Starting phenix.real_space_refine on Fri Sep 19 11:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elm_48155/09_2025/9elm_48155.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elm_48155/09_2025/9elm_48155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9elm_48155/09_2025/9elm_48155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elm_48155/09_2025/9elm_48155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9elm_48155/09_2025/9elm_48155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elm_48155/09_2025/9elm_48155.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 108 5.16 5 C 16137 2.51 5 N 4098 2.21 5 O 4932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25275 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8165 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 54, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8165 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 54, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8165 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 54, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "G" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 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: "C" 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 Time building chain proxies: 6.62, per 1000 atoms: 0.26 Number of scatterers: 25275 At special positions: 0 Unit cell: (138.574, 139.292, 188.116, 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 108 16.00 O 4932 8.00 N 4098 7.00 C 16137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.63 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.04 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=2.63 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.63 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 354 " " NAG A1306 " - " ASN A 343 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 354 " " NAG B1306 " - " ASN B 343 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 354 " " NAG C1306 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 282 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 801 " NAG-THR " NAG A1307 " - " THR A 236 " " NAG B1307 " - " THR B 236 " " NAG C1307 " - " THR C 236 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 42 sheets defined 27.2% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.522A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.048A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.884A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.546A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 626 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: 3.579A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.849A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.920A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.330A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1149 removed outlier: 3.577A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.522A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.048A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.884A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.546A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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 758 through 783 removed outlier: 3.579A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.849A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.920A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.330A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1149 removed outlier: 3.577A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.522A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.048A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.884A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.546A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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 758 through 783 removed outlier: 3.579A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.849A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.920A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.330A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1149 removed outlier: 3.577A pdb=" N LYS C1149 " --> pdb=" O LEU C1145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.813A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.185A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.754A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.918A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.587A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.324A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.925A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.853A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.596A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.393A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.501A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.501A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.520A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.813A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.185A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.918A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.587A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.925A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.852A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.596A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.501A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.664A 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: 6.501A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.520A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.813A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.755A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.918A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.587A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.925A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.853A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.596A 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: 6.501A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.501A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.520A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1072 hydrogen bonds defined for protein. 3027 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: 6.86 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 2852 1.24 - 1.38: 7165 1.38 - 1.53: 13365 1.53 - 1.68: 2337 1.68 - 1.83: 138 Bond restraints: 25857 Sorted by residual: bond pdb=" CG PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.503 1.213 0.290 3.40e-02 8.65e+02 7.28e+01 bond pdb=" CG PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 1.503 1.213 0.290 3.40e-02 8.65e+02 7.28e+01 bond pdb=" CG PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.503 1.213 0.290 3.40e-02 8.65e+02 7.27e+01 bond pdb=" CB PRO C 589 " pdb=" CG PRO C 589 " ideal model delta sigma weight residual 1.492 1.089 0.403 5.00e-02 4.00e+02 6.50e+01 bond pdb=" CB PRO A 589 " pdb=" CG PRO A 589 " ideal model delta sigma weight residual 1.492 1.089 0.403 5.00e-02 4.00e+02 6.50e+01 ... (remaining 25852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 35163 14.76 - 29.53: 3 29.53 - 44.29: 3 44.29 - 59.06: 0 59.06 - 73.82: 3 Bond angle restraints: 35172 Sorted by residual: angle pdb=" CB PRO C 589 " pdb=" CG PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 106.10 179.92 -73.82 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CB PRO B 589 " pdb=" CG PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 106.10 179.92 -73.82 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CB PRO A 589 " pdb=" CG PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 106.10 179.92 -73.82 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 589 " pdb=" CD PRO B 589 " pdb=" CG PRO B 589 " ideal model delta sigma weight residual 103.20 75.58 27.62 1.50e+00 4.44e-01 3.39e+02 angle pdb=" N PRO C 589 " pdb=" CD PRO C 589 " pdb=" CG PRO C 589 " ideal model delta sigma weight residual 103.20 75.58 27.62 1.50e+00 4.44e-01 3.39e+02 ... (remaining 35167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 15201 21.18 - 42.36: 633 42.36 - 63.55: 183 63.55 - 84.73: 74 84.73 - 105.91: 40 Dihedral angle restraints: 16131 sinusoidal: 7041 harmonic: 9090 Sorted by residual: dihedral pdb=" N PRO C 589 " pdb=" CG PRO C 589 " pdb=" CD PRO C 589 " pdb=" CB PRO C 589 " ideal model delta sinusoidal sigma weight residual 30.00 124.45 -94.45 1 1.50e+01 4.44e-03 4.60e+01 dihedral pdb=" N PRO B 589 " pdb=" CG PRO B 589 " pdb=" CD PRO B 589 " pdb=" CB PRO B 589 " ideal model delta sinusoidal sigma weight residual 30.00 122.76 -92.76 1 1.50e+01 4.44e-03 4.47e+01 dihedral pdb=" N PRO A 589 " pdb=" CG PRO A 589 " pdb=" CD PRO A 589 " pdb=" CB PRO A 589 " ideal model delta sinusoidal sigma weight residual 30.00 105.50 -75.50 1 1.50e+01 4.44e-03 3.20e+01 ... (remaining 16128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3659 0.101 - 0.202: 441 0.202 - 0.303: 37 0.303 - 0.404: 6 0.404 - 0.505: 3 Chirality restraints: 4146 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 4143 not shown) Planarity restraints: 4485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 133 " -0.026 2.00e-02 2.50e+03 3.56e-02 2.22e+01 pdb=" CG PHE A 133 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 133 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 133 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 133 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 133 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 133 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 133 " -0.026 2.00e-02 2.50e+03 3.56e-02 2.22e+01 pdb=" CG PHE B 133 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 133 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE B 133 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 133 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 133 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 133 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 133 " -0.026 2.00e-02 2.50e+03 3.56e-02 2.22e+01 pdb=" CG PHE C 133 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE C 133 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 133 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 133 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 133 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 133 " 0.001 2.00e-02 2.50e+03 ... (remaining 4482 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2308 2.74 - 3.28: 24585 3.28 - 3.82: 40695 3.82 - 4.36: 50975 4.36 - 4.90: 86798 Nonbonded interactions: 205361 Sorted by model distance: nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.205 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.205 3.120 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.205 3.120 nonbonded pdb=" O ILE A 231 " pdb=" NH2 ARG B 357 " model vdw 2.299 3.120 nonbonded pdb=" NH2 ARG A 357 " pdb=" O ILE C 231 " model vdw 2.299 3.120 ... (remaining 205356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 9.130 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: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.220 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.011 0.600 25950 Z= 0.479 Angle : 1.444 73.821 35412 Z= 0.727 Chirality : 0.067 0.505 4146 Planarity : 0.008 0.129 4452 Dihedral : 14.718 105.911 10167 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.14), residues: 3069 helix: 0.84 (0.17), residues: 741 sheet: 1.46 (0.20), residues: 609 loop : -0.19 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG A 498 TYR 0.031 0.004 TYR C 451 PHE 0.081 0.004 PHE A 133 TRP 0.042 0.005 TRP B 886 HIS 0.010 0.003 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00919 (25857) covalent geometry : angle 1.40621 (35172) SS BOND : bond 0.17317 ( 36) SS BOND : angle 4.71495 ( 72) hydrogen bonds : bond 0.12236 ( 1036) hydrogen bonds : angle 7.35962 ( 3027) link_BETA1-4 : bond 0.01322 ( 21) link_BETA1-4 : angle 4.90439 ( 63) link_NAG-ASN : bond 0.00539 ( 33) link_NAG-ASN : angle 3.23882 ( 99) link_NAG-THR : bond 0.00582 ( 3) link_NAG-THR : angle 5.00085 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.979 Fit side-chains REVERT: A 47 VAL cc_start: 0.8302 (m) cc_final: 0.8001 (p) REVERT: A 309 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 868 GLU cc_start: 0.8216 (tt0) cc_final: 0.7920 (mp0) REVERT: B 269 TYR cc_start: 0.7667 (m-10) cc_final: 0.7145 (m-10) REVERT: B 868 GLU cc_start: 0.8198 (tt0) cc_final: 0.7933 (mp0) REVERT: C 309 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7579 (mm-30) REVERT: C 868 GLU cc_start: 0.8187 (tt0) cc_final: 0.7841 (mp0) outliers start: 0 outliers final: 1 residues processed: 257 average time/residue: 0.5571 time to fit residues: 170.9038 Evaluate side-chains 212 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1005 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A 677 GLN A 762 GLN A 955 ASN B 339 HIS B 762 GLN B 955 ASN B1002 GLN C 49 HIS C 339 HIS C 955 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.203832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.136603 restraints weight = 27997.869| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.67 r_work: 0.3331 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25950 Z= 0.145 Angle : 0.690 13.457 35412 Z= 0.347 Chirality : 0.047 0.292 4146 Planarity : 0.004 0.064 4452 Dihedral : 8.031 62.405 4521 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.71 % Allowed : 8.52 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.14), residues: 3069 helix: 2.12 (0.18), residues: 732 sheet: 0.94 (0.19), residues: 645 loop : -0.30 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.021 0.002 TYR B1067 PHE 0.019 0.002 PHE C 43 TRP 0.014 0.002 TRP B 452 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00322 (25857) covalent geometry : angle 0.65044 (35172) SS BOND : bond 0.00241 ( 36) SS BOND : angle 0.94919 ( 72) hydrogen bonds : bond 0.05159 ( 1036) hydrogen bonds : angle 6.05838 ( 3027) link_BETA1-4 : bond 0.01005 ( 21) link_BETA1-4 : angle 3.75878 ( 63) link_NAG-ASN : bond 0.00759 ( 33) link_NAG-ASN : angle 3.17963 ( 99) link_NAG-THR : bond 0.00757 ( 3) link_NAG-THR : angle 2.34063 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.988 Fit side-chains REVERT: A 189 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6295 (mt) REVERT: A 269 TYR cc_start: 0.7969 (m-10) cc_final: 0.7734 (m-10) REVERT: A 309 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 571 ASP cc_start: 0.8107 (t70) cc_final: 0.7389 (t0) REVERT: A 690 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: A 868 GLU cc_start: 0.8272 (tt0) cc_final: 0.7933 (mp0) REVERT: B 189 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6278 (mt) REVERT: B 269 TYR cc_start: 0.7976 (m-10) cc_final: 0.7576 (m-80) REVERT: B 314 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: B 571 ASP cc_start: 0.8137 (t70) cc_final: 0.7432 (t0) REVERT: B 868 GLU cc_start: 0.8248 (tt0) cc_final: 0.7983 (mp0) REVERT: B 888 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.6780 (t80) REVERT: C 189 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6294 (mt) REVERT: C 231 ILE cc_start: 0.8134 (mt) cc_final: 0.7921 (mp) REVERT: C 309 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7549 (mm-30) REVERT: C 314 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: C 360 ASN cc_start: 0.7701 (t0) cc_final: 0.7493 (t0) REVERT: C 558 LYS cc_start: 0.7180 (mmpt) cc_final: 0.6942 (mmpt) REVERT: C 740 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8844 (tpp) REVERT: C 868 GLU cc_start: 0.8281 (tt0) cc_final: 0.7891 (mp0) REVERT: C 1005 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8323 (mm-40) outliers start: 47 outliers final: 16 residues processed: 274 average time/residue: 0.4192 time to fit residues: 142.6154 Evaluate side-chains 235 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 613 GLN A 762 GLN A 804 GLN A 935 GLN B 613 GLN B 677 GLN C 30 ASN C 613 GLN C 677 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.196435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127396 restraints weight = 27760.706| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.56 r_work: 0.3196 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 25950 Z= 0.274 Angle : 0.751 11.317 35412 Z= 0.377 Chirality : 0.052 0.277 4146 Planarity : 0.005 0.056 4452 Dihedral : 6.448 41.591 4518 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.13 % Allowed : 9.02 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.14), residues: 3069 helix: 1.91 (0.19), residues: 693 sheet: 0.79 (0.18), residues: 717 loop : -0.66 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 815 TYR 0.025 0.002 TYR B1067 PHE 0.024 0.003 PHE A 65 TRP 0.011 0.002 TRP A 452 HIS 0.010 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00665 (25857) covalent geometry : angle 0.70379 (35172) SS BOND : bond 0.00422 ( 36) SS BOND : angle 1.05052 ( 72) hydrogen bonds : bond 0.06013 ( 1036) hydrogen bonds : angle 6.10225 ( 3027) link_BETA1-4 : bond 0.01022 ( 21) link_BETA1-4 : angle 3.62624 ( 63) link_NAG-ASN : bond 0.00702 ( 33) link_NAG-ASN : angle 3.98825 ( 99) link_NAG-THR : bond 0.00729 ( 3) link_NAG-THR : angle 3.08018 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 225 time to evaluate : 0.984 Fit side-chains REVERT: A 30 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8144 (p0) REVERT: A 52 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8344 (tp40) REVERT: A 309 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 319 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7521 (ttp-170) REVERT: A 603 ASN cc_start: 0.8126 (m-40) cc_final: 0.7684 (t0) REVERT: A 675 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6557 (mp10) REVERT: A 690 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: A 868 GLU cc_start: 0.8437 (tt0) cc_final: 0.8064 (mp0) REVERT: B 52 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: B 54 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8632 (mp) REVERT: B 269 TYR cc_start: 0.8166 (m-10) cc_final: 0.7828 (m-10) REVERT: B 319 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7414 (ttp-170) REVERT: B 603 ASN cc_start: 0.8134 (m-40) cc_final: 0.7604 (t0) REVERT: B 675 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.6594 (mp10) REVERT: B 690 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: B 868 GLU cc_start: 0.8436 (tt0) cc_final: 0.8092 (mp0) REVERT: C 30 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8237 (p0) REVERT: C 52 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8311 (tp40) REVERT: C 603 ASN cc_start: 0.8027 (m-40) cc_final: 0.7564 (t0) REVERT: C 675 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: C 808 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: C 868 GLU cc_start: 0.8440 (tt0) cc_final: 0.8029 (mp0) outliers start: 86 outliers final: 27 residues processed: 278 average time/residue: 0.5108 time to fit residues: 171.4147 Evaluate side-chains 253 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 293 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN B 30 ASN B 613 GLN C 30 ASN C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.197029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126897 restraints weight = 27696.750| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.67 r_work: 0.3212 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25950 Z= 0.189 Angle : 0.651 10.977 35412 Z= 0.325 Chirality : 0.047 0.262 4146 Planarity : 0.004 0.045 4452 Dihedral : 5.961 42.762 4518 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.57 % Allowed : 9.46 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.14), residues: 3069 helix: 1.95 (0.19), residues: 696 sheet: 0.72 (0.18), residues: 723 loop : -0.75 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.021 0.002 TYR B1067 PHE 0.021 0.002 PHE A 65 TRP 0.013 0.002 TRP B 886 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00446 (25857) covalent geometry : angle 0.60549 (35172) SS BOND : bond 0.00290 ( 36) SS BOND : angle 0.80538 ( 72) hydrogen bonds : bond 0.05185 ( 1036) hydrogen bonds : angle 5.91591 ( 3027) link_BETA1-4 : bond 0.00983 ( 21) link_BETA1-4 : angle 3.30952 ( 63) link_NAG-ASN : bond 0.00628 ( 33) link_NAG-ASN : angle 3.66993 ( 99) link_NAG-THR : bond 0.00686 ( 3) link_NAG-THR : angle 2.70607 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 218 time to evaluate : 1.035 Fit side-chains REVERT: A 52 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8363 (tp40) REVERT: A 202 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7682 (mmtm) REVERT: A 309 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 514 SER cc_start: 0.7152 (OUTLIER) cc_final: 0.6762 (p) REVERT: A 571 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7874 (t70) REVERT: A 603 ASN cc_start: 0.8118 (m-40) cc_final: 0.7717 (t0) REVERT: A 675 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.6533 (mp10) REVERT: A 690 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: A 868 GLU cc_start: 0.8393 (tt0) cc_final: 0.8018 (mp0) REVERT: B 30 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8214 (p0) REVERT: B 52 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8360 (tp40) REVERT: B 54 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8610 (mp) REVERT: B 191 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 603 ASN cc_start: 0.8147 (m-40) cc_final: 0.7621 (t0) REVERT: B 675 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.6531 (mp10) REVERT: B 690 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: B 868 GLU cc_start: 0.8391 (tt0) cc_final: 0.8066 (mp0) REVERT: C 52 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8324 (tp40) REVERT: C 202 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7285 (mmtm) REVERT: C 603 ASN cc_start: 0.8033 (m-40) cc_final: 0.7633 (t0) REVERT: C 646 ARG cc_start: 0.8167 (mmp-170) cc_final: 0.7945 (mmp-170) REVERT: C 675 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: C 731 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8581 (mtp) REVERT: C 808 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: C 868 GLU cc_start: 0.8443 (tt0) cc_final: 0.8005 (mp0) outliers start: 98 outliers final: 39 residues processed: 283 average time/residue: 0.4958 time to fit residues: 170.7538 Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 147 optimal weight: 0.0270 chunk 208 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 314 GLN A 762 GLN B 30 ASN B 218 GLN B1119 ASN C 30 ASN C 218 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.198474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129942 restraints weight = 27608.050| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.52 r_work: 0.3249 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25950 Z= 0.128 Angle : 0.601 12.419 35412 Z= 0.298 Chirality : 0.045 0.268 4146 Planarity : 0.004 0.041 4452 Dihedral : 5.827 61.217 4518 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.87 % Allowed : 10.41 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3069 helix: 2.19 (0.19), residues: 693 sheet: 0.77 (0.18), residues: 711 loop : -0.72 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.020 0.001 TYR C1067 PHE 0.020 0.001 PHE C 65 TRP 0.011 0.001 TRP A 886 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00286 (25857) covalent geometry : angle 0.55828 (35172) SS BOND : bond 0.00198 ( 36) SS BOND : angle 0.74748 ( 72) hydrogen bonds : bond 0.04538 ( 1036) hydrogen bonds : angle 5.70976 ( 3027) link_BETA1-4 : bond 0.00937 ( 21) link_BETA1-4 : angle 3.09615 ( 63) link_NAG-ASN : bond 0.00645 ( 33) link_NAG-ASN : angle 3.39549 ( 99) link_NAG-THR : bond 0.00615 ( 3) link_NAG-THR : angle 2.50910 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 213 time to evaluate : 1.007 Fit side-chains REVERT: A 52 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8272 (tp40) REVERT: A 191 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 202 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7618 (mmtm) REVERT: A 309 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 514 SER cc_start: 0.7219 (OUTLIER) cc_final: 0.6860 (p) REVERT: A 547 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7211 (p) REVERT: A 603 ASN cc_start: 0.8098 (m-40) cc_final: 0.7741 (t0) REVERT: A 675 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.6506 (mp10) REVERT: A 690 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: A 868 GLU cc_start: 0.8415 (tt0) cc_final: 0.8037 (mp0) REVERT: B 30 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8294 (p0) REVERT: B 47 VAL cc_start: 0.8404 (p) cc_final: 0.8103 (m) REVERT: B 52 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8362 (tp40) REVERT: B 54 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8666 (mp) REVERT: B 191 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 269 TYR cc_start: 0.8165 (m-10) cc_final: 0.7911 (m-10) REVERT: B 577 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7336 (ttm170) REVERT: B 603 ASN cc_start: 0.8148 (m-40) cc_final: 0.7656 (t0) REVERT: B 675 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.6558 (mp10) REVERT: B 690 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: B 868 GLU cc_start: 0.8401 (tt0) cc_final: 0.8039 (mp0) REVERT: C 30 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8204 (p0) REVERT: C 52 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8373 (tp40) REVERT: C 191 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7979 (mt-10) REVERT: C 202 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7262 (mmtm) REVERT: C 514 SER cc_start: 0.7150 (OUTLIER) cc_final: 0.6805 (p) REVERT: C 603 ASN cc_start: 0.8016 (m-40) cc_final: 0.7640 (t0) REVERT: C 646 ARG cc_start: 0.8161 (mmp-170) cc_final: 0.7878 (mmp-170) REVERT: C 675 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: C 808 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: C 868 GLU cc_start: 0.8447 (tt0) cc_final: 0.8019 (mp0) outliers start: 79 outliers final: 35 residues processed: 262 average time/residue: 0.4797 time to fit residues: 153.3305 Evaluate side-chains 258 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 150 optimal weight: 0.1980 chunk 152 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 40 optimal weight: 0.0030 chunk 257 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 762 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 30 ASN C 30 ASN C 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.199188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130964 restraints weight = 27867.075| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.42 r_work: 0.3267 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25950 Z= 0.115 Angle : 0.575 11.652 35412 Z= 0.285 Chirality : 0.044 0.261 4146 Planarity : 0.004 0.036 4452 Dihedral : 5.510 51.518 4518 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.72 % Rotamer: Outliers : 2.62 % Allowed : 10.74 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.15), residues: 3069 helix: 2.24 (0.19), residues: 714 sheet: 0.75 (0.18), residues: 723 loop : -0.73 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.001 PHE C 562 TRP 0.011 0.001 TRP A 886 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00255 (25857) covalent geometry : angle 0.53367 (35172) SS BOND : bond 0.00177 ( 36) SS BOND : angle 0.72760 ( 72) hydrogen bonds : bond 0.04288 ( 1036) hydrogen bonds : angle 5.58116 ( 3027) link_BETA1-4 : bond 0.00918 ( 21) link_BETA1-4 : angle 2.95008 ( 63) link_NAG-ASN : bond 0.00593 ( 33) link_NAG-ASN : angle 3.31547 ( 99) link_NAG-THR : bond 0.00624 ( 3) link_NAG-THR : angle 2.36789 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 1.046 Fit side-chains REVERT: A 52 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8212 (tp40) REVERT: A 191 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 202 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7494 (mmtm) REVERT: A 269 TYR cc_start: 0.8034 (m-10) cc_final: 0.7753 (m-10) REVERT: A 309 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 514 SER cc_start: 0.7096 (OUTLIER) cc_final: 0.6737 (p) REVERT: A 547 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7142 (p) REVERT: A 603 ASN cc_start: 0.8063 (m-40) cc_final: 0.7672 (t0) REVERT: A 675 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.6434 (mp10) REVERT: A 690 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: A 868 GLU cc_start: 0.8306 (tt0) cc_final: 0.7861 (mp0) REVERT: B 47 VAL cc_start: 0.8282 (p) cc_final: 0.7980 (m) REVERT: B 52 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8280 (tp40) REVERT: B 54 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8570 (mp) REVERT: B 191 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 269 TYR cc_start: 0.8085 (m-10) cc_final: 0.7852 (m-10) REVERT: B 603 ASN cc_start: 0.8100 (m-40) cc_final: 0.7583 (t0) REVERT: B 675 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6523 (mp10) REVERT: B 690 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7376 (mt0) REVERT: B 740 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.7997 (ttp) REVERT: B 811 LYS cc_start: 0.6243 (mtmt) cc_final: 0.5937 (ptpt) REVERT: B 868 GLU cc_start: 0.8316 (tt0) cc_final: 0.7906 (mp0) REVERT: C 52 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8323 (tp40) REVERT: C 191 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7875 (mt-10) REVERT: C 514 SER cc_start: 0.6994 (OUTLIER) cc_final: 0.6683 (p) REVERT: C 549 THR cc_start: 0.8372 (m) cc_final: 0.8143 (t) REVERT: C 603 ASN cc_start: 0.8029 (m-40) cc_final: 0.7455 (t0) REVERT: C 646 ARG cc_start: 0.8057 (mmp-170) cc_final: 0.7851 (mmp-170) REVERT: C 675 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: C 808 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: C 868 GLU cc_start: 0.8364 (tt0) cc_final: 0.7845 (mp0) outliers start: 72 outliers final: 34 residues processed: 262 average time/residue: 0.5161 time to fit residues: 164.1919 Evaluate side-chains 264 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 195 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 762 GLN A 935 GLN C 30 ASN C 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.198473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126130 restraints weight = 27804.974| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.48 r_work: 0.3281 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25950 Z= 0.141 Angle : 0.582 11.004 35412 Z= 0.291 Chirality : 0.045 0.264 4146 Planarity : 0.004 0.038 4452 Dihedral : 5.235 42.953 4518 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.52 % Rotamer: Outliers : 2.91 % Allowed : 10.81 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3069 helix: 2.26 (0.19), residues: 711 sheet: 0.71 (0.18), residues: 741 loop : -0.77 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.021 0.001 TYR B1067 PHE 0.022 0.001 PHE C 562 TRP 0.016 0.001 TRP A 886 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00326 (25857) covalent geometry : angle 0.54252 (35172) SS BOND : bond 0.00218 ( 36) SS BOND : angle 0.70881 ( 72) hydrogen bonds : bond 0.04531 ( 1036) hydrogen bonds : angle 5.54873 ( 3027) link_BETA1-4 : bond 0.00906 ( 21) link_BETA1-4 : angle 2.83352 ( 63) link_NAG-ASN : bond 0.00599 ( 33) link_NAG-ASN : angle 3.31964 ( 99) link_NAG-THR : bond 0.00589 ( 3) link_NAG-THR : angle 2.22655 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 219 time to evaluate : 0.947 Fit side-chains REVERT: A 52 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8179 (tp40) REVERT: A 191 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 202 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7456 (mmtm) REVERT: A 269 TYR cc_start: 0.7981 (m-10) cc_final: 0.7689 (m-10) REVERT: A 309 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 396 TYR cc_start: 0.6607 (m-10) cc_final: 0.6360 (m-80) REVERT: A 514 SER cc_start: 0.7055 (OUTLIER) cc_final: 0.6687 (p) REVERT: A 603 ASN cc_start: 0.8038 (m-40) cc_final: 0.7650 (t0) REVERT: A 675 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6419 (mp10) REVERT: A 690 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: A 868 GLU cc_start: 0.8311 (tt0) cc_final: 0.7816 (mp0) REVERT: B 47 VAL cc_start: 0.8251 (p) cc_final: 0.7933 (m) REVERT: B 52 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8258 (tp40) REVERT: B 54 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 191 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 269 TYR cc_start: 0.8021 (m-10) cc_final: 0.7790 (m-10) REVERT: B 360 ASN cc_start: 0.7793 (t0) cc_final: 0.7449 (t0) REVERT: B 571 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (t70) REVERT: B 603 ASN cc_start: 0.8105 (m-40) cc_final: 0.7614 (t0) REVERT: B 675 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6449 (mp10) REVERT: B 690 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: B 868 GLU cc_start: 0.8319 (tt0) cc_final: 0.7863 (mp0) REVERT: C 52 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8278 (tp40) REVERT: C 191 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 202 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7066 (mmtm) REVERT: C 514 SER cc_start: 0.6986 (OUTLIER) cc_final: 0.6722 (p) REVERT: C 558 LYS cc_start: 0.7480 (mmpt) cc_final: 0.7232 (mmpt) REVERT: C 603 ASN cc_start: 0.8019 (m-40) cc_final: 0.7468 (t0) REVERT: C 675 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6548 (mp10) REVERT: C 808 ASP cc_start: 0.7960 (m-30) cc_final: 0.7672 (m-30) REVERT: C 868 GLU cc_start: 0.8361 (tt0) cc_final: 0.7798 (mp0) REVERT: C 1005 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8269 (mm-40) outliers start: 80 outliers final: 39 residues processed: 268 average time/residue: 0.5213 time to fit residues: 169.2739 Evaluate side-chains 263 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 284 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 199 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 762 GLN A 935 GLN B 30 ASN B 388 ASN C 30 ASN C 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.197209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125074 restraints weight = 27667.011| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.33 r_work: 0.3282 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25950 Z= 0.183 Angle : 0.620 11.092 35412 Z= 0.311 Chirality : 0.046 0.263 4146 Planarity : 0.004 0.038 4452 Dihedral : 5.426 45.102 4518 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 2.80 % Allowed : 10.84 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3069 helix: 2.21 (0.19), residues: 693 sheet: 0.69 (0.19), residues: 714 loop : -0.87 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.021 0.002 TYR C1067 PHE 0.020 0.002 PHE B 898 TRP 0.020 0.002 TRP A 886 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00434 (25857) covalent geometry : angle 0.58315 (35172) SS BOND : bond 0.00267 ( 36) SS BOND : angle 0.75075 ( 72) hydrogen bonds : bond 0.04939 ( 1036) hydrogen bonds : angle 5.66593 ( 3027) link_BETA1-4 : bond 0.00888 ( 21) link_BETA1-4 : angle 2.81031 ( 63) link_NAG-ASN : bond 0.00604 ( 33) link_NAG-ASN : angle 3.33520 ( 99) link_NAG-THR : bond 0.00602 ( 3) link_NAG-THR : angle 2.21494 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 223 time to evaluate : 1.074 Fit side-chains REVERT: A 52 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8174 (tp40) REVERT: A 191 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7859 (mt-10) REVERT: A 202 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7425 (mmtm) REVERT: A 269 TYR cc_start: 0.7977 (m-10) cc_final: 0.7714 (m-10) REVERT: A 309 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 319 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7463 (ttp-170) REVERT: A 396 TYR cc_start: 0.6595 (m-10) cc_final: 0.6302 (m-80) REVERT: A 514 SER cc_start: 0.7071 (OUTLIER) cc_final: 0.6735 (p) REVERT: A 603 ASN cc_start: 0.8043 (m-40) cc_final: 0.7669 (t0) REVERT: A 675 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6386 (mp10) REVERT: A 690 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: A 868 GLU cc_start: 0.8294 (tt0) cc_final: 0.7812 (mp0) REVERT: B 47 VAL cc_start: 0.8278 (p) cc_final: 0.7964 (m) REVERT: B 52 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8245 (tp40) REVERT: B 54 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8510 (mp) REVERT: B 191 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 269 TYR cc_start: 0.8013 (m-10) cc_final: 0.7769 (m-10) REVERT: B 319 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7300 (ttp-170) REVERT: B 360 ASN cc_start: 0.7775 (t0) cc_final: 0.7423 (t0) REVERT: B 396 TYR cc_start: 0.6525 (m-10) cc_final: 0.6297 (m-80) REVERT: B 571 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8077 (t70) REVERT: B 603 ASN cc_start: 0.8091 (m-40) cc_final: 0.7636 (t0) REVERT: B 675 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.6392 (mp10) REVERT: B 690 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7316 (mt0) REVERT: B 811 LYS cc_start: 0.6265 (mtmt) cc_final: 0.5916 (ptpt) REVERT: B 868 GLU cc_start: 0.8291 (tt0) cc_final: 0.7853 (mp0) REVERT: C 52 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8272 (tp40) REVERT: C 202 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7158 (mmtm) REVERT: C 396 TYR cc_start: 0.6601 (m-10) cc_final: 0.6208 (m-10) REVERT: C 514 SER cc_start: 0.6999 (OUTLIER) cc_final: 0.6742 (p) REVERT: C 603 ASN cc_start: 0.8014 (m-40) cc_final: 0.7666 (t0) REVERT: C 646 ARG cc_start: 0.8072 (mmp-170) cc_final: 0.7847 (mmp-170) REVERT: C 675 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6503 (mp10) REVERT: C 808 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: C 868 GLU cc_start: 0.8334 (tt0) cc_final: 0.7801 (mp0) outliers start: 77 outliers final: 40 residues processed: 269 average time/residue: 0.5068 time to fit residues: 164.8985 Evaluate side-chains 270 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 160 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 762 GLN A 935 GLN C 30 ASN C 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.198248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126271 restraints weight = 27784.497| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.08 r_work: 0.3315 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25950 Z= 0.140 Angle : 0.581 11.128 35412 Z= 0.291 Chirality : 0.045 0.261 4146 Planarity : 0.004 0.038 4452 Dihedral : 5.212 43.096 4518 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 2.33 % Allowed : 11.54 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3069 helix: 2.28 (0.19), residues: 711 sheet: 0.64 (0.19), residues: 714 loop : -0.85 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.020 0.001 TYR A1067 PHE 0.020 0.001 PHE A 65 TRP 0.013 0.001 TRP A 886 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00324 (25857) covalent geometry : angle 0.54550 (35172) SS BOND : bond 0.00210 ( 36) SS BOND : angle 0.74809 ( 72) hydrogen bonds : bond 0.04477 ( 1036) hydrogen bonds : angle 5.52426 ( 3027) link_BETA1-4 : bond 0.00880 ( 21) link_BETA1-4 : angle 2.71274 ( 63) link_NAG-ASN : bond 0.00584 ( 33) link_NAG-ASN : angle 3.13958 ( 99) link_NAG-THR : bond 0.00696 ( 3) link_NAG-THR : angle 2.10775 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 0.802 Fit side-chains REVERT: A 52 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8221 (tp40) REVERT: A 191 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 269 TYR cc_start: 0.7978 (m-10) cc_final: 0.7695 (m-10) REVERT: A 309 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 396 TYR cc_start: 0.6670 (m-10) cc_final: 0.6425 (m-80) REVERT: A 514 SER cc_start: 0.7213 (OUTLIER) cc_final: 0.6874 (p) REVERT: A 603 ASN cc_start: 0.8031 (m-40) cc_final: 0.7682 (t0) REVERT: A 675 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6471 (mp10) REVERT: A 690 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: A 868 GLU cc_start: 0.8318 (tt0) cc_final: 0.7906 (mp0) REVERT: B 47 VAL cc_start: 0.8282 (p) cc_final: 0.7959 (m) REVERT: B 52 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8261 (tp40) REVERT: B 54 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 269 TYR cc_start: 0.8032 (m-10) cc_final: 0.7810 (m-10) REVERT: B 319 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7371 (ttp-170) REVERT: B 360 ASN cc_start: 0.7779 (t0) cc_final: 0.7381 (t0) REVERT: B 396 TYR cc_start: 0.6564 (m-10) cc_final: 0.6334 (m-10) REVERT: B 603 ASN cc_start: 0.8092 (m-40) cc_final: 0.7679 (t0) REVERT: B 675 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6463 (mp10) REVERT: B 690 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: B 811 LYS cc_start: 0.6285 (mtmt) cc_final: 0.5991 (ptpt) REVERT: B 868 GLU cc_start: 0.8308 (tt0) cc_final: 0.7938 (mp0) REVERT: C 52 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8307 (tp40) REVERT: C 191 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7740 (mt-10) REVERT: C 202 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7129 (mmtm) REVERT: C 396 TYR cc_start: 0.6627 (m-10) cc_final: 0.6284 (m-80) REVERT: C 514 SER cc_start: 0.7138 (OUTLIER) cc_final: 0.6937 (p) REVERT: C 549 THR cc_start: 0.8411 (m) cc_final: 0.8173 (t) REVERT: C 603 ASN cc_start: 0.8013 (m-40) cc_final: 0.7547 (t0) REVERT: C 675 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: C 868 GLU cc_start: 0.8319 (tt0) cc_final: 0.7887 (mp0) outliers start: 64 outliers final: 39 residues processed: 255 average time/residue: 0.4501 time to fit residues: 139.2796 Evaluate side-chains 258 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 821 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 168 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 205 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 762 GLN C 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.198780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127256 restraints weight = 27776.220| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.04 r_work: 0.3334 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25950 Z= 0.126 Angle : 0.572 11.065 35412 Z= 0.286 Chirality : 0.045 0.263 4146 Planarity : 0.004 0.045 4452 Dihedral : 5.105 42.768 4518 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 1.93 % Allowed : 11.94 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3069 helix: 2.31 (0.19), residues: 711 sheet: 0.62 (0.19), residues: 714 loop : -0.83 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 995 TYR 0.021 0.001 TYR C 170 PHE 0.021 0.001 PHE A 65 TRP 0.011 0.001 TRP B 886 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00287 (25857) covalent geometry : angle 0.53740 (35172) SS BOND : bond 0.00189 ( 36) SS BOND : angle 0.74237 ( 72) hydrogen bonds : bond 0.04321 ( 1036) hydrogen bonds : angle 5.46593 ( 3027) link_BETA1-4 : bond 0.00875 ( 21) link_BETA1-4 : angle 2.65388 ( 63) link_NAG-ASN : bond 0.00584 ( 33) link_NAG-ASN : angle 3.08007 ( 99) link_NAG-THR : bond 0.00899 ( 3) link_NAG-THR : angle 1.91645 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8202 (tp40) REVERT: A 191 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 269 TYR cc_start: 0.7933 (m-10) cc_final: 0.7650 (m-10) REVERT: A 309 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 396 TYR cc_start: 0.6613 (m-10) cc_final: 0.6352 (m-80) REVERT: A 514 SER cc_start: 0.7166 (OUTLIER) cc_final: 0.6855 (p) REVERT: A 549 THR cc_start: 0.8413 (m) cc_final: 0.8200 (t) REVERT: A 603 ASN cc_start: 0.8036 (m-40) cc_final: 0.7686 (t0) REVERT: A 675 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6471 (mp10) REVERT: A 690 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: A 868 GLU cc_start: 0.8268 (tt0) cc_final: 0.7849 (mp0) REVERT: A 995 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: B 47 VAL cc_start: 0.8242 (p) cc_final: 0.7922 (m) REVERT: B 52 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8252 (tp40) REVERT: B 54 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8570 (mp) REVERT: B 269 TYR cc_start: 0.7995 (m-10) cc_final: 0.7716 (m-10) REVERT: B 396 TYR cc_start: 0.6564 (m-10) cc_final: 0.6336 (m-80) REVERT: B 603 ASN cc_start: 0.8074 (m-40) cc_final: 0.7647 (t0) REVERT: B 675 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.6447 (mp10) REVERT: B 690 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: B 868 GLU cc_start: 0.8284 (tt0) cc_final: 0.7874 (mp0) REVERT: C 52 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8280 (tp40) REVERT: C 191 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 202 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7088 (mmtm) REVERT: C 396 TYR cc_start: 0.6606 (m-10) cc_final: 0.6299 (m-80) REVERT: C 549 THR cc_start: 0.8380 (m) cc_final: 0.8147 (t) REVERT: C 603 ASN cc_start: 0.7991 (m-40) cc_final: 0.7522 (t0) REVERT: C 675 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6636 (mp10) REVERT: C 868 GLU cc_start: 0.8285 (tt0) cc_final: 0.7824 (mp0) REVERT: C 995 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7927 (mtm-85) REVERT: C 1005 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8225 (mm-40) outliers start: 53 outliers final: 34 residues processed: 253 average time/residue: 0.5103 time to fit residues: 156.4830 Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 156 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 0.0000 chunk 35 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN C 30 ASN C 314 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.197935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126445 restraints weight = 27686.113| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.36 r_work: 0.3298 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25950 Z= 0.153 Angle : 0.590 11.096 35412 Z= 0.295 Chirality : 0.045 0.265 4146 Planarity : 0.004 0.039 4452 Dihedral : 5.192 44.028 4518 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 1.97 % Allowed : 12.12 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3069 helix: 2.28 (0.19), residues: 711 sheet: 0.62 (0.19), residues: 714 loop : -0.86 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.021 0.001 TYR A1067 PHE 0.020 0.001 PHE A 65 TRP 0.012 0.001 TRP A 886 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00359 (25857) covalent geometry : angle 0.55600 (35172) SS BOND : bond 0.00254 ( 36) SS BOND : angle 0.75894 ( 72) hydrogen bonds : bond 0.04560 ( 1036) hydrogen bonds : angle 5.50571 ( 3027) link_BETA1-4 : bond 0.00864 ( 21) link_BETA1-4 : angle 2.64396 ( 63) link_NAG-ASN : bond 0.00577 ( 33) link_NAG-ASN : angle 3.10146 ( 99) link_NAG-THR : bond 0.00761 ( 3) link_NAG-THR : angle 1.96812 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12822.75 seconds wall clock time: 218 minutes 31.31 seconds (13111.31 seconds total)