Starting phenix.real_space_refine on Tue Jun 24 22:53:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co8_45773/06_2025/9co8_45773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co8_45773/06_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_45773/06_2025/9co8_45773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co8_45773/06_2025/9co8_45773.map" model { file = "/net/cci-nas-00/data/ceres_data/9co8_45773/06_2025/9co8_45773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co8_45773/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.90, per 1000 atoms: 0.58 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: 7.07 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: 4.09 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: 12.13 Time building geometry restraints manager: 8.39 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: 4.170 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: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 65.220 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.180 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.110 ------------------------------------------------------------------------------- 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 : 2.848 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: 1.1896 time to fit residues: 398.2238 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 : 2.781 ------------------------------------------------------------------------------- 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 = 0.153002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082648 restraints weight = 54695.142| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.28 r_work: 0.2907 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3628 (mpp) cc_final: 0.3036 (tmt) REVERT: B 175 MET cc_start: 0.2957 (OUTLIER) cc_final: 0.2691 (pmm) REVERT: B 399 ILE cc_start: 0.8304 (pt) cc_final: 0.8072 (pt) REVERT: B 782 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8524 (mptt) REVERT: B 1013 GLU cc_start: 0.8724 (tt0) cc_final: 0.8386 (tp30) REVERT: C 116 LEU cc_start: 0.6405 (mp) cc_final: 0.5999 (tt) REVERT: C 375 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7884 (mmmt) REVERT: C 387 LEU cc_start: 0.6823 (tt) cc_final: 0.6479 (tt) REVERT: A 34 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8769 (m) REVERT: A 116 LEU cc_start: 0.7847 (tp) cc_final: 0.7503 (mp) REVERT: A 120 ASN cc_start: 0.7651 (m-40) cc_final: 0.7164 (t0) REVERT: A 175 MET cc_start: 0.2181 (pmt) cc_final: 0.1735 (mmp) REVERT: A 223 LEU cc_start: 0.8313 (tp) cc_final: 0.8009 (tt) REVERT: A 327 PRO cc_start: 0.5411 (Cg_exo) cc_final: 0.4513 (Cg_endo) REVERT: A 736 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8507 (ttp) REVERT: A 776 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8222 (mm-30) REVERT: E 70 ILE cc_start: 0.6862 (tt) cc_final: 0.6470 (tp) REVERT: E 83 MET cc_start: 0.4511 (mmp) cc_final: 0.4258 (mmp) REVERT: D 34 THR cc_start: 0.3785 (OUTLIER) cc_final: 0.3416 (p) outliers start: 36 outliers final: 7 residues processed: 201 average time/residue: 1.0117 time to fit residues: 255.7661 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 : 3.209 ------------------------------------------------------------------------------- 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: 0.3980 chunk 186 optimal weight: 2.9990 chunk 335 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 206 optimal weight: 0.4980 chunk 332 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 191 optimal weight: 0.3980 chunk 168 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 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 144 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 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 = 0.4202 r_free = 0.4202 target = 0.152438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082274 restraints weight = 54431.877| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.23 r_work: 0.2914 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29785 Z= 0.121 Angle : 0.606 9.714 40591 Z= 0.303 Chirality : 0.046 0.372 4603 Planarity : 0.004 0.067 5201 Dihedral : 5.721 59.198 4614 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 1.16 % Allowed : 7.08 % Favored : 91.75 % 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: -1.02 (0.13), residues: 3633 helix: 1.38 (0.20), residues: 685 sheet: 0.45 (0.17), residues: 837 loop : -1.99 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 65 HIS 0.006 0.001 HIS E 30 PHE 0.027 0.001 PHE C 66 TYR 0.022 0.001 TYR B 366 ARG 0.011 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 16) link_NAG-ASN : angle 2.42420 ( 48) link_BETA1-4 : bond 0.00482 ( 16) link_BETA1-4 : angle 2.02144 ( 48) hydrogen bonds : bond 0.04361 ( 983) hydrogen bonds : angle 4.90067 ( 2745) SS BOND : bond 0.00415 ( 31) SS BOND : angle 1.30214 ( 62) covalent geometry : bond 0.00289 (29722) covalent geometry : angle 0.59527 (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 195 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3681 (mpp) cc_final: 0.3077 (tmt) REVERT: B 175 MET cc_start: 0.2973 (OUTLIER) cc_final: 0.2704 (pmm) REVERT: B 344 PHE cc_start: 0.6153 (m-10) cc_final: 0.5917 (m-10) REVERT: B 371 PHE cc_start: 0.8009 (m-80) cc_final: 0.7804 (m-80) REVERT: B 512 GLU cc_start: 0.8665 (tp30) cc_final: 0.8447 (tp30) REVERT: B 782 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8557 (mptt) REVERT: B 1013 GLU cc_start: 0.8706 (tt0) cc_final: 0.8386 (tp30) REVERT: C 116 LEU cc_start: 0.6546 (mp) cc_final: 0.6082 (tt) REVERT: C 194 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7892 (m110) REVERT: C 324 VAL cc_start: 0.7936 (t) cc_final: 0.7687 (p) REVERT: C 375 LYS cc_start: 0.8222 (mmmm) cc_final: 0.7976 (mmmt) REVERT: C 387 LEU cc_start: 0.7151 (tt) cc_final: 0.6732 (tt) REVERT: A 34 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8787 (m) REVERT: A 116 LEU cc_start: 0.7936 (tp) cc_final: 0.7524 (mp) REVERT: A 120 ASN cc_start: 0.7668 (m-40) cc_final: 0.7058 (t0) REVERT: A 175 MET cc_start: 0.2339 (pmt) cc_final: 0.1776 (mmp) REVERT: A 223 LEU cc_start: 0.8393 (tp) cc_final: 0.8110 (tt) REVERT: A 224 VAL cc_start: 0.8509 (t) cc_final: 0.7960 (p) REVERT: A 736 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8516 (ttp) REVERT: A 776 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 782 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8641 (mptt) REVERT: E 51 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7145 (mm) REVERT: F 83 MET cc_start: 0.0707 (mmt) cc_final: -0.2013 (ptp) REVERT: D 34 THR cc_start: 0.3875 (OUTLIER) cc_final: 0.3526 (p) outliers start: 37 outliers final: 9 residues processed: 182 average time/residue: 1.0568 time to fit residues: 238.5796 Evaluate side-chains 159 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 3.279 ------------------------------------------------------------------------------- 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 734 CYS Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 898 MET 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: 0.0980 chunk 341 optimal weight: 50.0000 chunk 314 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 154 optimal weight: 50.0000 chunk 60 optimal weight: 0.1980 chunk 81 optimal weight: 0.7980 chunk 279 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 258 optimal weight: 40.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 406 GLN B 998 GLN B1001 GLN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 GLN A1001 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084371 restraints weight = 55018.347| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.42 r_work: 0.2922 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 29785 Z= 0.104 Angle : 0.578 8.750 40591 Z= 0.288 Chirality : 0.045 0.350 4603 Planarity : 0.004 0.067 5201 Dihedral : 5.450 57.242 4614 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 1.10 % Allowed : 8.25 % Favored : 90.65 % 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: -0.80 (0.14), residues: 3633 helix: 1.77 (0.20), residues: 687 sheet: 0.54 (0.18), residues: 830 loop : -1.89 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 433 HIS 0.006 0.001 HIS E 32 PHE 0.041 0.001 PHE A 213 TYR 0.031 0.001 TYR B 38 ARG 0.007 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 16) link_NAG-ASN : angle 2.24550 ( 48) link_BETA1-4 : bond 0.00501 ( 16) link_BETA1-4 : angle 1.80526 ( 48) hydrogen bonds : bond 0.03837 ( 983) hydrogen bonds : angle 4.66047 ( 2745) SS BOND : bond 0.00578 ( 31) SS BOND : angle 1.32302 ( 62) covalent geometry : bond 0.00243 (29722) covalent geometry : angle 0.56869 (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 187 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 2.923 Fit side-chains revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7322 (m-10) cc_final: 0.7014 (m-10) REVERT: B 151 MET cc_start: 0.3768 (mpp) cc_final: 0.3112 (tmt) REVERT: B 175 MET cc_start: 0.3081 (OUTLIER) cc_final: 0.2816 (pmm) REVERT: B 205 HIS cc_start: 0.5661 (m170) cc_final: 0.5263 (m170) REVERT: B 344 PHE cc_start: 0.6379 (m-10) cc_final: 0.6126 (m-10) REVERT: B 418 TYR cc_start: 0.7197 (m-10) cc_final: 0.6759 (m-10) REVERT: B 512 GLU cc_start: 0.8718 (tp30) cc_final: 0.8436 (tp30) REVERT: B 782 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8610 (mptt) REVERT: B 1013 GLU cc_start: 0.8651 (tt0) cc_final: 0.8349 (tp30) REVERT: C 116 LEU cc_start: 0.6480 (mp) cc_final: 0.6031 (tt) REVERT: C 194 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7834 (m110) REVERT: C 324 VAL cc_start: 0.7905 (t) cc_final: 0.7677 (p) REVERT: C 375 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8191 (mmmt) REVERT: C 387 LEU cc_start: 0.7109 (tt) cc_final: 0.6669 (tt) REVERT: A 34 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8758 (m) REVERT: A 116 LEU cc_start: 0.7935 (tp) cc_final: 0.7489 (mp) REVERT: A 120 ASN cc_start: 0.7573 (m-40) cc_final: 0.6862 (t0) REVERT: A 175 MET cc_start: 0.2490 (pmt) cc_final: 0.2068 (mmp) REVERT: A 223 LEU cc_start: 0.8446 (tp) cc_final: 0.8142 (tt) REVERT: A 736 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8496 (ttp) REVERT: A 776 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 782 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8677 (mptt) REVERT: F 83 MET cc_start: 0.0254 (mmt) cc_final: -0.2226 (ptp) REVERT: D 34 THR cc_start: 0.3927 (OUTLIER) cc_final: 0.3543 (p) outliers start: 35 outliers final: 9 residues processed: 174 average time/residue: 1.0608 time to fit residues: 230.3326 Evaluate side-chains 161 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 3.011 ------------------------------------------------------------------------------- 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 734 CYS Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 194 ASN 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 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 A residue 736 MET 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: 7.9990 chunk 41 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 336 optimal weight: 40.0000 chunk 13 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 536 ASN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 GLN C1131 ASN A 489 GLN A1001 GLN A1131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.148157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077714 restraints weight = 54137.162| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.73 r_work: 0.2763 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 29785 Z= 0.266 Angle : 0.698 8.659 40591 Z= 0.350 Chirality : 0.050 0.501 4603 Planarity : 0.005 0.067 5201 Dihedral : 5.877 58.754 4614 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.17 % Favored : 94.69 % Rotamer: Outliers : 1.45 % Allowed : 9.13 % Favored : 89.42 % 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: -0.91 (0.14), residues: 3633 helix: 1.55 (0.20), residues: 683 sheet: 0.43 (0.18), residues: 820 loop : -1.88 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 433 HIS 0.008 0.002 HIS C1054 PHE 0.030 0.002 PHE A 213 TYR 0.038 0.002 TYR B 38 ARG 0.007 0.001 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 16) link_NAG-ASN : angle 2.70894 ( 48) link_BETA1-4 : bond 0.00345 ( 16) link_BETA1-4 : angle 2.04490 ( 48) hydrogen bonds : bond 0.06114 ( 983) hydrogen bonds : angle 4.97726 ( 2745) SS BOND : bond 0.00486 ( 31) SS BOND : angle 1.75843 ( 62) covalent geometry : bond 0.00655 (29722) covalent geometry : angle 0.68606 (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 205 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 2.869 Fit side-chains revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7622 (m-10) cc_final: 0.7292 (m-90) REVERT: B 151 MET cc_start: 0.3644 (mpp) cc_final: 0.3049 (tmt) REVERT: B 175 MET cc_start: 0.3162 (OUTLIER) cc_final: 0.2871 (pmm) REVERT: B 344 PHE cc_start: 0.7473 (m-10) cc_final: 0.7083 (m-80) REVERT: B 418 TYR cc_start: 0.7419 (m-10) cc_final: 0.7024 (m-10) REVERT: B 512 GLU cc_start: 0.8790 (tp30) cc_final: 0.8519 (tp30) REVERT: C 116 LEU cc_start: 0.6456 (mp) cc_final: 0.5963 (tt) REVERT: C 151 MET cc_start: 0.6457 (mmt) cc_final: 0.2613 (tmt) REVERT: C 194 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7907 (m110) REVERT: C 213 PHE cc_start: 0.7961 (m-80) cc_final: 0.7756 (m-80) REVERT: C 986 GLU cc_start: 0.8275 (pp20) cc_final: 0.8039 (pp20) REVERT: A 34 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8718 (m) REVERT: A 116 LEU cc_start: 0.7911 (tp) cc_final: 0.7426 (mp) REVERT: A 120 ASN cc_start: 0.7592 (m-40) cc_final: 0.6804 (t0) REVERT: A 175 MET cc_start: 0.2442 (pmt) cc_final: 0.1863 (mmp) REVERT: A 223 LEU cc_start: 0.8452 (tp) cc_final: 0.8154 (tt) REVERT: A 234 ARG cc_start: 0.7554 (mmt90) cc_final: 0.7223 (mmm-85) REVERT: E 50 CYS cc_start: 0.3281 (OUTLIER) cc_final: 0.2639 (m) REVERT: F 83 MET cc_start: 0.0358 (mmt) cc_final: -0.2165 (ptp) REVERT: D 34 THR cc_start: 0.3818 (OUTLIER) cc_final: 0.3448 (p) outliers start: 46 outliers final: 19 residues processed: 190 average time/residue: 1.0336 time to fit residues: 245.2708 Evaluate side-chains 174 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 3.045 ------------------------------------------------------------------------------- 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 194 ASN 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 C residue 970 SER Chi-restraints excluded: chain C residue 991 ARG 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 529 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain 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: 9.9990 chunk 58 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 275 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.0370 chunk 159 optimal weight: 3.9990 chunk 340 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 B1070 ASN C 988 GLN ** 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 = 0.4177 r_free = 0.4177 target = 0.151900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082854 restraints weight = 53953.779| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.93 r_work: 0.2827 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29785 Z= 0.112 Angle : 0.589 9.415 40591 Z= 0.293 Chirality : 0.045 0.373 4603 Planarity : 0.004 0.071 5201 Dihedral : 5.574 57.535 4614 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.49 % Favored : 95.40 % Rotamer: Outliers : 1.16 % Allowed : 10.14 % Favored : 88.70 % 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: 1.96 (0.20), residues: 681 sheet: 0.48 (0.18), residues: 830 loop : -1.82 (0.12), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 433 HIS 0.005 0.001 HIS E 32 PHE 0.028 0.001 PHE A 213 TYR 0.036 0.001 TYR E 110 ARG 0.006 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 16) link_NAG-ASN : angle 2.34982 ( 48) link_BETA1-4 : bond 0.00482 ( 16) link_BETA1-4 : angle 1.77962 ( 48) hydrogen bonds : bond 0.04310 ( 983) hydrogen bonds : angle 4.63263 ( 2745) SS BOND : bond 0.00578 ( 31) SS BOND : angle 1.38640 ( 62) covalent geometry : bond 0.00263 (29722) covalent geometry : angle 0.57929 (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 193 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7731 (m-10) cc_final: 0.7300 (m-90) REVERT: B 151 MET cc_start: 0.3575 (mpp) cc_final: 0.2972 (tmt) REVERT: B 175 MET cc_start: 0.3308 (OUTLIER) cc_final: 0.3014 (pmm) REVERT: B 344 PHE cc_start: 0.7341 (m-10) cc_final: 0.6972 (m-80) REVERT: B 418 TYR cc_start: 0.7368 (m-10) cc_final: 0.6962 (m-10) REVERT: B 512 GLU cc_start: 0.8823 (tp30) cc_final: 0.8441 (tp30) REVERT: B 782 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8748 (mptt) REVERT: B 998 GLN cc_start: 0.8585 (tp40) cc_final: 0.8268 (tt0) REVERT: C 116 LEU cc_start: 0.6247 (mp) cc_final: 0.5793 (tt) REVERT: C 151 MET cc_start: 0.6480 (mmt) cc_final: 0.2565 (tmt) REVERT: C 194 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7838 (m110) REVERT: C 213 PHE cc_start: 0.8042 (m-80) cc_final: 0.7756 (m-80) REVERT: C 324 VAL cc_start: 0.7925 (t) cc_final: 0.7698 (p) REVERT: C 387 LEU cc_start: 0.7013 (tt) cc_final: 0.6497 (tt) REVERT: C 570 ASP cc_start: 0.7436 (m-30) cc_final: 0.7068 (t0) REVERT: C 986 GLU cc_start: 0.8152 (pp20) cc_final: 0.7900 (pp20) REVERT: A 34 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8713 (m) REVERT: A 116 LEU cc_start: 0.7908 (tp) cc_final: 0.7416 (mp) REVERT: A 120 ASN cc_start: 0.7759 (m-40) cc_final: 0.6858 (t0) REVERT: A 132 PHE cc_start: 0.7817 (m-80) cc_final: 0.7616 (m-80) REVERT: A 175 MET cc_start: 0.2502 (pmt) cc_final: 0.2066 (mmp) REVERT: A 223 LEU cc_start: 0.8473 (tp) cc_final: 0.8176 (tt) REVERT: A 234 ARG cc_start: 0.7364 (mmt90) cc_final: 0.6909 (mmm-85) REVERT: A 898 MET cc_start: 0.9111 (mmt) cc_final: 0.8813 (mmt) REVERT: E 50 CYS cc_start: 0.4504 (OUTLIER) cc_final: 0.3488 (m) REVERT: F 83 MET cc_start: 0.0450 (mmt) cc_final: -0.2023 (ptp) REVERT: D 34 THR cc_start: 0.3739 (OUTLIER) cc_final: 0.3379 (p) outliers start: 37 outliers final: 13 residues processed: 181 average time/residue: 1.1273 time to fit residues: 253.2391 Evaluate side-chains 161 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain C residue 194 ASN 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 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 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: 2.9990 chunk 28 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 210 optimal weight: 0.0470 chunk 260 optimal weight: 30.0000 chunk 165 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 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 = 0.4187 r_free = 0.4187 target = 0.152923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080489 restraints weight = 55799.945| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.27 r_work: 0.2874 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29785 Z= 0.117 Angle : 0.579 10.257 40591 Z= 0.286 Chirality : 0.045 0.377 4603 Planarity : 0.004 0.066 5201 Dihedral : 5.363 56.948 4614 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 1.04 % Allowed : 10.92 % Favored : 88.04 % 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: -0.63 (0.14), residues: 3633 helix: 2.10 (0.21), residues: 681 sheet: 0.52 (0.18), residues: 824 loop : -1.77 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 433 HIS 0.005 0.001 HIS B 205 PHE 0.022 0.001 PHE C 66 TYR 0.019 0.001 TYR B 366 ARG 0.008 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 16) link_NAG-ASN : angle 2.34416 ( 48) link_BETA1-4 : bond 0.00388 ( 16) link_BETA1-4 : angle 1.71306 ( 48) hydrogen bonds : bond 0.04172 ( 983) hydrogen bonds : angle 4.49759 ( 2745) SS BOND : bond 0.00295 ( 31) SS BOND : angle 1.12615 ( 62) covalent geometry : bond 0.00283 (29722) covalent geometry : angle 0.56969 (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 181 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7727 (m-10) cc_final: 0.7468 (m-90) REVERT: B 151 MET cc_start: 0.3631 (mpp) cc_final: 0.2914 (tmt) REVERT: B 175 MET cc_start: 0.3275 (OUTLIER) cc_final: 0.2890 (pmm) REVERT: B 344 PHE cc_start: 0.7399 (m-10) cc_final: 0.7012 (m-80) REVERT: B 418 TYR cc_start: 0.7428 (m-10) cc_final: 0.7036 (m-10) REVERT: B 512 GLU cc_start: 0.8857 (tp30) cc_final: 0.8469 (tp30) REVERT: B 998 GLN cc_start: 0.8599 (tp40) cc_final: 0.8324 (tt0) REVERT: C 116 LEU cc_start: 0.6306 (mp) cc_final: 0.5829 (tt) REVERT: C 151 MET cc_start: 0.6458 (mmt) cc_final: 0.2556 (tmt) REVERT: C 194 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7851 (m110) REVERT: C 213 PHE cc_start: 0.7989 (m-80) cc_final: 0.7707 (m-80) REVERT: C 324 VAL cc_start: 0.8016 (t) cc_final: 0.7807 (p) REVERT: C 387 LEU cc_start: 0.7201 (tt) cc_final: 0.6664 (tt) REVERT: C 431 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7335 (pp) REVERT: A 34 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8712 (m) REVERT: A 116 LEU cc_start: 0.7919 (tp) cc_final: 0.7390 (mp) REVERT: A 120 ASN cc_start: 0.7782 (m-40) cc_final: 0.6878 (t0) REVERT: A 132 PHE cc_start: 0.7820 (m-80) cc_final: 0.7560 (m-80) REVERT: A 175 MET cc_start: 0.2378 (pmt) cc_final: 0.1909 (mmp) REVERT: A 223 LEU cc_start: 0.8494 (tp) cc_final: 0.8235 (tt) REVERT: A 234 ARG cc_start: 0.7347 (mmt90) cc_final: 0.6893 (mmm-85) REVERT: E 50 CYS cc_start: 0.3927 (OUTLIER) cc_final: 0.3212 (m) REVERT: F 83 MET cc_start: 0.0342 (mmt) cc_final: -0.2133 (ptp) REVERT: D 34 THR cc_start: 0.3606 (OUTLIER) cc_final: 0.3304 (p) outliers start: 33 outliers final: 15 residues processed: 175 average time/residue: 1.0595 time to fit residues: 232.2601 Evaluate side-chains 162 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 3.133 ------------------------------------------------------------------------------- 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 C residue 194 ASN 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 566 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 111 TYR 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: 0.0050 chunk 259 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 344 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 336 optimal weight: 50.0000 chunk 332 optimal weight: 20.0000 chunk 186 optimal weight: 0.9980 chunk 252 optimal weight: 0.0980 chunk 247 optimal weight: 0.7980 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.150546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.081170 restraints weight = 54454.591| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.47 r_work: 0.2847 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29785 Z= 0.131 Angle : 0.586 10.939 40591 Z= 0.289 Chirality : 0.045 0.382 4603 Planarity : 0.004 0.081 5201 Dihedral : 5.338 56.916 4614 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 1.13 % Allowed : 11.17 % Favored : 87.69 % 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: -0.61 (0.14), residues: 3633 helix: 2.10 (0.21), residues: 681 sheet: 0.54 (0.18), residues: 821 loop : -1.76 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 433 HIS 0.004 0.001 HIS E 32 PHE 0.023 0.001 PHE B 126 TYR 0.032 0.001 TYR E 110 ARG 0.009 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 16) link_NAG-ASN : angle 2.34799 ( 48) link_BETA1-4 : bond 0.00379 ( 16) link_BETA1-4 : angle 1.68843 ( 48) hydrogen bonds : bond 0.04254 ( 983) hydrogen bonds : angle 4.48298 ( 2745) SS BOND : bond 0.00383 ( 31) SS BOND : angle 1.21511 ( 62) covalent geometry : bond 0.00318 (29722) covalent geometry : angle 0.57689 (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 178 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7606 (m-10) cc_final: 0.7373 (m-90) REVERT: B 151 MET cc_start: 0.3602 (mpp) cc_final: 0.2944 (tmt) REVERT: B 175 MET cc_start: 0.3103 (OUTLIER) cc_final: 0.2896 (pmm) REVERT: B 344 PHE cc_start: 0.7523 (m-10) cc_final: 0.7135 (m-80) REVERT: B 418 TYR cc_start: 0.7419 (m-10) cc_final: 0.7025 (m-10) REVERT: B 512 GLU cc_start: 0.8851 (tp30) cc_final: 0.8428 (tp30) REVERT: B 782 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8761 (mptt) REVERT: B 998 GLN cc_start: 0.8555 (tp40) cc_final: 0.8287 (tt0) REVERT: C 116 LEU cc_start: 0.6196 (mp) cc_final: 0.5739 (tt) REVERT: C 151 MET cc_start: 0.6432 (mmt) cc_final: 0.2479 (tmt) REVERT: C 213 PHE cc_start: 0.8019 (m-80) cc_final: 0.7699 (m-80) REVERT: C 324 VAL cc_start: 0.7916 (t) cc_final: 0.7687 (p) REVERT: C 387 LEU cc_start: 0.7102 (tt) cc_final: 0.6545 (tt) REVERT: C 431 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7425 (pp) REVERT: C 570 ASP cc_start: 0.7389 (m-30) cc_final: 0.7083 (t0) REVERT: C 986 GLU cc_start: 0.8162 (pp20) cc_final: 0.7906 (pp20) REVERT: A 34 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8696 (m) REVERT: A 116 LEU cc_start: 0.7851 (tp) cc_final: 0.7336 (mp) REVERT: A 120 ASN cc_start: 0.7804 (m-40) cc_final: 0.6834 (t0) REVERT: A 132 PHE cc_start: 0.7833 (m-80) cc_final: 0.7326 (m-80) REVERT: A 175 MET cc_start: 0.2371 (pmt) cc_final: 0.1942 (mmp) REVERT: A 223 LEU cc_start: 0.8466 (tp) cc_final: 0.8203 (tt) REVERT: A 234 ARG cc_start: 0.7329 (mmt90) cc_final: 0.6901 (mmm-85) REVERT: A 898 MET cc_start: 0.9147 (mmt) cc_final: 0.8747 (mmt) REVERT: E 50 CYS cc_start: 0.4302 (OUTLIER) cc_final: 0.3505 (m) REVERT: E 90 ASP cc_start: 0.6603 (p0) cc_final: 0.6402 (p0) REVERT: F 83 MET cc_start: 0.0245 (mmt) cc_final: -0.2195 (ptp) REVERT: D 34 THR cc_start: 0.3693 (OUTLIER) cc_final: 0.3368 (p) outliers start: 36 outliers final: 18 residues processed: 170 average time/residue: 1.1431 time to fit residues: 241.4214 Evaluate side-chains 166 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain B residue 1067 GLN 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 581 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 239 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 25 optimal weight: 0.0770 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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 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 = 0.4184 r_free = 0.4184 target = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.081283 restraints weight = 54409.405| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.41 r_work: 0.2853 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2528 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= 0.127 Angle : 0.581 10.718 40591 Z= 0.286 Chirality : 0.045 0.385 4603 Planarity : 0.004 0.066 5201 Dihedral : 5.255 56.882 4614 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 1.01 % Allowed : 11.46 % Favored : 87.54 % 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: -0.58 (0.14), residues: 3633 helix: 2.12 (0.21), residues: 682 sheet: 0.56 (0.18), residues: 821 loop : -1.74 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 433 HIS 0.004 0.001 HIS E 32 PHE 0.024 0.001 PHE A 213 TYR 0.026 0.001 TYR C 168 ARG 0.009 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 16) link_NAG-ASN : angle 2.35916 ( 48) link_BETA1-4 : bond 0.00375 ( 16) link_BETA1-4 : angle 1.63837 ( 48) hydrogen bonds : bond 0.04225 ( 983) hydrogen bonds : angle 4.44009 ( 2745) SS BOND : bond 0.00329 ( 31) SS BOND : angle 1.13952 ( 62) covalent geometry : bond 0.00309 (29722) covalent geometry : angle 0.57161 (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 175 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TRP cc_start: 0.7629 (m-10) cc_final: 0.7417 (m-90) REVERT: B 151 MET cc_start: 0.3676 (mpp) cc_final: 0.2934 (tmt) REVERT: B 192 PHE cc_start: 0.8055 (m-10) cc_final: 0.7812 (m-10) REVERT: B 418 TYR cc_start: 0.7410 (m-10) cc_final: 0.7146 (m-10) REVERT: B 512 GLU cc_start: 0.8798 (tp30) cc_final: 0.8401 (tp30) REVERT: B 782 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8734 (mptt) REVERT: B 998 GLN cc_start: 0.8542 (tp40) cc_final: 0.8276 (tt0) REVERT: C 116 LEU cc_start: 0.6215 (mp) cc_final: 0.5755 (tt) REVERT: C 151 MET cc_start: 0.6440 (mmt) cc_final: 0.2530 (tmt) REVERT: C 213 PHE cc_start: 0.8033 (m-80) cc_final: 0.7748 (m-80) REVERT: C 324 VAL cc_start: 0.7870 (t) cc_final: 0.7611 (p) REVERT: C 387 LEU cc_start: 0.7164 (tt) cc_final: 0.6608 (tt) REVERT: C 431 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7472 (pp) REVERT: C 986 GLU cc_start: 0.8146 (pp20) cc_final: 0.7928 (pp20) REVERT: A 34 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8694 (m) REVERT: A 120 ASN cc_start: 0.7830 (m-40) cc_final: 0.6842 (t0) REVERT: A 175 MET cc_start: 0.2466 (pmt) cc_final: 0.2035 (mmp) REVERT: A 223 LEU cc_start: 0.8470 (tp) cc_final: 0.8233 (tt) REVERT: A 234 ARG cc_start: 0.7365 (mmt90) cc_final: 0.6915 (mmm-85) REVERT: A 898 MET cc_start: 0.9138 (mmt) cc_final: 0.8704 (mmt) REVERT: E 50 CYS cc_start: 0.3589 (OUTLIER) cc_final: 0.2959 (m) REVERT: E 90 ASP cc_start: 0.6466 (p0) cc_final: 0.6250 (p0) REVERT: F 83 MET cc_start: 0.0302 (mmt) cc_final: -0.2160 (ptp) REVERT: D 34 THR cc_start: 0.3638 (OUTLIER) cc_final: 0.3326 (p) outliers start: 32 outliers final: 14 residues processed: 168 average time/residue: 1.1073 time to fit residues: 228.6952 Evaluate side-chains 161 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 3.069 ------------------------------------------------------------------------------- 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 520 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain B residue 1067 GLN 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 581 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain D residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 316 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 289 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.153631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083760 restraints weight = 52954.546| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.82 r_work: 0.2832 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29785 Z= 0.132 Angle : 0.591 11.832 40591 Z= 0.291 Chirality : 0.045 0.387 4603 Planarity : 0.004 0.085 5201 Dihedral : 5.249 56.887 4614 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.46 % Rotamer: Outliers : 0.76 % Allowed : 11.87 % 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: -0.58 (0.14), residues: 3633 helix: 2.12 (0.21), residues: 682 sheet: 0.55 (0.18), residues: 825 loop : -1.74 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 433 HIS 0.005 0.001 HIS B 205 PHE 0.026 0.001 PHE A 851 TYR 0.030 0.001 TYR E 110 ARG 0.008 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 16) link_NAG-ASN : angle 2.36525 ( 48) link_BETA1-4 : bond 0.00376 ( 16) link_BETA1-4 : angle 1.63106 ( 48) hydrogen bonds : bond 0.04249 ( 983) hydrogen bonds : angle 4.42619 ( 2745) SS BOND : bond 0.00340 ( 31) SS BOND : angle 1.13709 ( 62) covalent geometry : bond 0.00321 (29722) covalent geometry : angle 0.58249 (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 164 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.3497 (mpp) cc_final: 0.2734 (tmt) REVERT: B 336 HIS cc_start: 0.8672 (p-80) cc_final: 0.8006 (t-170) REVERT: B 418 TYR cc_start: 0.7408 (m-10) cc_final: 0.7142 (m-10) REVERT: B 512 GLU cc_start: 0.8822 (tp30) cc_final: 0.8420 (tp30) REVERT: B 782 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8757 (mptt) REVERT: B 998 GLN cc_start: 0.8622 (tp40) cc_final: 0.8352 (tt0) REVERT: C 116 LEU cc_start: 0.6340 (mp) cc_final: 0.5852 (tt) REVERT: C 151 MET cc_start: 0.6449 (mmt) cc_final: 0.2675 (tmt) REVERT: C 213 PHE cc_start: 0.8056 (m-80) cc_final: 0.7808 (m-80) REVERT: C 324 VAL cc_start: 0.7924 (t) cc_final: 0.7663 (p) REVERT: C 387 LEU cc_start: 0.7145 (tt) cc_final: 0.6569 (tt) REVERT: C 431 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7439 (pp) REVERT: C 570 ASP cc_start: 0.7442 (m-30) cc_final: 0.7177 (t0) REVERT: C 986 GLU cc_start: 0.8189 (pp20) cc_final: 0.7969 (pp20) REVERT: A 34 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8724 (m) REVERT: A 120 ASN cc_start: 0.7922 (m-40) cc_final: 0.6873 (t0) REVERT: A 175 MET cc_start: 0.2484 (pmt) cc_final: 0.2050 (mmp) REVERT: A 223 LEU cc_start: 0.8483 (tp) cc_final: 0.8278 (tt) REVERT: A 234 ARG cc_start: 0.7386 (mmt90) cc_final: 0.6939 (mmm-85) REVERT: E 50 CYS cc_start: 0.3958 (OUTLIER) cc_final: 0.3103 (m) REVERT: E 90 ASP cc_start: 0.6439 (p0) cc_final: 0.6228 (p0) REVERT: F 83 MET cc_start: 0.0484 (mmt) cc_final: -0.2057 (ptp) outliers start: 24 outliers final: 15 residues processed: 158 average time/residue: 1.1832 time to fit residues: 233.8905 Evaluate side-chains 155 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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 520 VAL Chi-restraints excluded: chain B residue 782 LYS Chi-restraints excluded: chain B residue 1067 GLN 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 581 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 111 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 112 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 338 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 327 optimal weight: 30.0000 chunk 184 optimal weight: 0.0270 chunk 93 optimal weight: 3.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.153404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.084478 restraints weight = 52932.384| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.81 r_work: 0.2824 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29785 Z= 0.135 Angle : 0.590 11.993 40591 Z= 0.291 Chirality : 0.045 0.393 4603 Planarity : 0.004 0.075 5201 Dihedral : 5.234 57.090 4614 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 0.69 % Allowed : 11.84 % Favored : 87.47 % 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: 2.10 (0.21), residues: 683 sheet: 0.53 (0.18), residues: 826 loop : -1.75 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 433 HIS 0.004 0.001 HIS E 32 PHE 0.021 0.001 PHE C 192 TYR 0.028 0.001 TYR B 38 ARG 0.008 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 16) link_NAG-ASN : angle 2.38630 ( 48) link_BETA1-4 : bond 0.00373 ( 16) link_BETA1-4 : angle 1.61111 ( 48) hydrogen bonds : bond 0.04333 ( 983) hydrogen bonds : angle 4.43083 ( 2745) SS BOND : bond 0.00324 ( 31) SS BOND : angle 1.13844 ( 62) covalent geometry : bond 0.00330 (29722) covalent geometry : angle 0.58122 (40433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24028.78 seconds wall clock time: 415 minutes 59.31 seconds (24959.31 seconds total)