Starting phenix.real_space_refine on Mon Aug 25 15:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co8_45773/08_2025/9co8_45773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co8_45773/08_2025/9co8_45773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9co8_45773/08_2025/9co8_45773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co8_45773/08_2025/9co8_45773.map" model { file = "/net/cci-nas-00/data/ceres_data/9co8_45773/08_2025/9co8_45773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co8_45773/08_2025/9co8_45773.cif" } resolution = 2.99 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= 0.017 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 129 5.16 5 C 18472 2.51 5 N 4799 2.21 5 O 5626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29026 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8548 Classifications: {'peptide': 1090} Link IDs: {'PTRANS': 57, 'TRANS': 1032} Chain breaks: 2 Chain: "C" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8548 Classifications: {'peptide': 1090} Link IDs: {'PTRANS': 57, 'TRANS': 1032} Chain breaks: 2 Chain: "A" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8548 Classifications: {'peptide': 1090} Link IDs: {'PTRANS': 57, 'TRANS': 1032} Chain breaks: 2 Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "F" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "D" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "V" 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: "W" 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: "X" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "N" 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: "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: "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: 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: "S" 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: "T" 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: "U" 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 Time building chain proxies: 6.49, per 1000 atoms: 0.22 Number of scatterers: 29026 At special positions: 0 Unit cell: (144.309, 153.163, 234.613, 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 129 16.00 O 5626 8.00 N 4799 7.00 C 18472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.02 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.02 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.02 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 50 " - pdb=" SG CYS E 104 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 104 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG G 1 " - " ASN B 797 " " NAG H 1 " - " ASN B1094 " " NAG I 1 " - " ASN B1130 " " NAG K 1 " - " ASN C 705 " " NAG L 1 " - " ASN C 713 " " NAG M 1 " - " ASN C 797 " " NAG N 1 " - " ASN C1094 " " NAG O 1 " - " ASN C1130 " " NAG Q 1 " - " ASN A 705 " " NAG R 1 " - " ASN A 713 " " NAG S 1 " - " ASN A 797 " " NAG T 1 " - " ASN A1094 " " NAG U 1 " - " ASN A1130 " " NAG V 1 " - " ASN B 612 " " NAG W 1 " - " ASN B 705 " " NAG X 1 " - " ASN B 713 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 20.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.071A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 4.107A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 367' Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 613 through 620 removed outlier: 3.736A pdb=" N SER B 617 " --> pdb=" O CYS B 613 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.598A pdb=" N SER B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.794A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 759 " --> pdb=" O PHE B 755 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.952A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 882 through 886 removed outlier: 3.800A pdb=" N ALA B 886 " --> pdb=" O THR B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 909 through 914 Processing helix chain 'B' and resid 915 through 937 removed outlier: 4.066A pdb=" N ALA B 926 " --> pdb=" O GLN B 922 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 937 " --> pdb=" O SER B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.745A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.602A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.339A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B1029 " --> pdb=" O MET B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1146 removed outlier: 3.844A pdb=" N GLU B1146 " --> pdb=" O ASP B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.935A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.600A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.624A pdb=" N TYR C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.792A pdb=" N VAL C 616 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 750 removed outlier: 3.584A pdb=" N SER C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 removed outlier: 4.034A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 759 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 775 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.834A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 849 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 909 through 914 Processing helix chain 'C' and resid 915 through 937 removed outlier: 3.987A pdb=" N GLY C 928 " --> pdb=" O ASN C 924 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 935 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR C 937 " --> pdb=" O SER C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.623A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.689A pdb=" N LEU C 980 " --> pdb=" O ILE C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 1028 removed outlier: 4.045A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1146 removed outlier: 3.943A pdb=" N GLU C1146 " --> pdb=" O ASP C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.679A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 340 " --> pdb=" O HIS A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 340' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.860A pdb=" N GLN A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.607A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 850 removed outlier: 4.015A pdb=" N LYS A 850 " --> pdb=" O CYS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.510A pdb=" N GLY A 885 " --> pdb=" O TRP A 882 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 886 " --> pdb=" O THR A 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 882 through 886' Processing helix chain 'A' and resid 893 through 904 Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 915 through 937 removed outlier: 3.525A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 934 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.716A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 978 Processing helix chain 'A' and resid 981 through 1028 removed outlier: 4.063A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1142 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.861A pdb=" N ASP E 90 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR E 91 " --> pdb=" O LEU E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.631A pdb=" N ASP F 90 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 91 " --> pdb=" O LEU F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.972A pdb=" N THR D 91 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.771A pdb=" N SER B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASN B 62 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR B 266 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 264 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 185 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N SER B 203 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 44 removed outlier: 5.686A pdb=" N PHE B 44 " --> pdb=" O ARG C 563 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU C 321 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN C 538 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.950A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.593A pdb=" N SER B 170 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 125 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 119 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 115 " --> pdb=" O CYS B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.905A pdb=" N VAL B 591 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 314 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 589 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.774A pdb=" N GLU B 321 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASN B 538 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 571 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.993A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AA9, first strand: chain 'B' and resid 650 through 656 removed outlier: 5.973A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N VAL B 652 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 668 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 697 through 700 removed outlier: 6.635A pdb=" N ALA B 697 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS A 786 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN B 699 " --> pdb=" O LYS A 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 707 through 711 removed outlier: 4.007A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 714 through 724 removed outlier: 7.011A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.591A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 783 through 784 Processing sheet with id=AB6, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AB7, first strand: chain 'C' and resid 27 through 32 removed outlier: 3.769A pdb=" N SER C 28 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASN C 62 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR C 266 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 66 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR C 262 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 185 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER C 203 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 48 through 56 removed outlier: 3.630A pdb=" N VAL C 48 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 165 through 170 removed outlier: 5.599A pdb=" N PHE C 166 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 129 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 126 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 119 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS C 128 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP C 103 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN C 120 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG C 101 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY C 102 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.940A pdb=" N VAL C 591 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN C 314 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY C 589 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 352 through 355 removed outlier: 3.909A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN C 391 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 449 through 450 Processing sheet with id=AC4, first strand: chain 'C' and resid 650 through 656 removed outlier: 5.935A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N VAL C 652 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.918A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 714 through 724 removed outlier: 7.024A pdb=" N GLY C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER C1051 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C1057 " --> pdb=" O PRO C1049 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C1059 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER C1047 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.499A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 783 through 784 Processing sheet with id=AC9, first strand: chain 'C' and resid 1116 through 1118 Processing sheet with id=AD1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.716A pdb=" N SER A 61 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASN A 62 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TYR A 266 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 264 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 224 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER A 203 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 37 through 38 removed outlier: 7.138A pdb=" N VAL A 37 " --> pdb=" O LEU A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 50 through 56 Processing sheet with id=AD4, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.531A pdb=" N LEU A 117 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 115 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 103 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASN A 120 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG A 101 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 102 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 238 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 308 through 315 removed outlier: 7.016A pdb=" N VAL A 591 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN A 314 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY A 589 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 644 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 322 through 325 removed outlier: 6.270A pdb=" N ILE A 323 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 571 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AD8, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AD9, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.885A pdb=" N TYR A 470 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 485 " --> pdb=" O TYR A 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 650 through 656 removed outlier: 6.023A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL A 652 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA A 668 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 707 through 711 Processing sheet with id=AE3, first strand: chain 'A' and resid 714 through 724 removed outlier: 6.218A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.446A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AE6, first strand: chain 'A' and resid 1090 through 1093 Processing sheet with id=AE7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.560A pdb=" N GLN E 5 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 11 removed outlier: 5.787A pdb=" N GLY E 10 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N CYS E 50 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 59 " --> pdb=" O CYS E 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.608A pdb=" N MET F 83 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.113A pdb=" N VAL F 12 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR F 34 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N CYS F 50 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.172A pdb=" N GLY D 10 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 12 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR D 34 " --> pdb=" O CYS D 50 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N CYS D 50 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2745 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: 6.77 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8831 1.34 - 1.47: 7858 1.47 - 1.59: 12871 1.59 - 1.72: 0 1.72 - 1.85: 162 Bond restraints: 29722 Sorted by residual: bond pdb=" N VAL C 191 " pdb=" CA VAL C 191 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.53e+00 bond pdb=" N GLU C 189 " pdb=" CA GLU C 189 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.97e+00 bond pdb=" N SER A 526 " pdb=" CA SER A 526 " ideal model delta sigma weight residual 1.458 1.487 -0.028 1.19e-02 7.06e+03 5.70e+00 bond pdb=" N GLY A 522 " pdb=" CA GLY A 522 " ideal model delta sigma weight residual 1.443 1.475 -0.033 1.37e-02 5.33e+03 5.63e+00 ... (remaining 29717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 39074 2.48 - 4.96: 1159 4.96 - 7.44: 142 7.44 - 9.91: 43 9.91 - 12.39: 15 Bond angle restraints: 40433 Sorted by residual: angle pdb=" C ILE A 565 " pdb=" N VAL A 566 " pdb=" CA VAL A 566 " ideal model delta sigma weight residual 121.97 132.89 -10.92 1.80e+00 3.09e-01 3.68e+01 angle pdb=" C LEU D 29 " pdb=" N HIS D 30 " pdb=" CA HIS D 30 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 angle pdb=" C ILE B 69 " pdb=" N SER B 70 " pdb=" CA SER B 70 " ideal model delta sigma weight residual 121.54 132.02 -10.48 1.91e+00 2.74e-01 3.01e+01 angle pdb=" C GLY B 740 " pdb=" N ASP B 741 " pdb=" CA ASP B 741 " ideal model delta sigma weight residual 121.54 131.91 -10.37 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C GLY A 740 " pdb=" N ASP A 741 " pdb=" CA ASP A 741 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 ... (remaining 40428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 16525 17.66 - 35.31: 1232 35.31 - 52.97: 199 52.97 - 70.63: 42 70.63 - 88.28: 20 Dihedral angle restraints: 18018 sinusoidal: 7404 harmonic: 10614 Sorted by residual: dihedral pdb=" CB CYS C 658 " pdb=" SG CYS C 658 " pdb=" SG CYS C 667 " pdb=" CB CYS C 667 " ideal model delta sinusoidal sigma weight residual -86.00 -7.06 -78.94 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS B 477 " pdb=" SG CYS B 477 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -20.72 -65.28 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CB CYS C 613 " pdb=" SG CYS C 613 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual 93.00 40.41 52.59 1 1.00e+01 1.00e-02 3.77e+01 ... (remaining 18015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4382 0.126 - 0.252: 203 0.252 - 0.377: 11 0.377 - 0.503: 5 0.503 - 0.629: 2 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.63 2.00e-01 2.50e+01 9.89e+00 chirality pdb=" CB ILE A 208 " pdb=" CA ILE A 208 " pdb=" CG1 ILE A 208 " pdb=" CG2 ILE A 208 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CB ILE C 100 " pdb=" CA ILE C 100 " pdb=" CG1 ILE C 100 " pdb=" CG2 ILE C 100 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.11e+00 ... (remaining 4600 not shown) Planarity restraints: 5217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 713 " -0.055 2.00e-02 2.50e+03 5.00e-02 3.13e+01 pdb=" CG ASN C 713 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C 713 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 713 " 0.048 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 188 " -0.495 9.50e-02 1.11e+02 2.22e-01 3.02e+01 pdb=" NE ARG C 188 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG C 188 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 188 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 188 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 38 " -0.030 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR B 38 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 38 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 38 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 38 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 38 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 38 " -0.003 2.00e-02 2.50e+03 ... (remaining 5214 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3954 2.76 - 3.30: 25487 3.30 - 3.83: 45719 3.83 - 4.37: 52927 4.37 - 4.90: 93228 Nonbonded interactions: 221315 Sorted by model distance: nonbonded pdb=" OG SER B 70 " pdb=" O ASN B 73 " model vdw 2.231 3.040 nonbonded pdb=" O ALA A 875 " pdb=" OG1 THR A 879 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR B1112 " pdb=" OD1 ASP B1114 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR C 497 " pdb=" O PRO F 100 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASP B 564 " pdb=" OG1 THR B 568 " model vdw 2.299 3.040 ... (remaining 221310 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.920 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 : 0.005 0.070 29785 Z= 0.241 Angle : 1.001 12.394 40591 Z= 0.522 Chirality : 0.063 0.629 4603 Planarity : 0.008 0.222 5201 Dihedral : 12.634 88.284 11133 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.61 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.87 % 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: -1.94 (0.13), residues: 3633 helix: -0.42 (0.19), residues: 671 sheet: 0.15 (0.17), residues: 831 loop : -2.30 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 454 TYR 0.060 0.002 TYR B 38 PHE 0.046 0.003 PHE B 173 TRP 0.046 0.003 TRP C 882 HIS 0.013 0.002 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00520 (29722) covalent geometry : angle 0.98509 (40433) SS BOND : bond 0.00384 ( 31) SS BOND : angle 1.78960 ( 62) hydrogen bonds : bond 0.16271 ( 983) hydrogen bonds : angle 6.90297 ( 2745) link_BETA1-4 : bond 0.00670 ( 16) link_BETA1-4 : angle 2.93462 ( 48) link_NAG-ASN : bond 0.01024 ( 16) link_NAG-ASN : angle 4.05088 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3649 (mpp) cc_final: 0.2483 (tmt) REVERT: B 399 ILE cc_start: 0.8549 (pt) cc_final: 0.8306 (pt) REVERT: A 116 LEU cc_start: 0.7979 (tp) cc_final: 0.7664 (mm) REVERT: A 120 ASN cc_start: 0.8155 (m-40) cc_final: 0.7776 (t0) REVERT: F 83 MET cc_start: 0.2431 (mpp) cc_final: 0.1321 (ptp) REVERT: D 83 MET cc_start: 0.0704 (mpp) cc_final: -0.0383 (mmt) outliers start: 1 outliers final: 1 residues processed: 277 average time/residue: 0.5661 time to fit residues: 188.2781 Evaluate side-chains 164 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN B 144 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN B 897 GLN B 998 GLN B1001 GLN C 279 ASN C 318 GLN C 560 GLN C 609 GLN C 988 GLN C1121 ASN A 67 HIS A 144 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A1001 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.150563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080798 restraints weight = 54767.668| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.64 r_work: 0.2836 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29785 Z= 0.199 Angle : 0.688 9.200 40591 Z= 0.348 Chirality : 0.049 0.439 4603 Planarity : 0.005 0.067 5201 Dihedral : 6.217 61.619 4616 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 1.23 % Allowed : 5.57 % Favored : 93.20 % 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: -1.37 (0.13), residues: 3633 helix: 0.75 (0.20), residues: 686 sheet: 0.26 (0.17), residues: 839 loop : -2.11 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 505 TYR 0.046 0.002 TYR B 38 PHE 0.037 0.002 PHE C 66 TRP 0.022 0.002 TRP C 882 HIS 0.005 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00482 (29722) covalent geometry : angle 0.67450 (40433) SS BOND : bond 0.00377 ( 31) SS BOND : angle 1.72889 ( 62) hydrogen bonds : bond 0.05484 ( 983) hydrogen bonds : angle 5.30951 ( 2745) link_BETA1-4 : bond 0.00359 ( 16) link_BETA1-4 : angle 2.24316 ( 48) link_NAG-ASN : bond 0.00349 ( 16) link_NAG-ASN : angle 2.75395 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3645 (mpp) cc_final: 0.3083 (tmt) REVERT: B 175 MET cc_start: 0.2983 (OUTLIER) cc_final: 0.2727 (pmm) REVERT: B 399 ILE cc_start: 0.8394 (pt) cc_final: 0.8162 (pt) REVERT: B 782 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8614 (mptt) REVERT: C 116 LEU cc_start: 0.6455 (mp) cc_final: 0.6042 (tt) REVERT: C 375 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7850 (mmmt) REVERT: C 387 LEU cc_start: 0.6871 (tt) cc_final: 0.6478 (tt) REVERT: A 34 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8759 (m) REVERT: A 116 LEU cc_start: 0.7937 (tp) cc_final: 0.7564 (mp) REVERT: A 120 ASN cc_start: 0.7707 (m-40) cc_final: 0.7185 (t0) REVERT: A 132 PHE cc_start: 0.7701 (m-80) cc_final: 0.7263 (m-80) REVERT: A 175 MET cc_start: 0.2205 (pmt) cc_final: 0.1737 (mmp) REVERT: A 223 LEU cc_start: 0.8351 (tp) cc_final: 0.8032 (tt) REVERT: A 327 PRO cc_start: 0.5546 (Cg_exo) cc_final: 0.4717 (Cg_endo) REVERT: A 790 ILE cc_start: 0.9142 (mp) cc_final: 0.8897 (pp) REVERT: E 70 ILE cc_start: 0.6927 (tt) cc_final: 0.6579 (tp) REVERT: D 34 THR cc_start: 0.3767 (OUTLIER) cc_final: 0.3402 (p) outliers start: 39 outliers final: 8 residues processed: 207 average time/residue: 0.4600 time to fit residues: 118.3956 Evaluate side-chains 159 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 141 optimal weight: 10.0000 chunk 317 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 351 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN B 998 GLN B1001 GLN C 998 GLN A1001 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.150727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081300 restraints weight = 54901.954| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.72 r_work: 0.2833 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29785 Z= 0.142 Angle : 0.624 9.272 40591 Z= 0.312 Chirality : 0.046 0.396 4603 Planarity : 0.004 0.067 5201 Dihedral : 5.864 59.041 4614 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 1.16 % Allowed : 7.62 % Favored : 91.22 % 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: -1.07 (0.13), residues: 3633 helix: 1.31 (0.20), residues: 684 sheet: 0.40 (0.17), residues: 837 loop : -2.00 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 354 TYR 0.026 0.001 TYR C 168 PHE 0.023 0.001 PHE A 588 TRP 0.015 0.001 TRP C 882 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00342 (29722) covalent geometry : angle 0.61223 (40433) SS BOND : bond 0.00271 ( 31) SS BOND : angle 1.50311 ( 62) hydrogen bonds : bond 0.04774 ( 983) hydrogen bonds : angle 4.94747 ( 2745) link_BETA1-4 : bond 0.00412 ( 16) link_BETA1-4 : angle 2.06052 ( 48) link_NAG-ASN : bond 0.00378 ( 16) link_NAG-ASN : angle 2.45335 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7325 (m-10) cc_final: 0.6993 (m-10) REVERT: B 151 MET cc_start: 0.3593 (mpp) cc_final: 0.3085 (tmt) REVERT: B 175 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2783 (pmm) REVERT: B 205 HIS cc_start: 0.5757 (m170) cc_final: 0.5351 (m170) REVERT: B 418 TYR cc_start: 0.7370 (m-10) cc_final: 0.7140 (m-10) REVERT: B 512 GLU cc_start: 0.8684 (tp30) cc_final: 0.8455 (tp30) REVERT: B 736 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8641 (ttt) REVERT: B 782 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8648 (mptt) REVERT: C 116 LEU cc_start: 0.6508 (mp) cc_final: 0.6041 (tt) REVERT: C 324 VAL cc_start: 0.7841 (t) cc_final: 0.7585 (p) REVERT: C 354 ARG cc_start: 0.6155 (ptm-80) cc_final: 0.5787 (ptm-80) REVERT: C 387 LEU cc_start: 0.6993 (tt) cc_final: 0.6533 (tt) REVERT: C 570 ASP cc_start: 0.7370 (m-30) cc_final: 0.7009 (OUTLIER) REVERT: A 34 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8748 (m) REVERT: A 116 LEU cc_start: 0.7901 (tp) cc_final: 0.7501 (mp) REVERT: A 120 ASN cc_start: 0.7563 (m-40) cc_final: 0.6852 (t0) REVERT: A 175 MET cc_start: 0.2366 (pmt) cc_final: 0.1886 (mmp) REVERT: A 223 LEU cc_start: 0.8419 (tp) cc_final: 0.8118 (tt) REVERT: A 736 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8577 (ttt) REVERT: A 782 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8715 (mptt) REVERT: A 790 ILE cc_start: 0.9121 (mp) cc_final: 0.8919 (pp) REVERT: A 1006 GLN cc_start: 0.8531 (tt0) cc_final: 0.8224 (tt0) REVERT: E 51 ILE cc_start: 0.7676 (tt) cc_final: 0.7182 (mm) REVERT: F 83 MET cc_start: 0.0672 (mmt) cc_final: -0.2037 (ptp) REVERT: D 34 THR cc_start: 0.3918 (OUTLIER) cc_final: 0.3510 (p) outliers start: 37 outliers final: 12 residues processed: 181 average time/residue: 0.5333 time to fit residues: 118.6360 Evaluate side-chains 164 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 204 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 348 optimal weight: 50.0000 chunk 115 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN B 800 GLN B 931 GLN B 998 GLN C 144 HIS C1131 ASN A 205 HIS A 489 GLN A 951 ASN A1001 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.146376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076308 restraints weight = 54643.646| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.66 r_work: 0.2739 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 29785 Z= 0.322 Angle : 0.741 9.690 40591 Z= 0.373 Chirality : 0.052 0.542 4603 Planarity : 0.005 0.068 5201 Dihedral : 6.227 59.445 4614 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 1.57 % Allowed : 9.00 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.17 (0.13), residues: 3633 helix: 1.20 (0.20), residues: 690 sheet: 0.22 (0.17), residues: 839 loop : -2.00 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 354 TYR 0.049 0.002 TYR C 38 PHE 0.028 0.002 PHE A 588 TRP 0.026 0.002 TRP B 103 HIS 0.008 0.002 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00791 (29722) covalent geometry : angle 0.72680 (40433) SS BOND : bond 0.00596 ( 31) SS BOND : angle 2.11464 ( 62) hydrogen bonds : bond 0.06484 ( 983) hydrogen bonds : angle 5.15226 ( 2745) link_BETA1-4 : bond 0.00446 ( 16) link_BETA1-4 : angle 2.30357 ( 48) link_NAG-ASN : bond 0.00577 ( 16) link_NAG-ASN : angle 2.82728 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7637 (m-10) cc_final: 0.7220 (m-90) REVERT: B 151 MET cc_start: 0.3742 (mpp) cc_final: 0.3133 (tmt) REVERT: B 175 MET cc_start: 0.3146 (OUTLIER) cc_final: 0.2865 (pmm) REVERT: B 399 ILE cc_start: 0.8282 (pt) cc_final: 0.8076 (pt) REVERT: B 512 GLU cc_start: 0.8762 (tp30) cc_final: 0.8493 (tp30) REVERT: B 736 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8786 (ttt) REVERT: C 116 LEU cc_start: 0.6616 (mp) cc_final: 0.6097 (tp) REVERT: C 151 MET cc_start: 0.6527 (mmt) cc_final: 0.2724 (tmt) REVERT: C 198 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8215 (t80) REVERT: C 354 ARG cc_start: 0.6206 (ptm-80) cc_final: 0.5880 (ptm-80) REVERT: A 34 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8714 (m) REVERT: A 116 LEU cc_start: 0.7883 (tp) cc_final: 0.7418 (mp) REVERT: A 120 ASN cc_start: 0.7728 (m-40) cc_final: 0.6828 (t0) REVERT: A 175 MET cc_start: 0.2522 (pmt) cc_final: 0.1926 (mmp) REVERT: A 223 LEU cc_start: 0.8485 (tp) cc_final: 0.8186 (tt) REVERT: A 224 VAL cc_start: 0.8512 (t) cc_final: 0.8266 (t) REVERT: A 234 ARG cc_start: 0.7643 (mmt90) cc_final: 0.7283 (mmm-85) REVERT: A 1006 GLN cc_start: 0.8636 (tt0) cc_final: 0.8314 (tt0) REVERT: E 50 CYS cc_start: 0.3019 (OUTLIER) cc_final: 0.2230 (m) REVERT: F 83 MET cc_start: 0.0172 (mmt) cc_final: -0.2535 (ptp) REVERT: D 34 THR cc_start: 0.3885 (OUTLIER) cc_final: 0.3468 (p) outliers start: 50 outliers final: 16 residues processed: 187 average time/residue: 0.5755 time to fit residues: 131.4850 Evaluate side-chains 170 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 233 optimal weight: 0.0980 chunk 312 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 242 ASN B 897 GLN B 931 GLN B 951 ASN B 998 GLN B1070 ASN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.151497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082944 restraints weight = 54217.466| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.76 r_work: 0.2837 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29785 Z= 0.111 Angle : 0.599 9.209 40591 Z= 0.298 Chirality : 0.045 0.367 4603 Planarity : 0.004 0.067 5201 Dihedral : 5.796 59.742 4614 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.68 % Favored : 95.16 % Rotamer: Outliers : 1.32 % Allowed : 10.17 % Favored : 88.51 % 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: -0.87 (0.14), residues: 3633 helix: 1.79 (0.20), residues: 681 sheet: 0.40 (0.18), residues: 831 loop : -1.92 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.027 0.001 TYR C 168 PHE 0.030 0.001 PHE A 132 TRP 0.030 0.002 TRP A 433 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00257 (29722) covalent geometry : angle 0.58902 (40433) SS BOND : bond 0.00253 ( 31) SS BOND : angle 1.15646 ( 62) hydrogen bonds : bond 0.04333 ( 983) hydrogen bonds : angle 4.70384 ( 2745) link_BETA1-4 : bond 0.00504 ( 16) link_BETA1-4 : angle 1.94121 ( 48) link_NAG-ASN : bond 0.00542 ( 16) link_NAG-ASN : angle 2.39122 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7597 (m-10) cc_final: 0.7273 (m-90) REVERT: B 151 MET cc_start: 0.3696 (mpp) cc_final: 0.3070 (tmt) REVERT: B 175 MET cc_start: 0.3305 (OUTLIER) cc_final: 0.3006 (pmm) REVERT: B 205 HIS cc_start: 0.6081 (m170) cc_final: 0.5197 (m170) REVERT: B 354 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7245 (ttm170) REVERT: B 418 TYR cc_start: 0.7408 (m-10) cc_final: 0.6960 (m-10) REVERT: B 512 GLU cc_start: 0.8780 (tp30) cc_final: 0.8450 (tp30) REVERT: B 630 ARG cc_start: 0.6546 (ptp-110) cc_final: 0.6278 (mtm180) REVERT: B 782 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8777 (mptt) REVERT: C 116 LEU cc_start: 0.6295 (mp) cc_final: 0.5850 (tt) REVERT: C 151 MET cc_start: 0.6612 (mmt) cc_final: 0.2814 (tmt) REVERT: C 198 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8054 (t80) REVERT: C 324 VAL cc_start: 0.7897 (t) cc_final: 0.7637 (p) REVERT: C 354 ARG cc_start: 0.6639 (ptm-80) cc_final: 0.6302 (ptm-80) REVERT: C 387 LEU cc_start: 0.7106 (tt) cc_final: 0.6877 (tt) REVERT: C 998 GLN cc_start: 0.8650 (tt0) cc_final: 0.8444 (tt0) REVERT: A 34 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8696 (m) REVERT: A 116 LEU cc_start: 0.7867 (tp) cc_final: 0.7398 (mp) REVERT: A 120 ASN cc_start: 0.7803 (m-40) cc_final: 0.6738 (t0) REVERT: A 175 MET cc_start: 0.2465 (pmt) cc_final: 0.2100 (mmp) REVERT: A 223 LEU cc_start: 0.8452 (tp) cc_final: 0.8220 (tt) REVERT: A 224 VAL cc_start: 0.8616 (t) cc_final: 0.8331 (t) REVERT: A 234 ARG cc_start: 0.7459 (mmt90) cc_final: 0.7017 (mmm-85) REVERT: A 1006 GLN cc_start: 0.8525 (tt0) cc_final: 0.8196 (tt0) REVERT: E 51 ILE cc_start: 0.7573 (tt) cc_final: 0.7057 (mm) REVERT: F 83 MET cc_start: 0.0377 (mmt) cc_final: -0.2120 (ptp) REVERT: D 34 THR cc_start: 0.3833 (OUTLIER) cc_final: 0.3445 (p) outliers start: 42 outliers final: 12 residues processed: 190 average time/residue: 0.5811 time to fit residues: 134.0620 Evaluate side-chains 173 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 29 optimal weight: 3.9990 chunk 154 optimal weight: 0.1980 chunk 226 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 184 optimal weight: 0.0670 chunk 202 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 931 GLN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 ASN ** E 5 GLN ** 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 = 0.4161 r_free = 0.4161 target = 0.151108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077312 restraints weight = 55822.503| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.35 r_work: 0.2803 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29785 Z= 0.180 Angle : 0.631 10.012 40591 Z= 0.313 Chirality : 0.047 0.423 4603 Planarity : 0.004 0.071 5201 Dihedral : 5.742 59.624 4614 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.06 % Favored : 94.77 % Rotamer: Outliers : 1.45 % Allowed : 10.76 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.84 (0.14), residues: 3633 helix: 1.80 (0.20), residues: 686 sheet: 0.35 (0.18), residues: 838 loop : -1.87 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 354 TYR 0.025 0.001 TYR B 38 PHE 0.023 0.001 PHE A 588 TRP 0.036 0.002 TRP A 433 HIS 0.005 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00441 (29722) covalent geometry : angle 0.61992 (40433) SS BOND : bond 0.00485 ( 31) SS BOND : angle 1.39887 ( 62) hydrogen bonds : bond 0.04935 ( 983) hydrogen bonds : angle 4.71121 ( 2745) link_BETA1-4 : bond 0.00355 ( 16) link_BETA1-4 : angle 1.93012 ( 48) link_NAG-ASN : bond 0.00379 ( 16) link_NAG-ASN : angle 2.48967 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7531 (m-10) cc_final: 0.7303 (m-90) REVERT: B 151 MET cc_start: 0.3715 (mpp) cc_final: 0.3038 (tmt) REVERT: B 175 MET cc_start: 0.3281 (OUTLIER) cc_final: 0.3032 (pmm) REVERT: B 418 TYR cc_start: 0.7291 (m-10) cc_final: 0.6879 (m-10) REVERT: B 512 GLU cc_start: 0.8823 (tp30) cc_final: 0.8425 (tp30) REVERT: B 782 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8824 (mptt) REVERT: C 116 LEU cc_start: 0.6305 (mp) cc_final: 0.5846 (tt) REVERT: C 151 MET cc_start: 0.6623 (mmt) cc_final: 0.2945 (tmt) REVERT: C 324 VAL cc_start: 0.7935 (t) cc_final: 0.7669 (p) REVERT: C 354 ARG cc_start: 0.6745 (ptm-80) cc_final: 0.6423 (ptm-80) REVERT: C 1123 ASP cc_start: 0.8884 (m-30) cc_final: 0.8567 (m-30) REVERT: A 34 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8715 (m) REVERT: A 116 LEU cc_start: 0.7805 (tp) cc_final: 0.7306 (mp) REVERT: A 120 ASN cc_start: 0.7790 (m-40) cc_final: 0.6688 (t0) REVERT: A 175 MET cc_start: 0.2489 (pmt) cc_final: 0.2091 (mmp) REVERT: A 224 VAL cc_start: 0.8517 (t) cc_final: 0.8234 (t) REVERT: A 234 ARG cc_start: 0.7465 (mmt90) cc_final: 0.7016 (mmm-85) REVERT: A 790 ILE cc_start: 0.9057 (mp) cc_final: 0.8773 (pp) REVERT: A 1006 GLN cc_start: 0.8543 (tt0) cc_final: 0.8207 (tt0) REVERT: E 50 CYS cc_start: 0.2575 (OUTLIER) cc_final: 0.1760 (m) REVERT: F 83 MET cc_start: 0.0360 (mmt) cc_final: -0.2189 (ptp) REVERT: D 34 THR cc_start: 0.3762 (OUTLIER) cc_final: 0.3406 (p) outliers start: 46 outliers final: 17 residues processed: 186 average time/residue: 0.5354 time to fit residues: 122.6390 Evaluate side-chains 167 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 122 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 281 optimal weight: 0.7980 chunk 353 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 208 optimal weight: 0.3980 chunk 232 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 897 GLN B 931 GLN B 951 ASN A 194 ASN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.151833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083256 restraints weight = 54287.897| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.81 r_work: 0.2832 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29785 Z= 0.110 Angle : 0.588 10.321 40591 Z= 0.291 Chirality : 0.045 0.368 4603 Planarity : 0.004 0.066 5201 Dihedral : 5.512 56.504 4614 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 1.23 % Allowed : 11.68 % Favored : 87.09 % 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: -0.68 (0.14), residues: 3633 helix: 2.01 (0.21), residues: 684 sheet: 0.57 (0.18), residues: 814 loop : -1.83 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 354 TYR 0.019 0.001 TYR B 38 PHE 0.022 0.001 PHE B 126 TRP 0.029 0.001 TRP A 433 HIS 0.004 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00261 (29722) covalent geometry : angle 0.57894 (40433) SS BOND : bond 0.00299 ( 31) SS BOND : angle 1.09654 ( 62) hydrogen bonds : bond 0.04100 ( 983) hydrogen bonds : angle 4.52427 ( 2745) link_BETA1-4 : bond 0.00465 ( 16) link_BETA1-4 : angle 1.76964 ( 48) link_NAG-ASN : bond 0.00449 ( 16) link_NAG-ASN : angle 2.36314 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7575 (m-10) cc_final: 0.7311 (m-90) REVERT: B 151 MET cc_start: 0.3627 (mpp) cc_final: 0.2889 (tmt) REVERT: B 175 MET cc_start: 0.3155 (OUTLIER) cc_final: 0.2948 (pmm) REVERT: B 418 TYR cc_start: 0.7469 (m-10) cc_final: 0.7215 (m-10) REVERT: B 512 GLU cc_start: 0.8856 (tp30) cc_final: 0.8465 (tp30) REVERT: B 782 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8779 (mptt) REVERT: B 998 GLN cc_start: 0.8554 (tp40) cc_final: 0.8257 (tt0) REVERT: C 116 LEU cc_start: 0.6300 (mp) cc_final: 0.5866 (tt) REVERT: C 151 MET cc_start: 0.6673 (mmt) cc_final: 0.2960 (tmt) REVERT: C 198 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.8225 (t80) REVERT: C 324 VAL cc_start: 0.7975 (t) cc_final: 0.7738 (p) REVERT: C 354 ARG cc_start: 0.6867 (ptm-80) cc_final: 0.6560 (ptm-80) REVERT: C 387 LEU cc_start: 0.6969 (tt) cc_final: 0.6629 (tt) REVERT: C 1123 ASP cc_start: 0.8871 (m-30) cc_final: 0.8552 (m-30) REVERT: A 34 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8680 (m) REVERT: A 116 LEU cc_start: 0.7911 (tp) cc_final: 0.7401 (mp) REVERT: A 120 ASN cc_start: 0.7800 (m-40) cc_final: 0.6721 (t0) REVERT: A 175 MET cc_start: 0.2504 (pmt) cc_final: 0.2159 (mmp) REVERT: A 224 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 234 ARG cc_start: 0.7411 (mmt90) cc_final: 0.7053 (mmm-85) REVERT: A 1092 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8699 (m) REVERT: E 50 CYS cc_start: 0.2007 (OUTLIER) cc_final: 0.1188 (m) REVERT: E 70 ILE cc_start: 0.6260 (tp) cc_final: 0.5942 (tt) REVERT: F 83 MET cc_start: 0.0273 (mmt) cc_final: -0.2183 (ptp) REVERT: D 34 THR cc_start: 0.3639 (OUTLIER) cc_final: 0.3264 (p) outliers start: 39 outliers final: 18 residues processed: 182 average time/residue: 0.5699 time to fit residues: 126.1666 Evaluate side-chains 169 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 109 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 931 GLN C 186 ASN C1006 GLN A 951 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.150894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080346 restraints weight = 52676.055| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.70 r_work: 0.2739 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 29785 Z= 0.291 Angle : 0.704 11.171 40591 Z= 0.351 Chirality : 0.050 0.505 4603 Planarity : 0.005 0.082 5201 Dihedral : 5.930 59.980 4614 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 1.10 % Allowed : 12.59 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.88 (0.14), residues: 3633 helix: 1.61 (0.20), residues: 689 sheet: 0.41 (0.18), residues: 818 loop : -1.86 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 354 TYR 0.034 0.002 TYR B 38 PHE 0.034 0.002 PHE A 902 TRP 0.028 0.002 TRP B 103 HIS 0.007 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00710 (29722) covalent geometry : angle 0.69243 (40433) SS BOND : bond 0.00506 ( 31) SS BOND : angle 1.75243 ( 62) hydrogen bonds : bond 0.06050 ( 983) hydrogen bonds : angle 4.84114 ( 2745) link_BETA1-4 : bond 0.00323 ( 16) link_BETA1-4 : angle 2.05543 ( 48) link_NAG-ASN : bond 0.00466 ( 16) link_NAG-ASN : angle 2.72460 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3872 (mpp) cc_final: 0.3145 (tmt) REVERT: B 175 MET cc_start: 0.3230 (OUTLIER) cc_final: 0.2977 (pmm) REVERT: B 418 TYR cc_start: 0.7601 (m-10) cc_final: 0.7334 (m-10) REVERT: B 512 GLU cc_start: 0.8849 (tp30) cc_final: 0.8611 (tp30) REVERT: C 116 LEU cc_start: 0.6462 (mp) cc_final: 0.5963 (tp) REVERT: C 151 MET cc_start: 0.6580 (mmt) cc_final: 0.3165 (tmt) REVERT: C 198 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8239 (t80) REVERT: C 354 ARG cc_start: 0.6747 (ptm-80) cc_final: 0.6393 (ptm-80) REVERT: C 387 LEU cc_start: 0.6989 (tt) cc_final: 0.6639 (tt) REVERT: C 1123 ASP cc_start: 0.8919 (m-30) cc_final: 0.8572 (m-30) REVERT: A 34 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8704 (m) REVERT: A 116 LEU cc_start: 0.7883 (tp) cc_final: 0.7350 (mp) REVERT: A 120 ASN cc_start: 0.7874 (m-40) cc_final: 0.6827 (t0) REVERT: A 166 PHE cc_start: 0.7370 (t80) cc_final: 0.7123 (t80) REVERT: A 175 MET cc_start: 0.2499 (pmt) cc_final: 0.2064 (mmp) REVERT: A 224 VAL cc_start: 0.8476 (t) cc_final: 0.8100 (p) REVERT: A 234 ARG cc_start: 0.7557 (mmt90) cc_final: 0.7180 (mmm-85) REVERT: E 50 CYS cc_start: 0.1880 (OUTLIER) cc_final: 0.1337 (m) REVERT: F 83 MET cc_start: 0.0104 (mmt) cc_final: -0.2482 (ptp) REVERT: D 34 THR cc_start: 0.3631 (OUTLIER) cc_final: 0.3248 (p) outliers start: 35 outliers final: 17 residues processed: 171 average time/residue: 0.5018 time to fit residues: 106.5497 Evaluate side-chains 164 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 145 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 342 optimal weight: 40.0000 chunk 134 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN A 951 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.150421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080595 restraints weight = 54243.150| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.78 r_work: 0.2811 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29785 Z= 0.119 Angle : 0.604 11.015 40591 Z= 0.299 Chirality : 0.045 0.385 4603 Planarity : 0.004 0.068 5201 Dihedral : 5.613 57.883 4614 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.40 % Favored : 95.46 % Rotamer: Outliers : 1.04 % Allowed : 12.87 % Favored : 86.09 % 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: -0.72 (0.14), residues: 3633 helix: 1.89 (0.21), residues: 686 sheet: 0.50 (0.18), residues: 824 loop : -1.81 (0.12), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 354 TYR 0.030 0.001 TYR B 168 PHE 0.022 0.001 PHE B 126 TRP 0.025 0.001 TRP A 433 HIS 0.005 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00284 (29722) covalent geometry : angle 0.59442 (40433) SS BOND : bond 0.00285 ( 31) SS BOND : angle 1.11415 ( 62) hydrogen bonds : bond 0.04347 ( 983) hydrogen bonds : angle 4.55626 ( 2745) link_BETA1-4 : bond 0.00462 ( 16) link_BETA1-4 : angle 1.76498 ( 48) link_NAG-ASN : bond 0.00504 ( 16) link_NAG-ASN : angle 2.44523 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3812 (mpp) cc_final: 0.3075 (tmt) REVERT: B 175 MET cc_start: 0.3468 (OUTLIER) cc_final: 0.3180 (pmm) REVERT: B 418 TYR cc_start: 0.7587 (m-10) cc_final: 0.7327 (m-10) REVERT: B 512 GLU cc_start: 0.8828 (tp30) cc_final: 0.8372 (tp30) REVERT: C 116 LEU cc_start: 0.6484 (mp) cc_final: 0.5994 (tp) REVERT: C 151 MET cc_start: 0.6550 (mmt) cc_final: 0.3140 (tmt) REVERT: C 198 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8224 (t80) REVERT: C 324 VAL cc_start: 0.8011 (t) cc_final: 0.7741 (p) REVERT: C 354 ARG cc_start: 0.6891 (ptm-80) cc_final: 0.6575 (ptm-80) REVERT: C 387 LEU cc_start: 0.7020 (tt) cc_final: 0.6654 (tt) REVERT: A 34 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8694 (m) REVERT: A 116 LEU cc_start: 0.7953 (tp) cc_final: 0.7452 (mp) REVERT: A 120 ASN cc_start: 0.7866 (m-40) cc_final: 0.6763 (t0) REVERT: A 175 MET cc_start: 0.2453 (pmt) cc_final: 0.2049 (mmp) REVERT: A 234 ARG cc_start: 0.7441 (mmt90) cc_final: 0.7065 (mmm-85) REVERT: E 50 CYS cc_start: 0.1459 (OUTLIER) cc_final: 0.0754 (m) REVERT: E 70 ILE cc_start: 0.6341 (tp) cc_final: 0.5998 (tt) REVERT: F 83 MET cc_start: 0.0586 (mmt) cc_final: -0.2086 (ptp) REVERT: D 34 THR cc_start: 0.3443 (OUTLIER) cc_final: 0.3117 (p) outliers start: 33 outliers final: 16 residues processed: 165 average time/residue: 0.5509 time to fit residues: 111.9001 Evaluate side-chains 163 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 174 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 353 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 303 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.151121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.080133 restraints weight = 55367.633| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.54 r_work: 0.2802 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29785 Z= 0.147 Angle : 0.613 11.612 40591 Z= 0.303 Chirality : 0.046 0.406 4603 Planarity : 0.004 0.090 5201 Dihedral : 5.515 58.090 4614 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 0.91 % Allowed : 12.97 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.69 (0.14), residues: 3633 helix: 1.97 (0.21), residues: 689 sheet: 0.55 (0.18), residues: 808 loop : -1.81 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 354 TYR 0.028 0.001 TYR B 168 PHE 0.026 0.001 PHE A 199 TRP 0.024 0.001 TRP A 433 HIS 0.004 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00361 (29722) covalent geometry : angle 0.60360 (40433) SS BOND : bond 0.00320 ( 31) SS BOND : angle 1.23399 ( 62) hydrogen bonds : bond 0.04562 ( 983) hydrogen bonds : angle 4.53533 ( 2745) link_BETA1-4 : bond 0.00356 ( 16) link_BETA1-4 : angle 1.75510 ( 48) link_NAG-ASN : bond 0.00399 ( 16) link_NAG-ASN : angle 2.46916 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3797 (mpp) cc_final: 0.3077 (tmt) REVERT: B 175 MET cc_start: 0.3453 (OUTLIER) cc_final: 0.3179 (pmm) REVERT: B 418 TYR cc_start: 0.7606 (m-10) cc_final: 0.7304 (m-10) REVERT: B 512 GLU cc_start: 0.8803 (tp30) cc_final: 0.8376 (tp30) REVERT: B 998 GLN cc_start: 0.8599 (tp40) cc_final: 0.8301 (tt0) REVERT: C 116 LEU cc_start: 0.6513 (mp) cc_final: 0.6039 (tp) REVERT: C 151 MET cc_start: 0.6544 (mmt) cc_final: 0.3106 (tmt) REVERT: C 198 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8202 (t80) REVERT: C 324 VAL cc_start: 0.8020 (t) cc_final: 0.7744 (p) REVERT: C 354 ARG cc_start: 0.6890 (ptm-80) cc_final: 0.6553 (ptm-80) REVERT: C 387 LEU cc_start: 0.7022 (tt) cc_final: 0.6649 (tt) REVERT: C 1123 ASP cc_start: 0.8903 (m-30) cc_final: 0.8551 (m-30) REVERT: A 34 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8693 (m) REVERT: A 116 LEU cc_start: 0.7865 (tp) cc_final: 0.7357 (mp) REVERT: A 120 ASN cc_start: 0.7900 (m-40) cc_final: 0.6778 (t0) REVERT: A 175 MET cc_start: 0.2631 (pmt) cc_final: 0.2200 (mmp) REVERT: A 234 ARG cc_start: 0.7413 (mmt90) cc_final: 0.6790 (mtm-85) REVERT: A 1092 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8744 (m) REVERT: E 50 CYS cc_start: 0.1507 (OUTLIER) cc_final: 0.0883 (m) REVERT: E 70 ILE cc_start: 0.6251 (tp) cc_final: 0.5927 (tt) REVERT: F 83 MET cc_start: 0.0362 (mmt) cc_final: -0.2316 (ptp) REVERT: D 34 THR cc_start: 0.3439 (OUTLIER) cc_final: 0.3115 (p) outliers start: 29 outliers final: 17 residues processed: 167 average time/residue: 0.4909 time to fit residues: 101.4272 Evaluate side-chains 162 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 21 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 126 optimal weight: 0.4980 chunk 80 optimal weight: 0.0570 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 931 GLN A 951 ASN ** E 5 GLN ** 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 = 0.4179 r_free = 0.4179 target = 0.150790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082580 restraints weight = 54553.642| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.81 r_work: 0.2830 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29785 Z= 0.109 Angle : 0.591 11.333 40591 Z= 0.291 Chirality : 0.045 0.367 4603 Planarity : 0.004 0.069 5201 Dihedral : 5.302 55.770 4614 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 0.88 % Allowed : 13.03 % Favored : 86.09 % 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: -0.59 (0.14), residues: 3633 helix: 2.09 (0.21), residues: 684 sheet: 0.61 (0.18), residues: 811 loop : -1.76 (0.12), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 354 TYR 0.030 0.001 TYR B 168 PHE 0.032 0.001 PHE A 199 TRP 0.024 0.001 TRP A 433 HIS 0.004 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00263 (29722) covalent geometry : angle 0.58270 (40433) SS BOND : bond 0.00240 ( 31) SS BOND : angle 0.95624 ( 62) hydrogen bonds : bond 0.03940 ( 983) hydrogen bonds : angle 4.41538 ( 2745) link_BETA1-4 : bond 0.00431 ( 16) link_BETA1-4 : angle 1.63771 ( 48) link_NAG-ASN : bond 0.00471 ( 16) link_NAG-ASN : angle 2.39605 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10447.34 seconds wall clock time: 178 minutes 44.35 seconds (10724.35 seconds total)