Starting phenix.real_space_refine on Wed Feb 21 14:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6f_34501/02_2024/8h6f_34501.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6f_34501/02_2024/8h6f_34501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6f_34501/02_2024/8h6f_34501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6f_34501/02_2024/8h6f_34501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6f_34501/02_2024/8h6f_34501.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h6f_34501/02_2024/8h6f_34501.pdb" } resolution = 3.3 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= 0.075 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 124 5.16 5 C 19796 2.51 5 N 5120 2.21 5 O 5977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31017 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8096 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 6 Chain: "B" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8123 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 6 Chain: "C" Number of atoms: 8106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8106 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 6 Chain: "X" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2072 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 244} Chain: "Y" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2072 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 244} Chain: "Z" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2072 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 244} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.55, per 1000 atoms: 0.50 Number of scatterers: 31017 At special positions: 0 Unit cell: (153.994, 185.13, 228.888, 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 124 16.00 O 5977 8.00 N 5120 7.00 C 19796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.04 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 X 220 " - pdb=" SG CYS X 253 " distance=2.03 Simple disulfide: pdb=" SG CYS X 222 " - pdb=" SG CYS X 265 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 220 " - pdb=" SG CYS Y 253 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 222 " - pdb=" SG CYS Y 265 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 220 " - pdb=" SG CYS Z 253 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 222 " - pdb=" SG CYS Z 265 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 61 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG K 1 " - " ASN C1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.44 Conformation dependent library (CDL) restraints added in 6.0 seconds 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 42 sheets defined 23.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.676A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.495A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 4.166A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 422' Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.936A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.749A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.603A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.719A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.552A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 4.030A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.600A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.906A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.874A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.673A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.878A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.888A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.879A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.902A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.845A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.672A pdb=" N TRP B 633 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.911A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.538A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.639A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.156A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.992A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.876A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.649A pdb=" N PHE C 175 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 176 " --> pdb=" O GLN C 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 176' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.042A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.798A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.628A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.985A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 637 removed outlier: 4.092A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.592A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 4.098A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.564A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.684A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.576A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.970A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.510A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.039A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.753A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.856A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C1025 " --> pdb=" O SER C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.507A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 27 removed outlier: 3.975A pdb=" N LEU X 27 " --> pdb=" O ILE X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.708A pdb=" N SER X 43 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE X 44 " --> pdb=" O LEU X 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 40 through 44' Processing helix chain 'X' and resid 59 through 63 removed outlier: 3.833A pdb=" N TYR X 62 " --> pdb=" O GLY X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 83 removed outlier: 3.628A pdb=" N ALA X 81 " --> pdb=" O ASP X 78 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS X 83 " --> pdb=" O SER X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 104 through 108 removed outlier: 3.597A pdb=" N ASP X 107 " --> pdb=" O GLY X 104 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS X 108 " --> pdb=" O VAL X 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 104 through 108' Processing helix chain 'X' and resid 200 through 205 removed outlier: 4.678A pdb=" N ARG X 204 " --> pdb=" O GLY X 200 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU X 205 " --> pdb=" O VAL X 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 200 through 205' Processing helix chain 'X' and resid 225 through 235 Processing helix chain 'X' and resid 236 through 239 removed outlier: 3.792A pdb=" N VAL X 239 " --> pdb=" O SER X 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 236 through 239' Processing helix chain 'X' and resid 246 through 251 removed outlier: 3.675A pdb=" N SER X 250 " --> pdb=" O TRP X 246 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA X 251 " --> pdb=" O ALA X 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 246 through 251' Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 37 through 43 Processing helix chain 'Y' and resid 79 through 85 removed outlier: 3.544A pdb=" N LYS Y 83 " --> pdb=" O SER Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 225 through 235 removed outlier: 3.617A pdb=" N HIS Y 235 " --> pdb=" O TRP Y 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 27 Processing helix chain 'Z' and resid 37 through 44 removed outlier: 3.563A pdb=" N ILE Z 44 " --> pdb=" O GLU Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 removed outlier: 4.122A pdb=" N LEU Z 82 " --> pdb=" O ILE Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 201 through 205 removed outlier: 3.724A pdb=" N ARG Z 204 " --> pdb=" O VAL Z 201 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU Z 205 " --> pdb=" O PHE Z 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 201 through 205' Processing helix chain 'Z' and resid 223 through 235 removed outlier: 4.210A pdb=" N TYR Z 227 " --> pdb=" O PRO Z 223 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU Z 228 " --> pdb=" O GLY Z 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.757A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.073A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.756A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.682A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.905A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.794A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.271A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.947A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.709A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.739A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.876A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.288A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.643A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.963A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.542A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.806A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 355 through 357 removed outlier: 4.016A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 378 through 379 removed outlier: 4.128A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.217A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.591A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.612A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.612A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.517A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.823A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.161A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.566A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.566A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.620A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.919A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.632A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.243A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.779A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 812 hydrogen bonds defined for protein. 2223 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: 11.27 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9922 1.34 - 1.46: 6975 1.46 - 1.58: 14662 1.58 - 1.70: 0 1.70 - 1.82: 155 Bond restraints: 31714 Sorted by residual: bond pdb=" C ILE X 13 " pdb=" N PHE X 14 " ideal model delta sigma weight residual 1.331 1.376 -0.044 1.63e-02 3.76e+03 7.43e+00 bond pdb=" N SER C 155 " pdb=" CA SER C 155 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.18e-02 7.18e+03 7.42e+00 bond pdb=" CB ASN B 331 " pdb=" CG ASN B 331 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.21e+00 bond pdb=" CA ASP Y 164 " pdb=" CB ASP Y 164 " ideal model delta sigma weight residual 1.527 1.560 -0.033 1.75e-02 3.27e+03 3.66e+00 bond pdb=" N THR A1100 " pdb=" CA THR A1100 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.28e-02 6.10e+03 3.56e+00 ... (remaining 31709 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.28: 631 105.28 - 112.46: 16263 112.46 - 119.65: 10312 119.65 - 126.83: 15625 126.83 - 134.02: 339 Bond angle restraints: 43170 Sorted by residual: angle pdb=" N SER C 155 " pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 112.72 106.15 6.57 1.14e+00 7.69e-01 3.32e+01 angle pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 114.40 124.19 -9.79 2.30e+00 1.89e-01 1.81e+01 angle pdb=" N ARG X 72 " pdb=" CA ARG X 72 " pdb=" C ARG X 72 " ideal model delta sigma weight residual 111.55 106.38 5.17 1.37e+00 5.33e-01 1.43e+01 angle pdb=" CA GLN Y 12 " pdb=" CB GLN Y 12 " pdb=" CG GLN Y 12 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N ILE Z 79 " pdb=" CA ILE Z 79 " pdb=" C ILE Z 79 " ideal model delta sigma weight residual 112.43 109.02 3.41 9.20e-01 1.18e+00 1.37e+01 ... (remaining 43165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 16648 18.05 - 36.11: 2199 36.11 - 54.16: 511 54.16 - 72.22: 101 72.22 - 90.27: 37 Dihedral angle restraints: 19496 sinusoidal: 8137 harmonic: 11359 Sorted by residual: dihedral pdb=" CB CYS X 222 " pdb=" SG CYS X 222 " pdb=" SG CYS X 265 " pdb=" CB CYS X 265 " ideal model delta sinusoidal sigma weight residual -86.00 -176.27 90.27 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 0.77 -86.77 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -5.96 -80.04 1 1.00e+01 1.00e-02 7.94e+01 ... (remaining 19493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 4997 0.145 - 0.291: 22 0.291 - 0.436: 11 0.436 - 0.581: 2 0.581 - 0.727: 2 Chirality restraints: 5034 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.10e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.53e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.46e+01 ... (remaining 5031 not shown) Planarity restraints: 5569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG H 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.531 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " -0.348 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C1302 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " -0.140 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " -0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG C1306 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.164 2.00e-02 2.50e+03 ... (remaining 5566 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 757 2.70 - 3.25: 28578 3.25 - 3.80: 42715 3.80 - 4.35: 53114 4.35 - 4.90: 91733 Nonbonded interactions: 216897 Sorted by model distance: nonbonded pdb=" O THR A 108 " pdb=" OG1 THR A 236 " model vdw 2.148 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.204 2.440 nonbonded pdb=" OG SER A 438 " pdb=" O ASP A 442 " model vdw 2.212 2.440 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.220 2.520 nonbonded pdb=" O SER C 746 " pdb=" OG SER C 750 " model vdw 2.242 2.440 ... (remaining 216892 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 139 or resid 153 through 186 or resid 188 throu \ gh 243 or resid 263 through 675 or resid 691 through 1149 or resid 1301 through \ 1307)) selection = (chain 'B' and (resid 26 through 139 or resid 153 through 186 or resid 188 throu \ gh 243 or resid 263 through 675 or resid 691 through 1149 or resid 1301 through \ 1307)) selection = (chain 'C' and (resid 26 through 175 or resid 188 through 243 or resid 263 throu \ gh 675 or resid 691 through 1149 or resid 1301 through 1307)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 5.840 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: 0.030 Extract box with map and model: 17.410 Check model and map are aligned: 0.460 Set scattering table: 0.240 Process input model: 78.210 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 31714 Z= 0.215 Angle : 0.617 9.790 43170 Z= 0.333 Chirality : 0.051 0.727 5034 Planarity : 0.016 0.299 5540 Dihedral : 16.751 89.687 12021 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 0.26 % Allowed : 27.93 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.50 (0.13), residues: 3842 helix: 1.34 (0.21), residues: 713 sheet: -0.42 (0.25), residues: 437 loop : -1.90 (0.11), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 218 HIS 0.007 0.001 HIS C 655 PHE 0.029 0.001 PHE C 192 TYR 0.016 0.001 TYR C 660 ARG 0.004 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1041 ASP cc_start: 0.6694 (t0) cc_final: 0.6384 (t0) REVERT: C 153 MET cc_start: 0.5157 (tpp) cc_final: 0.4920 (tpt) REVERT: X 63 LEU cc_start: -0.0087 (OUTLIER) cc_final: -0.0348 (mp) outliers start: 9 outliers final: 4 residues processed: 167 average time/residue: 0.3841 time to fit residues: 110.7594 Evaluate side-chains 157 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain X residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 0.0470 chunk 293 optimal weight: 0.0030 chunk 162 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 303 optimal weight: 0.0270 chunk 117 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 351 optimal weight: 40.0000 overall best weight: 0.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 710 ASN A1101 HIS B 66 HIS B 331 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 422 ASN ** X 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31714 Z= 0.139 Angle : 0.538 11.026 43170 Z= 0.262 Chirality : 0.044 0.323 5034 Planarity : 0.004 0.063 5540 Dihedral : 5.669 57.793 4867 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 2.20 % Allowed : 26.31 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.30 (0.13), residues: 3842 helix: 1.60 (0.21), residues: 725 sheet: -0.23 (0.25), residues: 449 loop : -1.83 (0.11), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.007 0.001 HIS B 66 PHE 0.018 0.001 PHE A 192 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 161 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6884 (mp) REVERT: B 488 CYS cc_start: 0.0965 (OUTLIER) cc_final: 0.0096 (t) REVERT: C 153 MET cc_start: 0.5139 (tpp) cc_final: 0.4852 (tpt) REVERT: C 377 PHE cc_start: -0.0279 (OUTLIER) cc_final: -0.1493 (m-10) REVERT: Z 142 MET cc_start: 0.1946 (OUTLIER) cc_final: 0.1451 (mtp) outliers start: 76 outliers final: 27 residues processed: 228 average time/residue: 0.3583 time to fit residues: 139.3801 Evaluate side-chains 172 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Z residue 142 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 239 optimal weight: 0.0070 chunk 96 optimal weight: 0.9980 chunk 352 optimal weight: 2.9990 chunk 380 optimal weight: 0.5980 chunk 313 optimal weight: 20.0000 chunk 349 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 907 ASN B 66 HIS B 321 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 949 GLN C 321 GLN C 907 ASN ** X 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31714 Z= 0.138 Angle : 0.499 9.704 43170 Z= 0.245 Chirality : 0.043 0.362 5034 Planarity : 0.004 0.062 5540 Dihedral : 5.374 59.297 4862 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 1.85 % Allowed : 26.54 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.19 (0.13), residues: 3842 helix: 1.72 (0.21), residues: 726 sheet: -0.12 (0.24), residues: 459 loop : -1.77 (0.11), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.006 0.001 HIS B 66 PHE 0.014 0.001 PHE C 65 TYR 0.018 0.001 TYR B1067 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 154 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1041 ASP cc_start: 0.6646 (t0) cc_final: 0.6398 (t0) REVERT: B 488 CYS cc_start: 0.0911 (OUTLIER) cc_final: 0.0076 (t) REVERT: C 377 PHE cc_start: -0.0274 (OUTLIER) cc_final: -0.1519 (m-10) REVERT: Z 142 MET cc_start: 0.2057 (OUTLIER) cc_final: 0.1407 (mtp) outliers start: 64 outliers final: 38 residues processed: 211 average time/residue: 0.3751 time to fit residues: 135.7530 Evaluate side-chains 186 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 17 ASP Chi-restraints excluded: chain Z residue 142 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 30.0000 chunk 264 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 168 optimal weight: 0.5980 chunk 236 optimal weight: 20.0000 chunk 353 optimal weight: 0.8980 chunk 374 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 334 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN X 42 ASN ** X 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31714 Z= 0.174 Angle : 0.500 9.607 43170 Z= 0.247 Chirality : 0.044 0.359 5034 Planarity : 0.004 0.116 5540 Dihedral : 5.306 59.706 4862 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 2.63 % Allowed : 26.40 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.17 (0.13), residues: 3842 helix: 1.66 (0.21), residues: 734 sheet: -0.11 (0.24), residues: 460 loop : -1.75 (0.11), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 231 HIS 0.007 0.001 HIS B 66 PHE 0.021 0.001 PHE A 194 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 153 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.3784 (OUTLIER) cc_final: 0.3464 (t80) REVERT: A 1041 ASP cc_start: 0.6638 (t0) cc_final: 0.6378 (t0) REVERT: B 488 CYS cc_start: 0.0872 (OUTLIER) cc_final: 0.0051 (t) REVERT: C 192 PHE cc_start: 0.7271 (m-10) cc_final: 0.7048 (m-10) REVERT: C 377 PHE cc_start: -0.0239 (OUTLIER) cc_final: -0.1535 (m-10) REVERT: Y 111 ASN cc_start: 0.1582 (OUTLIER) cc_final: -0.1354 (t0) REVERT: Z 142 MET cc_start: 0.1983 (OUTLIER) cc_final: 0.1302 (mtp) outliers start: 91 outliers final: 62 residues processed: 234 average time/residue: 0.3903 time to fit residues: 156.2068 Evaluate side-chains 207 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 140 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 111 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 17 ASP Chi-restraints excluded: chain Z residue 142 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 20.0000 chunk 212 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 319 optimal weight: 0.5980 chunk 258 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN Z 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31714 Z= 0.286 Angle : 0.553 9.638 43170 Z= 0.277 Chirality : 0.046 0.358 5034 Planarity : 0.004 0.062 5540 Dihedral : 5.471 59.790 4862 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 3.50 % Allowed : 25.88 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.30 (0.13), residues: 3842 helix: 1.38 (0.20), residues: 739 sheet: -0.32 (0.24), residues: 482 loop : -1.77 (0.11), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.024 0.001 HIS B 66 PHE 0.031 0.002 PHE B 65 TYR 0.032 0.001 TYR B 265 ARG 0.004 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 151 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.3757 (OUTLIER) cc_final: 0.3451 (t80) REVERT: A 1041 ASP cc_start: 0.6769 (t0) cc_final: 0.6513 (t0) REVERT: B 488 CYS cc_start: 0.0970 (OUTLIER) cc_final: 0.0056 (t) REVERT: B 1029 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8134 (ttp) REVERT: B 1041 ASP cc_start: 0.7597 (t0) cc_final: 0.7370 (t0) REVERT: C 377 PHE cc_start: -0.0149 (OUTLIER) cc_final: -0.1398 (m-80) REVERT: Y 111 ASN cc_start: 0.1627 (OUTLIER) cc_final: -0.1400 (t0) REVERT: Z 142 MET cc_start: 0.2100 (OUTLIER) cc_final: 0.1331 (mtp) REVERT: Z 155 ASP cc_start: 0.2684 (OUTLIER) cc_final: 0.1462 (m-30) outliers start: 121 outliers final: 86 residues processed: 257 average time/residue: 0.3778 time to fit residues: 165.5623 Evaluate side-chains 231 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 138 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 111 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 17 ASP Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 155 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 0.6980 chunk 336 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 374 optimal weight: 30.0000 chunk 310 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 907 ASN B 66 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31714 Z= 0.164 Angle : 0.495 9.604 43170 Z= 0.246 Chirality : 0.044 0.352 5034 Planarity : 0.004 0.060 5540 Dihedral : 5.287 58.563 4862 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 3.04 % Allowed : 26.25 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.18 (0.13), residues: 3842 helix: 1.58 (0.21), residues: 734 sheet: -0.33 (0.24), residues: 485 loop : -1.70 (0.11), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.004 0.001 HIS C 655 PHE 0.019 0.001 PHE C 92 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 152 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.3768 (OUTLIER) cc_final: 0.3400 (t80) REVERT: A 1041 ASP cc_start: 0.6718 (t0) cc_final: 0.6513 (t0) REVERT: B 488 CYS cc_start: 0.1038 (OUTLIER) cc_final: 0.0067 (t) REVERT: C 377 PHE cc_start: -0.0097 (OUTLIER) cc_final: -0.1350 (m-80) REVERT: Y 111 ASN cc_start: 0.1625 (OUTLIER) cc_final: -0.1366 (t0) REVERT: Z 142 MET cc_start: 0.1996 (OUTLIER) cc_final: 0.1311 (mtp) REVERT: Z 155 ASP cc_start: 0.2635 (OUTLIER) cc_final: 0.1441 (m-30) REVERT: Z 169 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.5802 (mm-40) outliers start: 105 outliers final: 72 residues processed: 242 average time/residue: 0.3880 time to fit residues: 161.4836 Evaluate side-chains 220 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 141 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 111 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 265 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 273 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 315 optimal weight: 0.0170 chunk 209 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 233 optimal weight: 30.0000 chunk 227 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 overall best weight: 2.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 360 ASN C 321 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN X 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 31714 Z= 0.388 Angle : 0.621 9.834 43170 Z= 0.313 Chirality : 0.048 0.366 5034 Planarity : 0.005 0.061 5540 Dihedral : 5.805 59.300 4862 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.14 % Favored : 93.83 % Rotamer: Outliers : 3.62 % Allowed : 25.90 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.49 (0.13), residues: 3842 helix: 1.15 (0.20), residues: 739 sheet: -0.56 (0.24), residues: 483 loop : -1.84 (0.11), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.007 0.001 HIS C1064 PHE 0.028 0.002 PHE B1121 TYR 0.038 0.002 TYR B 265 ARG 0.012 0.001 ARG Z 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 145 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.5528 (m-40) cc_final: 0.4850 (p0) REVERT: A 153 MET cc_start: 0.2917 (mpp) cc_final: 0.2207 (tmm) REVERT: A 318 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7764 (p90) REVERT: A 338 PHE cc_start: 0.4061 (OUTLIER) cc_final: 0.3673 (t80) REVERT: A 1041 ASP cc_start: 0.6820 (t0) cc_final: 0.6599 (t0) REVERT: B 318 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8012 (p90) REVERT: B 488 CYS cc_start: 0.0851 (OUTLIER) cc_final: -0.0121 (t) REVERT: C 153 MET cc_start: 0.4608 (mmt) cc_final: 0.0698 (ttm) REVERT: C 377 PHE cc_start: 0.0004 (OUTLIER) cc_final: -0.1210 (m-80) REVERT: C 995 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7730 (ttm-80) REVERT: Y 111 ASN cc_start: 0.1750 (OUTLIER) cc_final: -0.1361 (t0) REVERT: Z 142 MET cc_start: 0.1992 (OUTLIER) cc_final: 0.1305 (mtp) REVERT: Z 155 ASP cc_start: 0.2735 (OUTLIER) cc_final: 0.1469 (m-30) outliers start: 125 outliers final: 91 residues processed: 256 average time/residue: 0.3813 time to fit residues: 167.8126 Evaluate side-chains 235 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 135 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 111 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 17 ASP Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 142 MET Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 197 VAL Chi-restraints excluded: chain Z residue 265 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 222 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 254 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 chunk 34 optimal weight: 30.0000 chunk 293 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN C 321 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31714 Z= 0.151 Angle : 0.501 9.596 43170 Z= 0.251 Chirality : 0.044 0.356 5034 Planarity : 0.004 0.058 5540 Dihedral : 5.423 58.945 4862 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 2.49 % Allowed : 26.92 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.21 (0.13), residues: 3842 helix: 1.49 (0.21), residues: 734 sheet: -0.47 (0.24), residues: 484 loop : -1.66 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS C 655 PHE 0.025 0.001 PHE C 192 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 150 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.5543 (m-40) cc_final: 0.4867 (p0) REVERT: A 153 MET cc_start: 0.2820 (mpp) cc_final: 0.2099 (tmm) REVERT: A 338 PHE cc_start: 0.4006 (OUTLIER) cc_final: 0.3573 (t80) REVERT: B 488 CYS cc_start: 0.0840 (OUTLIER) cc_final: -0.0140 (t) REVERT: C 153 MET cc_start: 0.4602 (mmt) cc_final: 0.0788 (ttm) REVERT: C 377 PHE cc_start: -0.0077 (OUTLIER) cc_final: -0.1260 (m-80) REVERT: Y 111 ASN cc_start: 0.1634 (OUTLIER) cc_final: -0.1402 (t0) REVERT: Z 155 ASP cc_start: 0.2615 (OUTLIER) cc_final: 0.1380 (m-30) REVERT: Z 169 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.5683 (mm-40) outliers start: 86 outliers final: 68 residues processed: 225 average time/residue: 0.3734 time to fit residues: 144.7219 Evaluate side-chains 213 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 139 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 111 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 17 ASP Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 6.9990 chunk 357 optimal weight: 1.9990 chunk 326 optimal weight: 0.0770 chunk 347 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 314 optimal weight: 0.0050 chunk 328 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 overall best weight: 1.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31714 Z= 0.203 Angle : 0.519 9.582 43170 Z= 0.260 Chirality : 0.044 0.356 5034 Planarity : 0.004 0.059 5540 Dihedral : 5.408 58.539 4862 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 2.72 % Allowed : 26.66 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.17 (0.13), residues: 3842 helix: 1.45 (0.20), residues: 740 sheet: -0.43 (0.24), residues: 489 loop : -1.63 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 633 HIS 0.004 0.001 HIS C 655 PHE 0.027 0.001 PHE C 192 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 140 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.5532 (m-40) cc_final: 0.4849 (p0) REVERT: A 153 MET cc_start: 0.2781 (mpp) cc_final: 0.2082 (tmm) REVERT: A 194 PHE cc_start: 0.7052 (m-10) cc_final: 0.6813 (m-10) REVERT: A 237 ARG cc_start: 0.5987 (ptt90) cc_final: 0.5677 (ptt90) REVERT: A 338 PHE cc_start: 0.4051 (OUTLIER) cc_final: 0.3639 (t80) REVERT: B 488 CYS cc_start: 0.0845 (OUTLIER) cc_final: -0.0118 (t) REVERT: C 153 MET cc_start: 0.4747 (mmt) cc_final: 0.0602 (ttm) REVERT: C 377 PHE cc_start: -0.0009 (OUTLIER) cc_final: -0.1235 (m-80) REVERT: Y 111 ASN cc_start: 0.1624 (OUTLIER) cc_final: -0.1408 (t0) REVERT: Z 155 ASP cc_start: 0.2604 (OUTLIER) cc_final: 0.1387 (m-30) REVERT: Z 169 GLN cc_start: 0.6527 (OUTLIER) cc_final: 0.5656 (mm-40) outliers start: 94 outliers final: 79 residues processed: 225 average time/residue: 0.3703 time to fit residues: 144.8772 Evaluate side-chains 221 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 136 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 186 ASP Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 111 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 17 ASP Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 3.9990 chunk 367 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 174 optimal weight: 0.0970 chunk 255 optimal weight: 6.9990 chunk 385 optimal weight: 0.6980 chunk 354 optimal weight: 0.0070 chunk 307 optimal weight: 0.3980 chunk 31 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 188 optimal weight: 0.0570 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 321 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 31714 Z= 0.132 Angle : 0.486 9.509 43170 Z= 0.244 Chirality : 0.043 0.354 5034 Planarity : 0.004 0.057 5540 Dihedral : 5.175 57.312 4862 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 1.97 % Allowed : 27.35 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.02 (0.14), residues: 3842 helix: 1.64 (0.21), residues: 737 sheet: -0.33 (0.23), residues: 500 loop : -1.55 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.004 0.000 HIS C 655 PHE 0.033 0.001 PHE C 192 TYR 0.017 0.001 TYR B1067 ARG 0.004 0.000 ARG A 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 151 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2792 (mpp) cc_final: 0.2046 (tmm) REVERT: A 338 PHE cc_start: 0.3984 (OUTLIER) cc_final: 0.3539 (t80) REVERT: B 127 VAL cc_start: 0.7286 (OUTLIER) cc_final: 0.7084 (m) REVERT: B 488 CYS cc_start: 0.0840 (OUTLIER) cc_final: -0.0137 (t) REVERT: C 153 MET cc_start: 0.4711 (mmt) cc_final: 0.0902 (ttm) REVERT: C 377 PHE cc_start: -0.0128 (OUTLIER) cc_final: -0.1299 (m-80) REVERT: Y 111 ASN cc_start: 0.1526 (OUTLIER) cc_final: -0.1445 (t0) REVERT: Z 30 LYS cc_start: 0.0924 (mmtp) cc_final: -0.1048 (ptpp) REVERT: Z 155 ASP cc_start: 0.2588 (OUTLIER) cc_final: 0.1393 (m-30) REVERT: Z 169 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.5631 (mm-40) outliers start: 68 outliers final: 52 residues processed: 212 average time/residue: 0.4164 time to fit residues: 153.2240 Evaluate side-chains 198 residues out of total 3455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 139 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 111 ASN Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Z residue 66 VAL Chi-restraints excluded: chain Z residue 155 ASP Chi-restraints excluded: chain Z residue 169 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 30.0000 chunk 327 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 128 optimal weight: 0.0770 chunk 315 optimal weight: 8.9990 chunk 38 optimal weight: 0.0020 chunk 56 optimal weight: 0.8980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 66 HIS C 321 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.252028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.206142 restraints weight = 37126.883| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.47 r_work: 0.4075 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31714 Z= 0.138 Angle : 0.485 9.523 43170 Z= 0.242 Chirality : 0.043 0.354 5034 Planarity : 0.004 0.064 5540 Dihedral : 5.099 56.944 4862 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 2.00 % Allowed : 27.29 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.94 (0.14), residues: 3842 helix: 1.74 (0.21), residues: 737 sheet: -0.25 (0.23), residues: 501 loop : -1.51 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 104 HIS 0.009 0.001 HIS B 66 PHE 0.032 0.001 PHE C 192 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5841.37 seconds wall clock time: 107 minutes 18.39 seconds (6438.39 seconds total)