 4713 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 6.23 % Allowed : 18.68 % Favored : 75.10 % 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: -2.29 (0.13), residues: 3522 helix: 0.70 (0.21), residues: 658 sheet: -1.39 (0.17), residues: 799 loop : -2.44 (0.12), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 436 HIS 0.025 0.002 HIS C 519 PHE 0.032 0.002 PHE C 541 TYR 0.026 0.002 TYR B1067 ARG 0.009 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 506 time to evaluate : 3.191 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: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6394 (t0) cc_final: 0.5586 (t0) REVERT: A 127 VAL cc_start: 0.8361 (t) cc_final: 0.8059 (m) REVERT: A 128 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7657 (mp) REVERT: A 129 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7866 (tppt) REVERT: A 184 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5598 (m-10) REVERT: A 281 GLU cc_start: 0.7176 (pm20) cc_final: 0.6933 (pm20) REVERT: A 516 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6043 (tm-30) REVERT: A 517 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7368 (pp) REVERT: A 776 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8219 (ttpp) REVERT: A 790 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7761 (mmmm) REVERT: A 796 TYR cc_start: 0.8462 (t80) cc_final: 0.8093 (t80) REVERT: A 990 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 30 ASN cc_start: 0.7746 (t0) cc_final: 0.7476 (t0) REVERT: B 52 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 186 ASN cc_start: 0.7779 (p0) cc_final: 0.7218 (p0) REVERT: B 224 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6738 (mm-30) REVERT: B 237 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7753 (mtp-110) REVERT: B 282 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.6545 (m-40) REVERT: B 338 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7769 (t80) REVERT: B 340 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6643 (tm-30) REVERT: B 347 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8267 (m-10) REVERT: B 421 TYR cc_start: 0.8458 (m-80) cc_final: 0.8255 (m-80) REVERT: B 470 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8101 (t) REVERT: B 472 ILE cc_start: 0.8172 (tp) cc_final: 0.7419 (mm) REVERT: B 762 GLN cc_start: 0.7333 (pp30) cc_final: 0.7084 (pp30) REVERT: B 765 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.6658 (mtm-85) REVERT: B 933 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8213 (mtmm) REVERT: B 983 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7488 (mtm110) REVERT: B 995 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7531 (mtm-85) REVERT: B 1091 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7646 (ttp-170) REVERT: C 88 ASP cc_start: 0.6898 (m-30) cc_final: 0.6653 (m-30) REVERT: C 170 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6749 (t80) REVERT: C 188 ARG cc_start: 0.7237 (ptp-170) cc_final: 0.7028 (mtp180) REVERT: C 218 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: C 317 ASN cc_start: 0.8006 (m110) cc_final: 0.7776 (m-40) REVERT: C 324 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7224 (mm-30) REVERT: C 407 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6201 (t) REVERT: C 461 LEU cc_start: -0.1250 (OUTLIER) cc_final: -0.1513 (pp) REVERT: C 585 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7273 (mt) REVERT: C 779 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7760 (tm-30) REVERT: C 814 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7574 (mppt) REVERT: C 957 GLN cc_start: 0.7573 (tt0) cc_final: 0.7109 (tt0) REVERT: D 18 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7216 (mm) REVERT: D 33 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 56 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6959 (tpp80) REVERT: D 82 MET cc_start: 0.6373 (ppp) cc_final: 0.5754 (ppp) REVERT: E 3 GLN cc_start: 0.4086 (OUTLIER) cc_final: 0.3819 (tm-30) REVERT: E 31 ASP cc_start: 0.5906 (OUTLIER) cc_final: 0.5600 (p0) REVERT: E 92 MET cc_start: 0.4629 (tpp) cc_final: 0.4002 (tpp) REVERT: E 99 TRP cc_start: 0.4386 (OUTLIER) cc_final: 0.3104 (t60) REVERT: F 110 GLN cc_start: 0.3656 (OUTLIER) cc_final: 0.3209 (pm20) REVERT: G 28 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.4064 (p90) REVERT: G 32 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: G 34 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6620 (tpt) REVERT: G 83 MET cc_start: 0.6722 (ptp) cc_final: 0.6201 (ptp) outliers start: 192 outliers final: 99 residues processed: 642 average time/residue: 1.2862 time to fit residues: 978.0556 Evaluate side-chains 591 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 467 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 8.9990 chunk 242 optimal weight: 50.0000 chunk 167 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 323 optimal weight: 20.0000 chunk 342 optimal weight: 0.0870 chunk 168 optimal weight: 0.9980 chunk 306 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 641 ASN A 895 GLN B 49 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 66 HIS C 121 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 641 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29010 Z= 0.216 Angle : 0.609 10.910 39489 Z= 0.306 Chirality : 0.045 0.281 4562 Planarity : 0.004 0.040 5055 Dihedral : 6.645 81.292 4695 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 5.64 % Allowed : 20.72 % Favored : 73.64 % 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: -1.98 (0.14), residues: 3522 helix: 0.95 (0.21), residues: 660 sheet: -1.10 (0.17), residues: 789 loop : -2.27 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 47 HIS 0.004 0.001 HIS B1088 PHE 0.033 0.001 PHE C 541 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 472 time to evaluate : 3.444 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: A 127 VAL cc_start: 0.8315 (t) cc_final: 0.8026 (m) REVERT: A 128 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 129 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7588 (tppp) REVERT: A 281 GLU cc_start: 0.7133 (pm20) cc_final: 0.6793 (pm20) REVERT: A 394 ASN cc_start: 0.6824 (t0) cc_final: 0.6309 (m-40) REVERT: A 516 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.5802 (tm-30) REVERT: A 517 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7696 (tm) REVERT: A 518 LEU cc_start: 0.8279 (mt) cc_final: 0.7684 (mt) REVERT: A 776 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8190 (ttpp) REVERT: A 790 LYS cc_start: 0.8075 (tptt) cc_final: 0.7830 (mtpp) REVERT: A 990 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 52 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7234 (tm-30) REVERT: B 186 ASN cc_start: 0.7782 (p0) cc_final: 0.6123 (p0) REVERT: B 188 ARG cc_start: 0.7927 (ptp90) cc_final: 0.7205 (mtt-85) REVERT: B 224 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6628 (mm-30) REVERT: B 237 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7811 (mtp-110) REVERT: B 338 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 340 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6613 (tm-30) REVERT: B 378 LYS cc_start: 0.7659 (mppt) cc_final: 0.7434 (mppt) REVERT: B 421 TYR cc_start: 0.8445 (m-10) cc_final: 0.8198 (m-80) REVERT: B 455 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8344 (mt) REVERT: B 472 ILE cc_start: 0.8068 (tp) cc_final: 0.7819 (mm) REVERT: B 752 LEU cc_start: 0.8275 (tp) cc_final: 0.8062 (tt) REVERT: B 765 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.6608 (mtm-85) REVERT: B 869 MET cc_start: 0.8573 (mtp) cc_final: 0.8336 (mtt) REVERT: B 933 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8216 (mtmm) REVERT: B 1091 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7620 (ttp-110) REVERT: C 88 ASP cc_start: 0.6774 (m-30) cc_final: 0.6551 (m-30) REVERT: C 237 ARG cc_start: 0.6970 (mtm-85) cc_final: 0.6659 (mtp85) REVERT: C 317 ASN cc_start: 0.7994 (m110) cc_final: 0.7763 (m-40) REVERT: C 324 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7192 (mm-30) REVERT: C 407 VAL cc_start: 0.6438 (OUTLIER) cc_final: 0.6184 (t) REVERT: C 461 LEU cc_start: -0.1376 (OUTLIER) cc_final: -0.1662 (pp) REVERT: C 740 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7688 (ttp) REVERT: C 779 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: C 814 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7575 (mppt) REVERT: C 918 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: C 957 GLN cc_start: 0.7533 (tt0) cc_final: 0.7064 (tt0) REVERT: C 990 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: D 18 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7096 (mm) REVERT: D 56 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.6929 (tpp80) REVERT: D 82 MET cc_start: 0.6366 (ppp) cc_final: 0.5674 (ppp) REVERT: E 3 GLN cc_start: 0.4043 (OUTLIER) cc_final: 0.3748 (tm-30) REVERT: E 4 LEU cc_start: -0.4795 (OUTLIER) cc_final: -0.5096 (tt) REVERT: E 31 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5626 (p0) REVERT: E 92 MET cc_start: 0.4860 (tpp) cc_final: 0.4204 (tpp) REVERT: E 99 TRP cc_start: 0.4384 (OUTLIER) cc_final: 0.3114 (t60) REVERT: G 28 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.4045 (p90) REVERT: G 32 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: G 34 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6536 (tpt) REVERT: G 47 TRP cc_start: 0.8273 (t60) cc_final: 0.7959 (t60) REVERT: G 83 MET cc_start: 0.6810 (ptp) cc_final: 0.6263 (ptp) outliers start: 174 outliers final: 93 residues processed: 605 average time/residue: 1.3597 time to fit residues: 988.6791 Evaluate side-chains 568 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 453 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 174 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 641 ASN A 901 GLN B 30 ASN B 49 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 30 ASN C 66 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 755 GLN C 960 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29010 Z= 0.396 Angle : 0.670 12.079 39489 Z= 0.340 Chirality : 0.048 0.304 4562 Planarity : 0.005 0.082 5055 Dihedral : 6.725 81.530 4684 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.45 % Rotamer: Outliers : 6.74 % Allowed : 20.30 % Favored : 72.96 % 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: -1.91 (0.14), residues: 3522 helix: 0.75 (0.21), residues: 687 sheet: -0.99 (0.18), residues: 783 loop : -2.20 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 436 HIS 0.007 0.001 HIS A 205 PHE 0.034 0.002 PHE C 541 TYR 0.025 0.002 TYR B1067 ARG 0.015 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 494 time to evaluate : 3.405 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 127 VAL cc_start: 0.8348 (t) cc_final: 0.8002 (m) REVERT: A 128 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 129 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7721 (tppt) REVERT: A 169 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: A 394 ASN cc_start: 0.6882 (t0) cc_final: 0.6523 (m-40) REVERT: A 516 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: A 517 LEU cc_start: 0.8156 (tm) cc_final: 0.7519 (tm) REVERT: A 776 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8200 (ttpp) REVERT: A 988 GLU cc_start: 0.7239 (pp20) cc_final: 0.6932 (tm-30) REVERT: A 990 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 1002 GLN cc_start: 0.7442 (tp40) cc_final: 0.7006 (tp40) REVERT: B 52 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 186 ASN cc_start: 0.7750 (p0) cc_final: 0.7007 (p0) REVERT: B 224 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6640 (mm-30) REVERT: B 237 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7847 (mtp-110) REVERT: B 340 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6750 (tm-30) REVERT: B 347 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8133 (m-10) REVERT: B 361 CYS cc_start: 0.5400 (t) cc_final: 0.5080 (t) REVERT: B 440 LYS cc_start: 0.7991 (tppt) cc_final: 0.7788 (tppt) REVERT: B 752 LEU cc_start: 0.8352 (tp) cc_final: 0.8080 (tt) REVERT: B 762 GLN cc_start: 0.7407 (pp30) cc_final: 0.7114 (pp30) REVERT: B 765 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.6922 (mtm-85) REVERT: B 776 LYS cc_start: 0.8431 (ttpp) cc_final: 0.7888 (ttpp) REVERT: B 780 GLU cc_start: 0.7471 (pt0) cc_final: 0.7099 (pm20) REVERT: B 933 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8268 (mtmm) REVERT: B 995 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7578 (mtm-85) REVERT: B 1091 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7689 (ttp-170) REVERT: C 170 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6365 (t80) REVERT: C 317 ASN cc_start: 0.8044 (m110) cc_final: 0.7786 (m-40) REVERT: C 324 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7117 (mm-30) REVERT: C 407 VAL cc_start: 0.6440 (OUTLIER) cc_final: 0.6194 (t) REVERT: C 461 LEU cc_start: -0.1390 (OUTLIER) cc_final: -0.1684 (pp) REVERT: C 754 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7487 (mm) REVERT: C 779 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: C 814 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7546 (mppt) REVERT: C 918 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6840 (mm-30) REVERT: C 957 GLN cc_start: 0.7608 (tt0) cc_final: 0.7140 (tt0) REVERT: C 990 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: C 1002 GLN cc_start: 0.7660 (tt0) cc_final: 0.7438 (tp40) REVERT: C 1041 ASP cc_start: 0.7393 (t0) cc_final: 0.7005 (t0) REVERT: D 18 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.6858 (mm) REVERT: D 56 ARG cc_start: 0.8410 (mpp80) cc_final: 0.8164 (mpp80) REVERT: D 82 MET cc_start: 0.6328 (ppp) cc_final: 0.5410 (ppp) REVERT: E 3 GLN cc_start: 0.4306 (OUTLIER) cc_final: 0.4012 (tm-30) REVERT: E 4 LEU cc_start: -0.4689 (OUTLIER) cc_final: -0.5135 (tt) REVERT: E 31 ASP cc_start: 0.5657 (OUTLIER) cc_final: 0.5232 (p0) REVERT: E 92 MET cc_start: 0.5130 (tpp) cc_final: 0.4470 (tpp) REVERT: E 99 TRP cc_start: 0.4416 (OUTLIER) cc_final: 0.3116 (t60) REVERT: F 36 TRP cc_start: 0.4754 (t60) cc_final: 0.4466 (t60) REVERT: F 82 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.5088 (ppp) REVERT: F 110 GLN cc_start: 0.3682 (OUTLIER) cc_final: 0.3218 (pm20) REVERT: G 28 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5932 (p90) REVERT: G 34 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6551 (tpt) REVERT: G 47 TRP cc_start: 0.8272 (t60) cc_final: 0.8006 (t60) REVERT: G 83 MET cc_start: 0.6823 (ptp) cc_final: 0.6245 (ptp) outliers start: 208 outliers final: 106 residues processed: 650 average time/residue: 1.2594 time to fit residues: 971.4319 Evaluate side-chains 599 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 471 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 0.0980 chunk 308 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 342 optimal weight: 8.9990 chunk 284 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 115 GLN A 205 HIS A 280 ASN A 641 ASN A 895 GLN A 901 GLN B 173 GLN B 343 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN C 66 HIS C 205 HIS C 234 ASN C 239 GLN C 409 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 641 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29010 Z= 0.195 Angle : 0.629 12.188 39489 Z= 0.313 Chirality : 0.045 0.363 4562 Planarity : 0.004 0.061 5055 Dihedral : 6.307 81.581 4680 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 5.93 % Allowed : 21.30 % Favored : 72.76 % 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: -1.69 (0.14), residues: 3522 helix: 1.04 (0.21), residues: 678 sheet: -0.96 (0.17), residues: 801 loop : -2.03 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 436 HIS 0.011 0.001 HIS C 205 PHE 0.035 0.001 PHE C 541 TYR 0.019 0.001 TYR C1067 ARG 0.011 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 472 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: 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 127 VAL cc_start: 0.8284 (t) cc_final: 0.7941 (m) REVERT: A 128 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 129 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7553 (tppp) REVERT: A 169 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: A 394 ASN cc_start: 0.6917 (t0) cc_final: 0.6378 (m-40) REVERT: A 516 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.5969 (tm-30) REVERT: A 517 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7595 (tm) REVERT: A 776 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8184 (ttpp) REVERT: A 933 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8110 (mtpp) REVERT: A 990 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 52 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 186 ASN cc_start: 0.7759 (p0) cc_final: 0.6998 (p0) REVERT: B 224 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6595 (mm-30) REVERT: B 237 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7812 (mtp-110) REVERT: B 340 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6693 (tm-30) REVERT: B 472 ILE cc_start: 0.8038 (tp) cc_final: 0.7791 (mm) REVERT: B 574 ASP cc_start: 0.7054 (t0) cc_final: 0.6791 (t0) REVERT: B 588 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8347 (p) REVERT: B 752 LEU cc_start: 0.8228 (tp) cc_final: 0.7965 (tt) REVERT: B 765 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.6901 (mtm-85) REVERT: B 776 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7891 (ttpp) REVERT: B 933 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8229 (mtmm) REVERT: B 983 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7377 (mtm110) REVERT: B 1014 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7449 (mtp180) REVERT: B 1031 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: B 1091 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7669 (ttp-110) REVERT: B 1141 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7124 (tm) REVERT: C 129 LYS cc_start: 0.7340 (mppt) cc_final: 0.6987 (mppt) REVERT: C 170 TYR cc_start: 0.7175 (t80) cc_final: 0.5765 (t80) REVERT: C 237 ARG cc_start: 0.7020 (mtp-110) cc_final: 0.6727 (mtp85) REVERT: C 317 ASN cc_start: 0.8016 (m110) cc_final: 0.7797 (m-40) REVERT: C 320 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8396 (m) REVERT: C 321 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7876 (mm110) REVERT: C 324 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7151 (mm-30) REVERT: C 407 VAL cc_start: 0.6426 (OUTLIER) cc_final: 0.6177 (t) REVERT: C 461 LEU cc_start: -0.1378 (OUTLIER) cc_final: -0.1690 (pp) REVERT: C 565 PHE cc_start: 0.6369 (m-10) cc_final: 0.6143 (m-10) REVERT: C 740 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7624 (ttp) REVERT: C 814 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7569 (mppt) REVERT: C 918 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: C 957 GLN cc_start: 0.7565 (tt0) cc_final: 0.7109 (tt0) REVERT: C 976 VAL cc_start: 0.8658 (t) cc_final: 0.8368 (m) REVERT: C 990 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: C 1041 ASP cc_start: 0.7353 (t0) cc_final: 0.6964 (t0) REVERT: D 18 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7494 (mm) REVERT: D 33 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7180 (tm-30) REVERT: D 82 MET cc_start: 0.6300 (ppp) cc_final: 0.5861 (ppp) REVERT: E 4 LEU cc_start: -0.4912 (OUTLIER) cc_final: -0.5214 (tt) REVERT: E 31 ASP cc_start: 0.5679 (OUTLIER) cc_final: 0.5298 (p0) REVERT: E 92 MET cc_start: 0.5250 (tpp) cc_final: 0.4612 (tpp) REVERT: E 99 TRP cc_start: 0.4388 (OUTLIER) cc_final: 0.3090 (t60) REVERT: F 34 MET cc_start: 0.4009 (mmm) cc_final: 0.3715 (mmp) REVERT: F 36 TRP cc_start: 0.4570 (t60) cc_final: 0.4298 (t60) REVERT: F 77 MET cc_start: 0.3698 (ppp) cc_final: 0.2405 (tpt) REVERT: F 110 GLN cc_start: 0.3648 (OUTLIER) cc_final: 0.3209 (pm20) REVERT: G 28 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.4115 (p90) REVERT: G 32 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: G 34 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6493 (tpt) REVERT: G 47 TRP cc_start: 0.8285 (t60) cc_final: 0.8044 (t60) REVERT: G 83 MET cc_start: 0.6860 (ptp) cc_final: 0.6278 (ptp) outliers start: 183 outliers final: 87 residues processed: 615 average time/residue: 1.2639 time to fit residues: 923.9054 Evaluate side-chains 580 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 468 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 30.0000 chunk 38 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 341 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 580 GLN A 641 ASN A 895 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN C 30 ASN C 66 HIS C 205 HIS C 239 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 641 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29010 Z= 0.257 Angle : 0.647 12.064 39489 Z= 0.323 Chirality : 0.047 0.488 4562 Planarity : 0.004 0.056 5055 Dihedral : 6.139 81.707 4674 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.87 % Favored : 93.10 % Rotamer: Outliers : 5.22 % Allowed : 23.05 % Favored : 71.73 % 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: -1.60 (0.14), residues: 3522 helix: 0.99 (0.21), residues: 691 sheet: -0.85 (0.18), residues: 790 loop : -1.96 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 64 HIS 0.023 0.001 HIS C 205 PHE 0.034 0.002 PHE C 541 TYR 0.022 0.001 TYR A 904 ARG 0.013 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 467 time to evaluate : 3.020 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: symmetry clash REVERT: A 127 VAL cc_start: 0.8310 (t) cc_final: 0.7931 (m) REVERT: A 128 ILE cc_start: 0.8028 (mt) cc_final: 0.7778 (mp) REVERT: A 129 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7679 (tppp) REVERT: A 169 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: A 394 ASN cc_start: 0.6928 (t0) cc_final: 0.6407 (m-40) REVERT: A 516 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5998 (tm-30) REVERT: A 517 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7570 (tm) REVERT: A 776 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8166 (ttpp) REVERT: A 990 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 52 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 186 ASN cc_start: 0.7794 (p0) cc_final: 0.6135 (p0) REVERT: B 188 ARG cc_start: 0.7910 (ptp90) cc_final: 0.7132 (mtt-85) REVERT: B 224 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6618 (mm-30) REVERT: B 237 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7737 (mtp-110) REVERT: B 340 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6730 (tm-30) REVERT: B 574 ASP cc_start: 0.7077 (t0) cc_final: 0.6805 (t0) REVERT: B 588 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8358 (p) REVERT: B 752 LEU cc_start: 0.8264 (tp) cc_final: 0.7994 (tt) REVERT: B 773 GLU cc_start: 0.7397 (tt0) cc_final: 0.7078 (tt0) REVERT: B 933 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8244 (mtmm) REVERT: B 1014 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7452 (mtp180) REVERT: B 1107 ARG cc_start: 0.7411 (mtt180) cc_final: 0.7204 (mtt180) REVERT: B 1141 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7151 (tm) REVERT: B 1144 GLU cc_start: 0.6971 (pp20) cc_final: 0.6712 (pp20) REVERT: C 129 LYS cc_start: 0.7306 (mppt) cc_final: 0.6954 (mmpt) REVERT: C 170 TYR cc_start: 0.7219 (t80) cc_final: 0.5961 (t80) REVERT: C 317 ASN cc_start: 0.8059 (m110) cc_final: 0.7824 (m-40) REVERT: C 320 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8410 (m) REVERT: C 324 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 407 VAL cc_start: 0.6418 (OUTLIER) cc_final: 0.6174 (t) REVERT: C 461 LEU cc_start: -0.1403 (OUTLIER) cc_final: -0.1716 (pp) REVERT: C 546 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6788 (mt) REVERT: C 558 LYS cc_start: 0.7899 (pttm) cc_final: 0.7687 (pttm) REVERT: C 740 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7629 (ttp) REVERT: C 814 LYS cc_start: 0.7998 (mmtm) cc_final: 0.7571 (mppt) REVERT: C 918 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: C 957 GLN cc_start: 0.7603 (tt0) cc_final: 0.7292 (mt0) REVERT: C 964 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (tmtt) REVERT: C 990 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: C 1002 GLN cc_start: 0.7590 (tt0) cc_final: 0.7333 (tp40) REVERT: C 1041 ASP cc_start: 0.7391 (t0) cc_final: 0.6991 (t0) REVERT: D 18 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7471 (mm) REVERT: D 33 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7314 (tm-30) REVERT: D 82 MET cc_start: 0.6311 (ppp) cc_final: 0.5829 (ppp) REVERT: E 4 LEU cc_start: -0.4826 (OUTLIER) cc_final: -0.5174 (tt) REVERT: E 31 ASP cc_start: 0.5695 (OUTLIER) cc_final: 0.5306 (p0) REVERT: E 92 MET cc_start: 0.5187 (tpp) cc_final: 0.4553 (tpp) REVERT: E 99 TRP cc_start: 0.4449 (OUTLIER) cc_final: 0.3122 (t60) REVERT: F 36 TRP cc_start: 0.4571 (t-100) cc_final: 0.4326 (t60) REVERT: F 77 MET cc_start: 0.3883 (ppp) cc_final: 0.2387 (tpt) REVERT: F 82 MET cc_start: 0.7026 (tpt) cc_final: 0.5965 (pp-130) REVERT: F 110 GLN cc_start: 0.3673 (OUTLIER) cc_final: 0.3237 (pm20) REVERT: G 28 TYR cc_start: 0.6565 (OUTLIER) cc_final: 0.5960 (p90) REVERT: G 34 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6583 (tpt) REVERT: G 47 TRP cc_start: 0.8303 (t60) cc_final: 0.8060 (t60) REVERT: G 83 MET cc_start: 0.6903 (ptp) cc_final: 0.6335 (ptp) outliers start: 161 outliers final: 92 residues processed: 591 average time/residue: 1.2779 time to fit residues: 891.8664 Evaluate side-chains 574 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 460 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 580 GLN A 641 ASN A 895 GLN A 901 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 474 GLN C 487 ASN C 641 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29010 Z= 0.245 Angle : 0.655 13.446 39489 Z= 0.326 Chirality : 0.046 0.226 4562 Planarity : 0.005 0.075 5055 Dihedral : 6.051 81.689 4670 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.36 % Rotamer: Outliers : 4.93 % Allowed : 23.70 % Favored : 71.37 % 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: -1.51 (0.14), residues: 3522 helix: 1.00 (0.21), residues: 696 sheet: -0.86 (0.18), residues: 807 loop : -1.86 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 436 HIS 0.022 0.001 HIS C 205 PHE 0.035 0.002 PHE C 541 TYR 0.020 0.001 TYR B1067 ARG 0.019 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 480 time to evaluate : 3.296 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: symmetry clash REVERT: A 96 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6771 (mp0) REVERT: A 127 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.7937 (m) REVERT: A 128 ILE cc_start: 0.8043 (mt) cc_final: 0.7782 (mp) REVERT: A 129 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7656 (tppp) REVERT: A 169 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: A 188 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7308 (mmt-90) REVERT: A 229 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7021 (mp) REVERT: A 394 ASN cc_start: 0.6861 (t0) cc_final: 0.6366 (m-40) REVERT: A 516 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6000 (tm-30) REVERT: A 517 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7558 (tm) REVERT: A 776 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8156 (ttpp) REVERT: A 933 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8119 (mtpp) REVERT: A 990 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: B 52 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 96 GLU cc_start: 0.7414 (pm20) cc_final: 0.7183 (pm20) REVERT: B 186 ASN cc_start: 0.7770 (p0) cc_final: 0.6404 (p0) REVERT: B 188 ARG cc_start: 0.7863 (ptp90) cc_final: 0.7181 (mtt-85) REVERT: B 237 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7672 (mtp-110) REVERT: B 340 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6736 (tm-30) REVERT: B 574 ASP cc_start: 0.7054 (t0) cc_final: 0.6758 (t0) REVERT: B 588 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8367 (p) REVERT: B 752 LEU cc_start: 0.8251 (tp) cc_final: 0.7998 (tt) REVERT: B 773 GLU cc_start: 0.7188 (tt0) cc_final: 0.6853 (tt0) REVERT: B 776 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8033 (ttpp) REVERT: B 780 GLU cc_start: 0.7570 (pp20) cc_final: 0.7098 (pm20) REVERT: B 933 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8232 (mtmm) REVERT: B 1014 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7453 (mtp180) REVERT: B 1019 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7246 (ttp80) REVERT: B 1141 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.6980 (tm) REVERT: C 121 ASN cc_start: 0.6725 (t0) cc_final: 0.6244 (t0) REVERT: C 129 LYS cc_start: 0.7354 (mppt) cc_final: 0.6559 (mmtm) REVERT: C 170 TYR cc_start: 0.7285 (t80) cc_final: 0.5774 (t80) REVERT: C 317 ASN cc_start: 0.8066 (m110) cc_final: 0.7821 (m-40) REVERT: C 320 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8405 (m) REVERT: C 324 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7178 (mm-30) REVERT: C 407 VAL cc_start: 0.6396 (OUTLIER) cc_final: 0.6153 (t) REVERT: C 461 LEU cc_start: -0.1404 (OUTLIER) cc_final: -0.1740 (pp) REVERT: C 546 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7344 (mt) REVERT: C 558 LYS cc_start: 0.7916 (pttm) cc_final: 0.7672 (pttm) REVERT: C 740 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7679 (ttp) REVERT: C 814 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7556 (mppt) REVERT: C 825 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8286 (mtmt) REVERT: C 918 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6704 (mm-30) REVERT: C 957 GLN cc_start: 0.7601 (tt0) cc_final: 0.7264 (tt0) REVERT: C 976 VAL cc_start: 0.8680 (t) cc_final: 0.8382 (m) REVERT: C 990 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: C 1002 GLN cc_start: 0.7572 (tt0) cc_final: 0.7333 (tp40) REVERT: C 1041 ASP cc_start: 0.7395 (t0) cc_final: 0.6991 (t0) REVERT: D 18 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7447 (mm) REVERT: D 33 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7285 (tm-30) REVERT: D 82 MET cc_start: 0.6295 (ppp) cc_final: 0.5799 (ppp) REVERT: E 4 LEU cc_start: -0.4846 (OUTLIER) cc_final: -0.5172 (tt) REVERT: E 31 ASP cc_start: 0.5695 (OUTLIER) cc_final: 0.5294 (p0) REVERT: E 92 MET cc_start: 0.5280 (tpp) cc_final: 0.4666 (tpp) REVERT: E 99 TRP cc_start: 0.4417 (OUTLIER) cc_final: 0.3098 (t60) REVERT: F 77 MET cc_start: 0.3831 (ppp) cc_final: 0.2586 (tpt) REVERT: F 82 MET cc_start: 0.6804 (tpt) cc_final: 0.5712 (pp-130) REVERT: F 110 GLN cc_start: 0.3692 (OUTLIER) cc_final: 0.3253 (pm20) REVERT: G 28 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.5994 (p90) REVERT: G 34 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6580 (tpt) REVERT: G 83 MET cc_start: 0.6864 (ptp) cc_final: 0.6241 (ptp) REVERT: G 93 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7827 (pt) outliers start: 152 outliers final: 91 residues processed: 595 average time/residue: 1.2732 time to fit residues: 900.0133 Evaluate side-chains 574 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 459 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 6.9990 chunk 326 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 317 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 249 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 300 optimal weight: 0.9990 chunk 316 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 580 GLN A 641 ASN A 895 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 641 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29010 Z= 0.235 Angle : 0.662 14.033 39489 Z= 0.330 Chirality : 0.046 0.218 4562 Planarity : 0.005 0.080 5055 Dihedral : 5.978 81.636 4670 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.04 % Favored : 92.93 % Rotamer: Outliers : 4.60 % Allowed : 24.58 % Favored : 70.82 % 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: -1.44 (0.14), residues: 3522 helix: 1.03 (0.21), residues: 696 sheet: -0.77 (0.18), residues: 804 loop : -1.83 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 47 HIS 0.024 0.001 HIS C 205 PHE 0.033 0.002 PHE C 541 TYR 0.026 0.001 TYR C 266 ARG 0.019 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 470 time to evaluate : 3.191 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: symmetry clash REVERT: A 127 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7925 (m) REVERT: A 128 ILE cc_start: 0.8045 (mt) cc_final: 0.7791 (mp) REVERT: A 129 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7628 (tppp) REVERT: A 169 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: A 188 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7352 (mmt-90) REVERT: A 229 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7164 (mt) REVERT: A 346 ARG cc_start: 0.4014 (OUTLIER) cc_final: 0.2557 (pmt-80) REVERT: A 394 ASN cc_start: 0.6854 (t0) cc_final: 0.6320 (m-40) REVERT: A 516 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5762 (tm-30) REVERT: A 517 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7720 (tm) REVERT: A 518 LEU cc_start: 0.8172 (mt) cc_final: 0.7707 (mt) REVERT: A 776 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8162 (ttpp) REVERT: A 933 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8105 (mtpp) REVERT: A 990 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: B 52 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 96 GLU cc_start: 0.7409 (pm20) cc_final: 0.7116 (pm20) REVERT: B 186 ASN cc_start: 0.7765 (p0) cc_final: 0.6386 (p0) REVERT: B 188 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7187 (mtt-85) REVERT: B 224 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6654 (mm-30) REVERT: B 237 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7722 (mtp-110) REVERT: B 340 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 440 LYS cc_start: 0.8055 (tppt) cc_final: 0.7728 (tppt) REVERT: B 574 ASP cc_start: 0.7052 (t0) cc_final: 0.6766 (t0) REVERT: B 588 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8372 (p) REVERT: B 752 LEU cc_start: 0.8262 (tp) cc_final: 0.8009 (tt) REVERT: B 776 LYS cc_start: 0.8498 (ttpp) cc_final: 0.7994 (ttpp) REVERT: B 780 GLU cc_start: 0.7554 (pp20) cc_final: 0.7090 (pm20) REVERT: B 933 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8239 (mtmm) REVERT: B 1014 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7458 (mtp180) REVERT: B 1019 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7352 (ttp80) REVERT: C 121 ASN cc_start: 0.6614 (t0) cc_final: 0.6175 (t0) REVERT: C 129 LYS cc_start: 0.7373 (mppt) cc_final: 0.7056 (mptt) REVERT: C 170 TYR cc_start: 0.7346 (t80) cc_final: 0.5886 (t80) REVERT: C 237 ARG cc_start: 0.6966 (mtp-110) cc_final: 0.6674 (mtp85) REVERT: C 317 ASN cc_start: 0.8072 (m110) cc_final: 0.7831 (m-40) REVERT: C 320 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 324 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7180 (mm-30) REVERT: C 461 LEU cc_start: -0.1429 (OUTLIER) cc_final: -0.1768 (pp) REVERT: C 558 LYS cc_start: 0.7903 (pttm) cc_final: 0.7647 (pttm) REVERT: C 740 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7598 (ttp) REVERT: C 814 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7568 (mppt) REVERT: C 825 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8265 (mtmt) REVERT: C 976 VAL cc_start: 0.8650 (t) cc_final: 0.8401 (m) REVERT: C 990 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: C 1002 GLN cc_start: 0.7579 (tt0) cc_final: 0.7337 (tp40) REVERT: C 1041 ASP cc_start: 0.7397 (t0) cc_final: 0.6992 (t0) REVERT: D 82 MET cc_start: 0.6286 (ppp) cc_final: 0.5963 (ppp) REVERT: E 4 LEU cc_start: -0.4950 (OUTLIER) cc_final: -0.5269 (tt) REVERT: E 31 ASP cc_start: 0.5694 (OUTLIER) cc_final: 0.5307 (p0) REVERT: E 92 MET cc_start: 0.5427 (tpp) cc_final: 0.4851 (tpp) REVERT: E 99 TRP cc_start: 0.4459 (OUTLIER) cc_final: 0.3120 (t60) REVERT: F 77 MET cc_start: 0.3730 (ppp) cc_final: 0.2335 (tmm) REVERT: F 82 MET cc_start: 0.6656 (tpt) cc_final: 0.5661 (pp-130) REVERT: F 99 TRP cc_start: 0.5338 (OUTLIER) cc_final: 0.4868 (t60) REVERT: F 110 GLN cc_start: 0.3717 (OUTLIER) cc_final: 0.3266 (pm20) REVERT: G 28 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6024 (p90) REVERT: G 34 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6722 (tpt) REVERT: G 83 MET cc_start: 0.6875 (ptp) cc_final: 0.6255 (ptp) REVERT: G 93 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7822 (pt) outliers start: 142 outliers final: 88 residues processed: 580 average time/residue: 1.3833 time to fit residues: 961.1559 Evaluate side-chains 570 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 460 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 0.8980 chunk 336 optimal weight: 8.9990 chunk 205 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 352 optimal weight: 3.9990 chunk 324 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 580 GLN A 641 ASN A 895 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 205 HIS C 641 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS D 73 ASN G 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 29010 Z= 0.459 Angle : 0.755 11.728 39489 Z= 0.380 Chirality : 0.050 0.224 4562 Planarity : 0.005 0.078 5055 Dihedral : 6.405 81.584 4666 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 4.47 % Allowed : 25.00 % Favored : 70.53 % 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: -1.59 (0.14), residues: 3522 helix: 0.75 (0.21), residues: 703 sheet: -0.83 (0.18), residues: 824 loop : -1.89 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP G 47 HIS 0.025 0.002 HIS C 205 PHE 0.034 0.002 PHE C 541 TYR 0.032 0.002 TYR C 266 ARG 0.019 0.001 ARG B 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 477 time to evaluate : 3.189 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.7984 (m) REVERT: A 128 ILE cc_start: 0.8067 (mt) cc_final: 0.7802 (mp) REVERT: A 129 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7592 (tppp) REVERT: A 169 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: A 229 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7919 (mt) REVERT: A 394 ASN cc_start: 0.6945 (t0) cc_final: 0.6567 (m-40) REVERT: A 428 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6003 (p0) REVERT: A 516 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6306 (tm-30) REVERT: A 517 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7598 (tp) REVERT: A 776 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8190 (ttpp) REVERT: A 990 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 52 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7302 (tm-30) REVERT: B 129 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7854 (mtmm) REVERT: B 188 ARG cc_start: 0.7872 (ptp90) cc_final: 0.7479 (mtt-85) REVERT: B 237 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7738 (mtp-110) REVERT: B 280 ASN cc_start: 0.6878 (t0) cc_final: 0.6642 (t0) REVERT: B 340 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6773 (tm-30) REVERT: B 440 LYS cc_start: 0.8145 (tppt) cc_final: 0.7837 (tppt) REVERT: B 574 ASP cc_start: 0.7111 (t0) cc_final: 0.6806 (t0) REVERT: B 752 LEU cc_start: 0.8400 (tp) cc_final: 0.8119 (tt) REVERT: B 933 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8278 (mtmm) REVERT: B 1014 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7468 (mtp180) REVERT: C 121 ASN cc_start: 0.6656 (t0) cc_final: 0.6208 (t0) REVERT: C 129 LYS cc_start: 0.7351 (mppt) cc_final: 0.7103 (mptt) REVERT: C 170 TYR cc_start: 0.7574 (t80) cc_final: 0.6500 (t80) REVERT: C 228 ASP cc_start: 0.7321 (t0) cc_final: 0.7065 (t0) REVERT: C 317 ASN cc_start: 0.8103 (m110) cc_final: 0.7852 (m-40) REVERT: C 320 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8402 (m) REVERT: C 324 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7155 (mm-30) REVERT: C 461 LEU cc_start: -0.1257 (OUTLIER) cc_final: -0.1607 (pp) REVERT: C 814 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7543 (mppt) REVERT: C 825 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8277 (mtmt) REVERT: C 902 MET cc_start: 0.8392 (mmm) cc_final: 0.8184 (mmp) REVERT: C 990 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: C 1002 GLN cc_start: 0.7637 (tt0) cc_final: 0.7435 (tp40) REVERT: C 1041 ASP cc_start: 0.7439 (t0) cc_final: 0.7039 (t0) REVERT: D 82 MET cc_start: 0.6357 (ppp) cc_final: 0.5953 (ppp) REVERT: E 4 LEU cc_start: -0.4848 (OUTLIER) cc_final: -0.5225 (tt) REVERT: E 92 MET cc_start: 0.5486 (tpp) cc_final: 0.4839 (tpp) REVERT: E 99 TRP cc_start: 0.4449 (OUTLIER) cc_final: 0.3085 (t60) REVERT: F 77 MET cc_start: 0.3434 (ppp) cc_final: 0.3084 (ppp) REVERT: F 82 MET cc_start: 0.6602 (tpt) cc_final: 0.5532 (pp-130) REVERT: F 110 GLN cc_start: 0.3817 (OUTLIER) cc_final: 0.3338 (pm20) REVERT: G 28 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.6074 (p90) REVERT: G 34 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6783 (tpt) REVERT: G 83 MET cc_start: 0.6866 (ptp) cc_final: 0.6229 (ptp) REVERT: G 93 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7884 (pt) outliers start: 138 outliers final: 89 residues processed: 582 average time/residue: 1.2601 time to fit residues: 865.9949 Evaluate side-chains 569 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 463 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 99 TRP Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 0.5980 chunk 299 optimal weight: 0.9990 chunk 86 optimal weight: 0.0020 chunk 258 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 281 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 580 GLN A 641 ASN A 895 GLN A 901 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 641 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS G 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.163843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125156 restraints weight = 46507.571| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.74 r_work: 0.3384 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29010 Z= 0.210 Angle : 0.697 12.537 39489 Z= 0.347 Chirality : 0.046 0.308 4562 Planarity : 0.005 0.082 5055 Dihedral : 6.149 81.622 4663 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.33 % Rotamer: Outliers : 3.76 % Allowed : 25.71 % Favored : 70.53 % 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: -1.41 (0.14), residues: 3522 helix: 0.98 (0.21), residues: 696 sheet: -0.77 (0.18), residues: 829 loop : -1.77 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 436 HIS 0.010 0.001 HIS C 205 PHE 0.036 0.001 PHE C 541 TYR 0.044 0.001 TYR A 904 ARG 0.020 0.001 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14078.24 seconds wall clock time: 249 minutes 18.85 seconds (14958.85 seconds total)