Starting phenix.real_space_refine on Tue May 27 00:42:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co8_45773/05_2025/9co8_45773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co8_45773/05_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_45773/05_2025/9co8_45773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co8_45773/05_2025/9co8_45773.map" model { file = "/net/cci-nas-00/data/ceres_data/9co8_45773/05_2025/9co8_45773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co8_45773/05_2025/9co8_45773.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.98, per 1000 atoms: 0.55 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: 7.03 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 4.07 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: 12.32 Time building geometry restraints manager: 8.20 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: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.280 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 63.130 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.190 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.050 ------------------------------------------------------------------------------- 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 : 4.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (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 TRP 0.046 0.003 TRP C 882 HIS 0.013 0.002 HIS D 32 PHE 0.046 0.003 PHE B 173 TYR 0.060 0.002 TYR B 38 ARG 0.016 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.01024 ( 16) link_NAG-ASN : angle 4.05088 ( 48) link_BETA1-4 : bond 0.00670 ( 16) link_BETA1-4 : angle 2.93462 ( 48) hydrogen bonds : bond 0.16271 ( 983) hydrogen bonds : angle 6.90297 ( 2745) SS BOND : bond 0.00384 ( 31) SS BOND : angle 1.78960 ( 62) covalent geometry : bond 0.00520 (29722) covalent geometry : angle 0.98509 (40433) *********************** 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 : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3649 (mpp) cc_final: 0.2484 (tmt) REVERT: B 399 ILE cc_start: 0.8549 (pt) cc_final: 0.8304 (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: 1.1562 time to fit residues: 388.0417 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 : 3.720 ------------------------------------------------------------------------------- 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 306 optimal weight: 0.3980 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 185 optimal weight: 0.0570 chunk 146 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 329 optimal weight: 30.0000 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN ** 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 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1121 ASN A 144 HIS A 609 GLN A1001 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.152963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082895 restraints weight = 54643.132| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.26 r_work: 0.2907 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 29785 Z= 0.130 Angle : 0.650 9.099 40591 Z= 0.329 Chirality : 0.047 0.388 4603 Planarity : 0.005 0.066 5201 Dihedral : 6.092 61.581 4616 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 1.13 % Allowed : 5.51 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3633 helix: 0.78 (0.20), residues: 684 sheet: 0.32 (0.17), residues: 838 loop : -2.09 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 65 HIS 0.004 0.001 HIS D 32 PHE 0.036 0.001 PHE C 66 TYR 0.036 0.001 TYR B 38 ARG 0.009 0.001 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 16) link_NAG-ASN : angle 2.70643 ( 48) link_BETA1-4 : bond 0.00458 ( 16) link_BETA1-4 : angle 2.22651 ( 48) hydrogen bonds : bond 0.04843 ( 983) hydrogen bonds : angle 5.27241 ( 2745) SS BOND : bond 0.00292 ( 31) SS BOND : angle 1.40531 ( 62) covalent geometry : bond 0.00309 (29722) covalent geometry : angle 0.63765 (40433) *********************** 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 215 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3631 (mpp) cc_final: 0.3021 (tmt) REVERT: B 175 MET cc_start: 0.2941 (OUTLIER) cc_final: 0.2674 (pmm) REVERT: B 399 ILE cc_start: 0.8425 (pt) cc_final: 0.8193 (pt) REVERT: B 782 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8531 (mptt) REVERT: B 1013 GLU cc_start: 0.8720 (tt0) cc_final: 0.8385 (tp30) REVERT: C 116 LEU cc_start: 0.6593 (mp) cc_final: 0.6153 (tt) REVERT: C 375 LYS cc_start: 0.8193 (mmmm) cc_final: 0.7893 (mmmt) REVERT: C 387 LEU cc_start: 0.6971 (tt) cc_final: 0.6612 (tt) REVERT: A 34 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8770 (m) REVERT: A 116 LEU cc_start: 0.7957 (tp) cc_final: 0.7581 (mp) REVERT: A 120 ASN cc_start: 0.7698 (m-40) cc_final: 0.7245 (t0) REVERT: A 175 MET cc_start: 0.2181 (pmt) cc_final: 0.1705 (mmp) REVERT: A 223 LEU cc_start: 0.8337 (tp) cc_final: 0.8036 (tt) REVERT: A 327 PRO cc_start: 0.5413 (Cg_exo) cc_final: 0.4501 (Cg_endo) REVERT: A 736 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8511 (ttp) REVERT: A 776 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8226 (mm-30) REVERT: E 70 ILE cc_start: 0.6853 (tt) cc_final: 0.6462 (tp) REVERT: E 83 MET cc_start: 0.4515 (mmp) cc_final: 0.4264 (mmp) REVERT: D 34 THR cc_start: 0.3781 (OUTLIER) cc_final: 0.3417 (p) outliers start: 36 outliers final: 7 residues processed: 201 average time/residue: 0.9816 time to fit residues: 248.6445 Evaluate side-chains 154 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 507 VAL 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 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 A residue 736 MET 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 121 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 206 optimal weight: 0.3980 chunk 332 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 191 optimal weight: 0.4980 chunk 168 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 144 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 998 GLN B1001 GLN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 GLN A 67 HIS A1001 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.152078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081170 restraints weight = 54263.691| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.29 r_work: 0.2880 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1620 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= 0.133 Angle : 0.613 10.520 40591 Z= 0.306 Chirality : 0.046 0.386 4603 Planarity : 0.004 0.066 5201 Dihedral : 5.733 59.975 4614 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.85 % Rotamer: Outliers : 1.26 % Allowed : 7.15 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3633 helix: 1.41 (0.20), residues: 688 sheet: 0.44 (0.17), residues: 840 loop : -1.98 (0.12), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 65 HIS 0.005 0.001 HIS D 32 PHE 0.028 0.001 PHE C 66 TYR 0.022 0.001 TYR B 366 ARG 0.009 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 16) link_NAG-ASN : angle 2.42026 ( 48) link_BETA1-4 : bond 0.00409 ( 16) link_BETA1-4 : angle 2.00529 ( 48) hydrogen bonds : bond 0.04548 ( 983) hydrogen bonds : angle 4.88728 ( 2745) SS BOND : bond 0.00374 ( 31) SS BOND : angle 1.38839 ( 62) covalent geometry : bond 0.00322 (29722) covalent geometry : angle 0.60240 (40433) *********************** 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 201 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3730 (mpp) cc_final: 0.3124 (tmt) REVERT: B 175 MET cc_start: 0.2995 (OUTLIER) cc_final: 0.2725 (pmm) REVERT: B 205 HIS cc_start: 0.5817 (m170) cc_final: 0.5447 (m170) REVERT: B 344 PHE cc_start: 0.6310 (m-10) cc_final: 0.6087 (m-10) REVERT: B 512 GLU cc_start: 0.8663 (tp30) cc_final: 0.8431 (tp30) REVERT: B 736 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8674 (ttt) REVERT: B 782 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8579 (mptt) REVERT: B 1013 GLU cc_start: 0.8717 (tt0) cc_final: 0.8391 (tp30) REVERT: C 116 LEU cc_start: 0.6438 (mp) cc_final: 0.5989 (tt) REVERT: C 194 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7888 (m110) REVERT: C 198 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8260 (t80) REVERT: C 324 VAL cc_start: 0.7925 (t) cc_final: 0.7670 (p) REVERT: C 354 ARG cc_start: 0.6194 (ptm-80) cc_final: 0.5852 (ptm-80) REVERT: C 387 LEU cc_start: 0.7109 (tt) cc_final: 0.6656 (tt) REVERT: A 34 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8761 (m) REVERT: A 116 LEU cc_start: 0.7891 (tp) cc_final: 0.7484 (mp) REVERT: A 120 ASN cc_start: 0.7551 (m-40) cc_final: 0.6886 (t0) REVERT: A 175 MET cc_start: 0.2353 (pmt) cc_final: 0.1795 (mmp) REVERT: A 223 LEU cc_start: 0.8393 (tp) cc_final: 0.8072 (tt) REVERT: A 782 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8690 (mptt) REVERT: E 51 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7039 (mm) REVERT: F 83 MET cc_start: 0.0581 (mmt) cc_final: -0.1976 (ptp) REVERT: D 34 THR cc_start: 0.3910 (OUTLIER) cc_final: 0.3555 (p) outliers start: 40 outliers final: 9 residues processed: 189 average time/residue: 1.0059 time to fit residues: 237.4077 Evaluate side-chains 162 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 3.040 ------------------------------------------------------------------------------- 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 194 ASN 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 566 VAL Chi-restraints excluded: chain C residue 581 LEU 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 782 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 4.9990 chunk 341 optimal weight: 30.0000 chunk 314 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 998 GLN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.152038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082682 restraints weight = 54968.183| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.42 r_work: 0.2887 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29785 Z= 0.116 Angle : 0.591 9.342 40591 Z= 0.294 Chirality : 0.045 0.372 4603 Planarity : 0.004 0.067 5201 Dihedral : 5.551 58.477 4614 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.54 % Rotamer: Outliers : 1.26 % Allowed : 8.37 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3633 helix: 1.71 (0.20), residues: 689 sheet: 0.46 (0.17), residues: 836 loop : -1.90 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 433 HIS 0.005 0.001 HIS D 32 PHE 0.038 0.001 PHE A 213 TYR 0.028 0.001 TYR B 38 ARG 0.009 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 16) link_NAG-ASN : angle 2.30125 ( 48) link_BETA1-4 : bond 0.00394 ( 16) link_BETA1-4 : angle 1.82713 ( 48) hydrogen bonds : bond 0.04152 ( 983) hydrogen bonds : angle 4.70704 ( 2745) SS BOND : bond 0.00419 ( 31) SS BOND : angle 1.35858 ( 62) covalent geometry : bond 0.00278 (29722) covalent geometry : angle 0.58120 (40433) *********************** 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 190 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7303 (m-10) cc_final: 0.6935 (m-10) REVERT: B 151 MET cc_start: 0.3662 (mpp) cc_final: 0.3055 (tmt) REVERT: B 175 MET cc_start: 0.3107 (OUTLIER) cc_final: 0.2840 (pmm) REVERT: B 418 TYR cc_start: 0.7166 (m-10) cc_final: 0.6770 (m-10) REVERT: B 512 GLU cc_start: 0.8724 (tp30) cc_final: 0.8430 (tp30) REVERT: B 782 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8622 (mptt) REVERT: B 1013 GLU cc_start: 0.8714 (tt0) cc_final: 0.8387 (tp30) REVERT: C 116 LEU cc_start: 0.6541 (mp) cc_final: 0.6078 (tt) REVERT: C 194 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7839 (m110) REVERT: C 198 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8275 (t80) REVERT: C 324 VAL cc_start: 0.7938 (t) cc_final: 0.7703 (p) REVERT: C 354 ARG cc_start: 0.6426 (ptm-80) cc_final: 0.6104 (ptm-80) REVERT: C 387 LEU cc_start: 0.7095 (tt) cc_final: 0.6605 (tt) REVERT: A 34 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8768 (m) REVERT: A 116 LEU cc_start: 0.7915 (tp) cc_final: 0.7475 (mp) REVERT: A 120 ASN cc_start: 0.7618 (m-40) cc_final: 0.6890 (t0) REVERT: A 175 MET cc_start: 0.2451 (pmt) cc_final: 0.2010 (mmp) REVERT: A 223 LEU cc_start: 0.8423 (tp) cc_final: 0.8118 (tt) REVERT: A 782 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8716 (mptt) REVERT: F 83 MET cc_start: 0.0448 (mmt) cc_final: -0.2108 (ptp) REVERT: D 34 THR cc_start: 0.3828 (OUTLIER) cc_final: 0.3493 (p) outliers start: 40 outliers final: 12 residues processed: 177 average time/residue: 1.0175 time to fit residues: 226.6139 Evaluate side-chains 163 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 3.157 ------------------------------------------------------------------------------- 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 578 LEU Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 194 ASN 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 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 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 782 LYS 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 70 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 336 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 289 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 274 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 800 GLN B 931 GLN B 998 GLN C 536 ASN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 GLN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A1001 GLN A1131 ASN E 32 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.148476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077787 restraints weight = 54141.719| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.70 r_work: 0.2771 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29785 Z= 0.242 Angle : 0.683 13.991 40591 Z= 0.341 Chirality : 0.049 0.487 4603 Planarity : 0.005 0.066 5201 Dihedral : 5.852 59.165 4614 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 1.42 % Allowed : 9.00 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3633 helix: 1.62 (0.20), residues: 680 sheet: 0.41 (0.18), residues: 829 loop : -1.89 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 433 HIS 0.007 0.002 HIS C1054 PHE 0.028 0.002 PHE C 66 TYR 0.035 0.002 TYR B 38 ARG 0.005 0.001 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 16) link_NAG-ASN : angle 2.65088 ( 48) link_BETA1-4 : bond 0.00326 ( 16) link_BETA1-4 : angle 2.01785 ( 48) hydrogen bonds : bond 0.05878 ( 983) hydrogen bonds : angle 4.92333 ( 2745) SS BOND : bond 0.00463 ( 31) SS BOND : angle 1.72407 ( 62) covalent geometry : bond 0.00591 (29722) covalent geometry : angle 0.67149 (40433) *********************** 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 202 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7566 (m-10) cc_final: 0.7170 (m-90) REVERT: B 151 MET cc_start: 0.3662 (mpp) cc_final: 0.3064 (tmt) REVERT: B 175 MET cc_start: 0.3146 (OUTLIER) cc_final: 0.2851 (pmm) REVERT: B 205 HIS cc_start: 0.6199 (m170) cc_final: 0.5786 (m170) REVERT: B 344 PHE cc_start: 0.7019 (m-10) cc_final: 0.6689 (m-80) REVERT: B 418 TYR cc_start: 0.7306 (m-10) cc_final: 0.7026 (m-10) REVERT: B 512 GLU cc_start: 0.8784 (tp30) cc_final: 0.8516 (tp30) REVERT: C 116 LEU cc_start: 0.6461 (mp) cc_final: 0.5966 (tt) REVERT: C 151 MET cc_start: 0.6540 (mmt) cc_final: 0.2617 (tmt) REVERT: C 213 PHE cc_start: 0.8083 (m-80) cc_final: 0.7870 (m-80) REVERT: C 354 ARG cc_start: 0.6416 (ptm-80) cc_final: 0.6073 (ptm-80) REVERT: A 34 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 116 LEU cc_start: 0.7903 (tp) cc_final: 0.7408 (mp) REVERT: A 120 ASN cc_start: 0.7639 (m-40) cc_final: 0.6815 (t0) REVERT: A 175 MET cc_start: 0.2487 (pmt) cc_final: 0.1950 (mmp) REVERT: A 223 LEU cc_start: 0.8472 (tp) cc_final: 0.8170 (tt) REVERT: A 234 ARG cc_start: 0.7557 (mmt90) cc_final: 0.7221 (mmm-85) REVERT: E 50 CYS cc_start: 0.3454 (OUTLIER) cc_final: 0.2719 (m) REVERT: F 83 MET cc_start: 0.0333 (mmt) cc_final: -0.2175 (ptp) REVERT: D 34 THR cc_start: 0.3821 (OUTLIER) cc_final: 0.3447 (p) outliers start: 45 outliers final: 18 residues processed: 186 average time/residue: 1.1129 time to fit residues: 260.7321 Evaluate side-chains 169 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 3.022 ------------------------------------------------------------------------------- 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 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 578 LEU 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 970 SER 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 353 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 120 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 340 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 B 951 ASN B1070 ASN C 988 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 = 0.4196 r_free = 0.4196 target = 0.152384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083548 restraints weight = 54177.149| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.59 r_work: 0.2849 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29785 Z= 0.109 Angle : 0.584 9.048 40591 Z= 0.289 Chirality : 0.045 0.372 4603 Planarity : 0.004 0.068 5201 Dihedral : 5.531 56.665 4614 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 1.29 % Allowed : 10.07 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3633 helix: 1.99 (0.20), residues: 681 sheet: 0.49 (0.18), residues: 833 loop : -1.84 (0.12), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 433 HIS 0.004 0.001 HIS D 32 PHE 0.024 0.001 PHE C 66 TYR 0.038 0.001 TYR C 38 ARG 0.006 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 16) link_NAG-ASN : angle 2.35373 ( 48) link_BETA1-4 : bond 0.00461 ( 16) link_BETA1-4 : angle 1.75894 ( 48) hydrogen bonds : bond 0.04181 ( 983) hydrogen bonds : angle 4.57136 ( 2745) SS BOND : bond 0.00313 ( 31) SS BOND : angle 1.13168 ( 62) covalent geometry : bond 0.00257 (29722) covalent geometry : angle 0.57431 (40433) *********************** 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 194 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7553 (m-10) cc_final: 0.7200 (m-90) REVERT: B 151 MET cc_start: 0.3580 (mpp) cc_final: 0.2956 (tmt) REVERT: B 175 MET cc_start: 0.3250 (OUTLIER) cc_final: 0.2961 (pmm) REVERT: B 192 PHE cc_start: 0.8121 (m-10) cc_final: 0.7908 (m-10) REVERT: B 344 PHE cc_start: 0.6866 (m-10) cc_final: 0.6365 (m-80) REVERT: B 418 TYR cc_start: 0.7378 (m-10) cc_final: 0.6983 (m-10) REVERT: B 512 GLU cc_start: 0.8834 (tp30) cc_final: 0.8442 (tp30) REVERT: B 782 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8736 (mptt) REVERT: B 998 GLN cc_start: 0.8552 (tp40) cc_final: 0.8243 (tt0) REVERT: C 116 LEU cc_start: 0.6232 (mp) cc_final: 0.5778 (tt) REVERT: C 151 MET cc_start: 0.6487 (mmt) cc_final: 0.2567 (tmt) REVERT: C 198 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.8090 (t80) REVERT: C 213 PHE cc_start: 0.8070 (m-80) cc_final: 0.7821 (m-80) REVERT: C 324 VAL cc_start: 0.7933 (t) cc_final: 0.7707 (p) REVERT: C 354 ARG cc_start: 0.6842 (ptm-80) cc_final: 0.6583 (ptm-80) REVERT: C 387 LEU cc_start: 0.7042 (tt) cc_final: 0.6507 (tt) REVERT: C 570 ASP cc_start: 0.7387 (m-30) cc_final: 0.7065 (t0) REVERT: A 34 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 116 LEU cc_start: 0.7884 (tp) cc_final: 0.7391 (mp) REVERT: A 120 ASN cc_start: 0.7805 (m-40) cc_final: 0.6884 (t0) REVERT: A 132 PHE cc_start: 0.7831 (m-80) cc_final: 0.7603 (m-80) REVERT: A 175 MET cc_start: 0.2412 (pmt) cc_final: 0.2031 (mmp) REVERT: A 223 LEU cc_start: 0.8480 (tp) cc_final: 0.8193 (tt) REVERT: A 234 ARG cc_start: 0.7358 (mmt90) cc_final: 0.6903 (mmm-85) REVERT: E 50 CYS cc_start: 0.2427 (OUTLIER) cc_final: 0.1812 (m) REVERT: F 83 MET cc_start: 0.0363 (mmt) cc_final: -0.2094 (ptp) REVERT: D 34 THR cc_start: 0.3756 (OUTLIER) cc_final: 0.3394 (p) outliers start: 41 outliers final: 14 residues processed: 180 average time/residue: 1.1033 time to fit residues: 246.9152 Evaluate side-chains 163 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 3.019 ------------------------------------------------------------------------------- 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 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 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 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 185 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 260 optimal weight: 30.0000 chunk 165 optimal weight: 0.0980 chunk 205 optimal weight: 0.8980 chunk 258 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 156 optimal weight: 0.0270 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 236 GLN B 242 ASN B 951 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.154846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083771 restraints weight = 53076.904| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.44 r_work: 0.2890 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29785 Z= 0.104 Angle : 0.570 10.016 40591 Z= 0.281 Chirality : 0.044 0.359 4603 Planarity : 0.004 0.068 5201 Dihedral : 5.240 55.984 4614 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 1.10 % Allowed : 10.70 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3633 helix: 2.17 (0.21), residues: 679 sheet: 0.56 (0.18), residues: 832 loop : -1.78 (0.12), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 433 HIS 0.004 0.001 HIS E 30 PHE 0.024 0.001 PHE B 126 TYR 0.032 0.001 TYR A 168 ARG 0.007 0.000 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 16) link_NAG-ASN : angle 2.31830 ( 48) link_BETA1-4 : bond 0.00371 ( 16) link_BETA1-4 : angle 1.66675 ( 48) hydrogen bonds : bond 0.03871 ( 983) hydrogen bonds : angle 4.40481 ( 2745) SS BOND : bond 0.00286 ( 31) SS BOND : angle 1.00015 ( 62) covalent geometry : bond 0.00247 (29722) covalent geometry : angle 0.56151 (40433) *********************** 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 182 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7660 (m-10) cc_final: 0.7422 (m-90) REVERT: B 151 MET cc_start: 0.3638 (mpp) cc_final: 0.2849 (tmt) REVERT: B 175 MET cc_start: 0.3203 (OUTLIER) cc_final: 0.2968 (pmm) REVERT: B 266 TYR cc_start: 0.8405 (m-80) cc_final: 0.8204 (m-80) REVERT: B 344 PHE cc_start: 0.6970 (m-10) cc_final: 0.6616 (m-80) REVERT: B 418 TYR cc_start: 0.7376 (m-10) cc_final: 0.6987 (m-10) REVERT: B 512 GLU cc_start: 0.8864 (tp30) cc_final: 0.8511 (tp30) REVERT: B 782 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8705 (mptt) REVERT: B 998 GLN cc_start: 0.8568 (tp40) cc_final: 0.8332 (tt0) REVERT: B 1013 GLU cc_start: 0.8654 (tt0) cc_final: 0.8392 (tp30) REVERT: C 116 LEU cc_start: 0.6281 (mp) cc_final: 0.5809 (tt) REVERT: C 151 MET cc_start: 0.6409 (mmt) cc_final: 0.2449 (tmt) REVERT: C 192 PHE cc_start: 0.7585 (m-10) cc_final: 0.7349 (m-10) REVERT: C 213 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: C 324 VAL cc_start: 0.8009 (t) cc_final: 0.7798 (p) REVERT: C 354 ARG cc_start: 0.6908 (ptm-80) cc_final: 0.6597 (ptm-80) REVERT: C 387 LEU cc_start: 0.7247 (tt) cc_final: 0.6741 (tt) REVERT: A 34 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8711 (m) REVERT: A 116 LEU cc_start: 0.7886 (tp) cc_final: 0.7355 (mp) REVERT: A 120 ASN cc_start: 0.7822 (m-40) cc_final: 0.6878 (t0) REVERT: A 132 PHE cc_start: 0.7778 (m-80) cc_final: 0.7221 (m-80) REVERT: A 175 MET cc_start: 0.2483 (pmt) cc_final: 0.2061 (mmp) REVERT: A 223 LEU cc_start: 0.8502 (tp) cc_final: 0.8257 (tt) REVERT: A 234 ARG cc_start: 0.7314 (mmt90) cc_final: 0.6872 (mmm-85) REVERT: E 50 CYS cc_start: 0.2560 (OUTLIER) cc_final: 0.2032 (m) REVERT: E 90 ASP cc_start: 0.6611 (p0) cc_final: 0.6406 (p0) REVERT: F 83 MET cc_start: 0.0310 (mmt) cc_final: -0.2145 (ptp) REVERT: D 34 THR cc_start: 0.3640 (OUTLIER) cc_final: 0.3346 (p) outliers start: 35 outliers final: 17 residues processed: 173 average time/residue: 1.0276 time to fit residues: 221.8416 Evaluate side-chains 163 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 3.221 ------------------------------------------------------------------------------- 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 C residue 213 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 THR 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 970 SER 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 E residue 50 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 238 optimal weight: 9.9990 chunk 259 optimal weight: 0.5980 chunk 35 optimal weight: 0.0040 chunk 344 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 336 optimal weight: 50.0000 chunk 332 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 252 optimal weight: 0.1980 chunk 247 optimal weight: 6.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 951 ASN 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 = 0.4207 r_free = 0.4207 target = 0.156242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.086522 restraints weight = 52507.318| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.66 r_work: 0.2873 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29785 Z= 0.108 Angle : 0.568 10.589 40591 Z= 0.279 Chirality : 0.044 0.361 4603 Planarity : 0.004 0.079 5201 Dihedral : 5.139 55.682 4614 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Rotamer: Outliers : 0.98 % Allowed : 11.43 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3633 helix: 2.22 (0.21), residues: 677 sheet: 0.60 (0.18), residues: 832 loop : -1.74 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 433 HIS 0.004 0.001 HIS E 30 PHE 0.025 0.001 PHE A 851 TYR 0.030 0.001 TYR B 168 ARG 0.007 0.000 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 16) link_NAG-ASN : angle 2.30861 ( 48) link_BETA1-4 : bond 0.00413 ( 16) link_BETA1-4 : angle 1.60196 ( 48) hydrogen bonds : bond 0.03865 ( 983) hydrogen bonds : angle 4.36694 ( 2745) SS BOND : bond 0.00280 ( 31) SS BOND : angle 0.99117 ( 62) covalent geometry : bond 0.00261 (29722) covalent geometry : angle 0.55961 (40433) *********************** 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 175 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3697 (mpp) cc_final: 0.2904 (tmt) REVERT: B 344 PHE cc_start: 0.7046 (m-10) cc_final: 0.6598 (m-80) REVERT: B 418 TYR cc_start: 0.7296 (m-10) cc_final: 0.6973 (m-10) REVERT: B 512 GLU cc_start: 0.8833 (tp30) cc_final: 0.8448 (tp30) REVERT: B 782 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8753 (mptt) REVERT: B 998 GLN cc_start: 0.8532 (tp40) cc_final: 0.8281 (tt0) REVERT: B 1013 GLU cc_start: 0.8643 (tt0) cc_final: 0.8337 (tp30) REVERT: C 116 LEU cc_start: 0.6235 (mp) cc_final: 0.5788 (tt) REVERT: C 151 MET cc_start: 0.6429 (mmt) cc_final: 0.2455 (tmt) REVERT: C 324 VAL cc_start: 0.7910 (t) cc_final: 0.7674 (p) REVERT: C 354 ARG cc_start: 0.6873 (ptm-80) cc_final: 0.6566 (ptm-80) REVERT: C 387 LEU cc_start: 0.7153 (tt) cc_final: 0.6653 (tt) REVERT: C 431 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7426 (pp) REVERT: A 34 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8694 (m) REVERT: A 120 ASN cc_start: 0.7820 (m-40) cc_final: 0.6821 (t0) REVERT: A 132 PHE cc_start: 0.7800 (m-80) cc_final: 0.7287 (m-80) REVERT: A 175 MET cc_start: 0.2444 (pmt) cc_final: 0.2064 (mmp) REVERT: A 223 LEU cc_start: 0.8473 (tp) cc_final: 0.8244 (tt) REVERT: A 234 ARG cc_start: 0.7237 (mmt90) cc_final: 0.6822 (mmm-85) REVERT: E 50 CYS cc_start: 0.2061 (OUTLIER) cc_final: 0.1792 (m) REVERT: F 83 MET cc_start: 0.0458 (mmt) cc_final: -0.2062 (ptp) outliers start: 31 outliers final: 18 residues processed: 167 average time/residue: 1.1300 time to fit residues: 236.4176 Evaluate side-chains 161 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 431 ILE 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 927 ILE 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 E residue 50 CYS Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 239 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.155138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.084873 restraints weight = 52232.003| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.87 r_work: 0.2842 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29785 Z= 0.138 Angle : 0.593 11.431 40591 Z= 0.291 Chirality : 0.045 0.393 4603 Planarity : 0.004 0.071 5201 Dihedral : 5.186 57.206 4614 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 0.91 % Allowed : 11.71 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3633 helix: 2.14 (0.21), residues: 680 sheet: 0.55 (0.18), residues: 833 loop : -1.76 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 433 HIS 0.004 0.001 HIS E 30 PHE 0.024 0.001 PHE B 126 TYR 0.024 0.001 TYR C 168 ARG 0.006 0.000 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 16) link_NAG-ASN : angle 2.38000 ( 48) link_BETA1-4 : bond 0.00308 ( 16) link_BETA1-4 : angle 1.61760 ( 48) hydrogen bonds : bond 0.04324 ( 983) hydrogen bonds : angle 4.40981 ( 2745) SS BOND : bond 0.00314 ( 31) SS BOND : angle 1.16798 ( 62) covalent geometry : bond 0.00338 (29722) covalent geometry : angle 0.58395 (40433) *********************** 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 174 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3550 (mpp) cc_final: 0.2709 (tmt) REVERT: B 344 PHE cc_start: 0.7321 (m-10) cc_final: 0.6861 (m-80) REVERT: B 418 TYR cc_start: 0.7279 (m-10) cc_final: 0.7043 (m-10) REVERT: B 512 GLU cc_start: 0.8803 (tp30) cc_final: 0.8384 (tp30) REVERT: B 998 GLN cc_start: 0.8605 (tp40) cc_final: 0.8339 (tt0) REVERT: C 116 LEU cc_start: 0.6281 (mp) cc_final: 0.5830 (tt) REVERT: C 151 MET cc_start: 0.6486 (mmt) cc_final: 0.2662 (tmt) REVERT: C 324 VAL cc_start: 0.7963 (t) cc_final: 0.7734 (p) REVERT: C 354 ARG cc_start: 0.6864 (ptm-80) cc_final: 0.6559 (ptm-80) REVERT: C 387 LEU cc_start: 0.7216 (tt) cc_final: 0.6682 (tt) REVERT: C 431 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7436 (pp) REVERT: C 570 ASP cc_start: 0.7448 (m-30) cc_final: 0.7184 (t0) REVERT: A 34 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8717 (m) REVERT: A 120 ASN cc_start: 0.7871 (m-40) cc_final: 0.6851 (t0) REVERT: A 175 MET cc_start: 0.2471 (pmt) cc_final: 0.2075 (mmp) REVERT: A 223 LEU cc_start: 0.8483 (tp) cc_final: 0.8283 (tt) REVERT: A 234 ARG cc_start: 0.7328 (mmt90) cc_final: 0.6893 (mmm-85) REVERT: E 50 CYS cc_start: 0.2449 (OUTLIER) cc_final: 0.1756 (m) REVERT: F 83 MET cc_start: 0.0468 (mmt) cc_final: -0.2063 (ptp) outliers start: 29 outliers final: 16 residues processed: 167 average time/residue: 1.0426 time to fit residues: 216.9179 Evaluate side-chains 159 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 431 ILE 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 927 ILE 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 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain E residue 50 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 316 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 197 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088245 restraints weight = 51363.452| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.84 r_work: 0.2864 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29785 Z= 0.106 Angle : 0.575 11.942 40591 Z= 0.282 Chirality : 0.045 0.364 4603 Planarity : 0.004 0.066 5201 Dihedral : 5.082 55.614 4614 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 0.72 % Allowed : 12.02 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3633 helix: 2.21 (0.21), residues: 680 sheet: 0.63 (0.18), residues: 831 loop : -1.74 (0.12), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 433 HIS 0.004 0.001 HIS E 30 PHE 0.025 0.001 PHE A 851 TYR 0.027 0.001 TYR B 168 ARG 0.012 0.000 ARG B 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 16) link_NAG-ASN : angle 2.33040 ( 48) link_BETA1-4 : bond 0.00400 ( 16) link_BETA1-4 : angle 1.56178 ( 48) hydrogen bonds : bond 0.03861 ( 983) hydrogen bonds : angle 4.32362 ( 2745) SS BOND : bond 0.00262 ( 31) SS BOND : angle 0.99139 ( 62) covalent geometry : bond 0.00256 (29722) covalent geometry : angle 0.56615 (40433) ********************** 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 165 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3579 (mpp) cc_final: 0.2758 (tmt) REVERT: B 266 TYR cc_start: 0.8227 (m-80) cc_final: 0.7998 (m-80) REVERT: B 344 PHE cc_start: 0.7355 (m-10) cc_final: 0.6926 (m-80) REVERT: B 418 TYR cc_start: 0.7271 (m-10) cc_final: 0.7046 (m-10) REVERT: B 512 GLU cc_start: 0.8790 (tp30) cc_final: 0.8417 (tp30) REVERT: B 998 GLN cc_start: 0.8559 (tp40) cc_final: 0.8297 (tt0) REVERT: B 1013 GLU cc_start: 0.8653 (tt0) cc_final: 0.8338 (tp30) REVERT: C 116 LEU cc_start: 0.6225 (mp) cc_final: 0.5784 (tt) REVERT: C 151 MET cc_start: 0.6476 (mmt) cc_final: 0.2663 (tmt) REVERT: C 175 MET cc_start: 0.0499 (mmm) cc_final: 0.0053 (mmm) REVERT: C 324 VAL cc_start: 0.7871 (t) cc_final: 0.7636 (p) REVERT: C 354 ARG cc_start: 0.6905 (ptm-80) cc_final: 0.6588 (ptm-80) REVERT: C 387 LEU cc_start: 0.7132 (tt) cc_final: 0.6608 (tt) REVERT: C 431 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7426 (pp) REVERT: A 34 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8695 (m) REVERT: A 120 ASN cc_start: 0.7854 (m-40) cc_final: 0.6753 (t0) REVERT: A 175 MET cc_start: 0.2445 (pmt) cc_final: 0.2085 (mmp) REVERT: A 234 ARG cc_start: 0.7230 (mmt90) cc_final: 0.6796 (mmm-85) REVERT: E 50 CYS cc_start: 0.2246 (OUTLIER) cc_final: 0.1883 (m) REVERT: F 83 MET cc_start: 0.0374 (mmt) cc_final: -0.2131 (ptp) outliers start: 23 outliers final: 13 residues processed: 159 average time/residue: 1.1601 time to fit residues: 232.6296 Evaluate side-chains 152 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 431 ILE 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 927 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain E residue 50 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 112 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 chunk 258 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 327 optimal weight: 30.0000 chunk 184 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- 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 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.152187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.083760 restraints weight = 52839.692| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.11 r_work: 0.2787 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29785 Z= 0.188 Angle : 0.636 11.753 40591 Z= 0.313 Chirality : 0.047 0.433 4603 Planarity : 0.004 0.066 5201 Dihedral : 5.325 58.896 4614 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 0.79 % Allowed : 12.15 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3633 helix: 2.04 (0.21), residues: 682 sheet: 0.56 (0.18), residues: 810 loop : -1.78 (0.12), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 433 HIS 0.005 0.001 HIS A1054 PHE 0.025 0.002 PHE B 126 TYR 0.029 0.001 TYR B 38 ARG 0.006 0.000 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 16) link_NAG-ASN : angle 2.50232 ( 48) link_BETA1-4 : bond 0.00337 ( 16) link_BETA1-4 : angle 1.67697 ( 48) hydrogen bonds : bond 0.04977 ( 983) hydrogen bonds : angle 4.52005 ( 2745) SS BOND : bond 0.00405 ( 31) SS BOND : angle 1.38074 ( 62) covalent geometry : bond 0.00461 (29722) covalent geometry : angle 0.62623 (40433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21170.33 seconds wall clock time: 364 minutes 58.32 seconds (21898.32 seconds total)