Starting phenix.real_space_refine on Sat Jun 21 23:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdh_13919/06_2025/7qdh_13919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdh_13919/06_2025/7qdh_13919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qdh_13919/06_2025/7qdh_13919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdh_13919/06_2025/7qdh_13919.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdh_13919/06_2025/7qdh_13919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdh_13919/06_2025/7qdh_13919.cif" } resolution = 4.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 114 5.16 5 C 16372 2.51 5 N 4224 2.21 5 O 5002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25712 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8354 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 1015} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8369 Classifications: {'peptide': 1073} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 53, 'TRANS': 1019} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 8373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8373 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 54, 'TRANS': 1021} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.51, per 1000 atoms: 0.60 Number of scatterers: 25712 At special positions: 0 Unit cell: (162.4, 158.2, 193.2, 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 114 16.00 O 5002 8.00 N 4224 7.00 C 16372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.95 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.73 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.00 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.09 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.79 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.92 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.89 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.99 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.81 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.79 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.77 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.00 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.85 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.00 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.23 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.99 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.88 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.07 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.00 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.06 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 164 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 616 " " NAG E 1 " - " ASN A 717 " " NAG G 1 " - " ASN B 717 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN A 343 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN C 282 " " NAG P 1 " - " ASN C 343 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 3.4 seconds 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.9% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.734A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.509A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.582A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.427A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.957A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.568A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.019A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.507A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.032A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1031 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.919A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.513A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.873A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.541A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.582A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.022A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 829 removed outlier: 3.573A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.729A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.900A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 968 removed outlier: 3.503A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.906A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.609A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.800A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.779A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.573A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.154A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.669A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.649A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 4.008A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.824A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.749A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.923A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.589A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.195A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.990A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.630A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.902A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.510A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.966A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.526A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.501A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.421A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.661A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.684A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.435A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.544A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.913A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.588A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A1080 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.015A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.156A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.770A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.494A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.539A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.400A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.251A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.536A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.799A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 727 removed outlier: 3.928A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.142A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1080 through 1081 removed outlier: 6.446A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.903A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.770A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.646A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.568A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.122A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.633A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 665 through 667 removed outlier: 6.088A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 727 removed outlier: 3.879A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 727 removed outlier: 3.879A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.673A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.79 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.11: 3 1.11 - 1.32: 4505 1.32 - 1.53: 19463 1.53 - 1.75: 2187 1.75 - 1.96: 142 Bond restraints: 26300 Sorted by residual: bond pdb=" C SER B 940 " pdb=" O SER B 940 " ideal model delta sigma weight residual 1.237 0.902 0.334 1.17e-02 7.31e+03 8.17e+02 bond pdb=" C THR B 676 " pdb=" O THR B 676 " ideal model delta sigma weight residual 1.231 0.895 0.336 2.00e-02 2.50e+03 2.82e+02 bond pdb=" C SER A 940 " pdb=" O SER A 940 " ideal model delta sigma weight residual 1.236 1.021 0.214 1.31e-02 5.83e+03 2.68e+02 bond pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 1.456 1.326 0.130 9.80e-03 1.04e+04 1.75e+02 bond pdb=" CA ASN A 343 " pdb=" C ASN A 343 " ideal model delta sigma weight residual 1.526 1.614 -0.088 1.11e-02 8.12e+03 6.27e+01 ... (remaining 26295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 35130 4.42 - 8.85: 619 8.85 - 13.27: 47 13.27 - 17.69: 9 17.69 - 22.12: 2 Bond angle restraints: 35807 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 119.84 141.96 -22.12 1.25e+00 6.40e-01 3.13e+02 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 118.85 130.84 -11.99 1.09e+00 8.42e-01 1.21e+02 angle pdb=" N ALA C 989 " pdb=" CA ALA C 989 " pdb=" C ALA C 989 " ideal model delta sigma weight residual 112.38 100.73 11.65 1.22e+00 6.72e-01 9.12e+01 angle pdb=" N THR B 961 " pdb=" CA THR B 961 " pdb=" C THR B 961 " ideal model delta sigma weight residual 111.14 101.18 9.96 1.08e+00 8.57e-01 8.50e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.84 130.74 -10.90 1.25e+00 6.40e-01 7.61e+01 ... (remaining 35802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 15182 23.87 - 47.74: 881 47.74 - 71.61: 117 71.61 - 95.48: 37 95.48 - 119.35: 8 Dihedral angle restraints: 16225 sinusoidal: 6858 harmonic: 9367 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.45 -84.55 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -1.78 -84.22 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 11.24 81.76 1 1.00e+01 1.00e-02 8.22e+01 ... (remaining 16222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 4057 0.219 - 0.437: 112 0.437 - 0.656: 9 0.656 - 0.875: 3 0.875 - 1.093: 1 Chirality restraints: 4182 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.96e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.91e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.88e+01 ... (remaining 4179 not shown) Planarity restraints: 4619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " 0.003 2.00e-02 2.50e+03 3.17e-02 2.51e+01 pdb=" CG TRP A 64 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 940 " 0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C SER A 940 " -0.081 2.00e-02 2.50e+03 pdb=" O SER A 940 " 0.033 2.00e-02 2.50e+03 pdb=" N THR A 941 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 266 " -0.002 2.00e-02 2.50e+03 3.20e-02 2.04e+01 pdb=" CG TYR A 266 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 266 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 266 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 266 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 266 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 266 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 266 " 0.044 2.00e-02 2.50e+03 ... (remaining 4616 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 54 2.13 - 2.82: 8581 2.82 - 3.52: 36944 3.52 - 4.21: 59039 4.21 - 4.90: 98178 Nonbonded interactions: 202796 Sorted by model distance: nonbonded pdb=" CZ3 TRP C 353 " pdb=" CD1 TYR C 423 " model vdw 1.441 3.640 nonbonded pdb=" O ASP C 420 " pdb=" OD1 ASN C 460 " model vdw 1.591 3.040 nonbonded pdb=" NH1 ARG C 34 " pdb=" OG SER C 221 " model vdw 1.637 3.120 nonbonded pdb=" O ASN B 856 " pdb=" N LEU B 858 " model vdw 1.670 3.120 nonbonded pdb=" OD1 ASP B 578 " pdb=" OG1 THR B 581 " model vdw 1.684 3.040 ... (remaining 202791 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' and (resid 15 through 372 or (resid 373 and (name N or name CA or nam \ e C or name O or name CB )) or resid 374 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 515 or resid 52 \ 3 through 579 or (resid 580 and (name N or name CA or name C or name O or name C \ B )) or resid 581 through 616 or (resid 617 and (name N or name CA or name C or \ name CB or name SG )) or resid 618 through 939 or (resid 940 through 944 and (na \ me N or name CA or name C or name O or name CB )) or resid 945 through 1146 or r \ esid 1301 through 1306)) selection = (chain 'B' and (resid 15 through 372 or (resid 373 and (name N or name CA or nam \ e C or name O or name CB )) or resid 374 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 616 or (resid 6 \ 17 and (name N or name CA or name C or name CB or name SG )) or resid 618 throug \ h 621 or resid 641 through 827 or resid 854 through 939 or (resid 940 through 94 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 945 through \ 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 15 through 515 or resid 523 through 579 or (resid 580 and \ (name N or name CA or name C or name O or name CB )) or resid 581 through 827 or \ resid 854 through 1146 or resid 1301 through 1306)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.890 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: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.450 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.370 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 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 : 0.018 0.893 26386 Z= 1.039 Angle : 1.671 46.266 36017 Z= 0.997 Chirality : 0.096 1.093 4182 Planarity : 0.007 0.062 4587 Dihedral : 14.724 119.353 10077 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 62.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.02 % Favored : 95.61 % Rotamer: Outliers : 7.70 % Allowed : 10.57 % Favored : 81.73 % Cbeta Deviations : 0.53 % 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: 0.10 (0.14), residues: 3187 helix: 2.65 (0.20), residues: 634 sheet: 0.29 (0.21), residues: 616 loop : -0.94 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.005 TRP A 64 HIS 0.019 0.003 HIS B 245 PHE 0.049 0.005 PHE B 329 TYR 0.049 0.005 TYR A 266 ARG 0.030 0.003 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01451 ( 32) link_NAG-ASN : angle 7.39878 ( 96) link_BETA1-4 : bond 0.00312 ( 10) link_BETA1-4 : angle 2.00118 ( 30) hydrogen bonds : bond 0.28264 ( 872) hydrogen bonds : angle 9.68542 ( 2433) SS BOND : bond 0.35443 ( 42) SS BOND : angle 13.24096 ( 84) covalent geometry : bond 0.01085 (26300) covalent geometry : angle 1.49889 (35807) Misc. bond : bond 0.32817 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 693 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8103 (mmmt) REVERT: A 53 ASP cc_start: 0.7724 (t0) cc_final: 0.7391 (t0) REVERT: A 88 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: A 194 PHE cc_start: 0.7981 (m-80) cc_final: 0.7774 (m-80) REVERT: A 202 LYS cc_start: 0.7945 (mttt) cc_final: 0.7694 (mtmm) REVERT: A 240 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7463 (t) REVERT: A 241 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7448 (tp) REVERT: A 275 PHE cc_start: 0.5045 (m-10) cc_final: 0.4128 (m-10) REVERT: A 304 LYS cc_start: 0.8393 (tppp) cc_final: 0.7992 (tppp) REVERT: A 323 THR cc_start: 0.7940 (p) cc_final: 0.7622 (p) REVERT: A 380 TYR cc_start: 0.7925 (m-80) cc_final: 0.7464 (m-80) REVERT: A 386 LYS cc_start: 0.8258 (mttp) cc_final: 0.7925 (mmmm) REVERT: A 462 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7286 (ttpp) REVERT: A 562 PHE cc_start: 0.7989 (p90) cc_final: 0.7020 (p90) REVERT: A 585 LEU cc_start: 0.7793 (mt) cc_final: 0.7330 (mt) REVERT: A 592 PHE cc_start: 0.6830 (t80) cc_final: 0.6537 (t80) REVERT: A 751 ASN cc_start: 0.8597 (m110) cc_final: 0.8341 (m-40) REVERT: A 752 LEU cc_start: 0.8554 (mt) cc_final: 0.8198 (mp) REVERT: A 763 LEU cc_start: 0.8859 (mt) cc_final: 0.8524 (mt) REVERT: A 776 LYS cc_start: 0.8809 (tptm) cc_final: 0.8526 (tptm) REVERT: A 777 ASN cc_start: 0.8289 (m-40) cc_final: 0.7957 (m110) REVERT: A 796 ASP cc_start: 0.7799 (m-30) cc_final: 0.7365 (p0) REVERT: A 824 ASN cc_start: 0.7554 (m-40) cc_final: 0.7353 (m-40) REVERT: A 860 VAL cc_start: 0.7487 (t) cc_final: 0.7216 (p) REVERT: A 867 ASP cc_start: 0.7599 (m-30) cc_final: 0.7083 (p0) REVERT: A 917 TYR cc_start: 0.8281 (m-80) cc_final: 0.8036 (m-10) REVERT: A 968 SER cc_start: 0.8404 (m) cc_final: 0.8025 (t) REVERT: A 990 GLU cc_start: 0.8611 (tt0) cc_final: 0.8372 (mt-10) REVERT: A 991 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.8881 (m) REVERT: A 996 LEU cc_start: 0.8800 (mt) cc_final: 0.8514 (mt) REVERT: A 1115 ILE cc_start: -0.5528 (OUTLIER) cc_final: -0.5760 (tp) REVERT: A 1141 LEU cc_start: -0.7109 (OUTLIER) cc_final: -0.7952 (mt) REVERT: B 48 LEU cc_start: 0.8646 (mp) cc_final: 0.7966 (mp) REVERT: B 58 PHE cc_start: 0.7683 (m-80) cc_final: 0.7040 (m-80) REVERT: B 63 THR cc_start: 0.7989 (p) cc_final: 0.6726 (t) REVERT: B 64 TRP cc_start: 0.8335 (t60) cc_final: 0.8068 (t60) REVERT: B 65 PHE cc_start: 0.8121 (m-80) cc_final: 0.7453 (m-10) REVERT: B 119 ILE cc_start: 0.4067 (OUTLIER) cc_final: 0.3064 (pt) REVERT: B 122 ASN cc_start: 0.1670 (OUTLIER) cc_final: -0.0331 (m-40) REVERT: B 194 PHE cc_start: 0.6981 (m-80) cc_final: 0.6529 (m-80) REVERT: B 210 ILE cc_start: 0.3997 (tp) cc_final: 0.3507 (mm) REVERT: B 266 TYR cc_start: 0.5955 (m-10) cc_final: 0.5723 (m-10) REVERT: B 289 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6876 (p) REVERT: B 300 LYS cc_start: 0.7848 (mttt) cc_final: 0.7591 (mtmm) REVERT: B 306 PHE cc_start: 0.6531 (m-80) cc_final: 0.5190 (m-80) REVERT: B 312 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7763 (pt) REVERT: B 396 TYR cc_start: 0.8088 (m-80) cc_final: 0.7738 (m-80) REVERT: B 560 LEU cc_start: 0.8536 (mt) cc_final: 0.8248 (mt) REVERT: B 563 GLN cc_start: 0.6499 (mt0) cc_final: 0.6297 (mt0) REVERT: B 582 LEU cc_start: 0.8966 (tt) cc_final: 0.8762 (tp) REVERT: B 586 ASP cc_start: 0.6681 (m-30) cc_final: 0.6194 (m-30) REVERT: B 603 ASN cc_start: 0.8815 (t0) cc_final: 0.8484 (p0) REVERT: B 613 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6394 (mm110) REVERT: B 620 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.5890 (p) REVERT: B 656 VAL cc_start: 0.8712 (m) cc_final: 0.7655 (p) REVERT: B 765 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7514 (ttm110) REVERT: B 776 LYS cc_start: 0.8558 (tptp) cc_final: 0.8176 (mmmt) REVERT: B 822 LEU cc_start: 0.9116 (tp) cc_final: 0.8865 (mt) REVERT: B 869 MET cc_start: 0.8445 (mtt) cc_final: 0.8069 (mmp) REVERT: B 873 TYR cc_start: 0.7499 (m-80) cc_final: 0.7114 (m-80) REVERT: B 927 PHE cc_start: 0.8191 (t80) cc_final: 0.7893 (t80) REVERT: B 937 SER cc_start: 0.8696 (t) cc_final: 0.8453 (p) REVERT: B 954 GLN cc_start: 0.8562 (mt0) cc_final: 0.8335 (pp30) REVERT: B 955 ASN cc_start: 0.8403 (m110) cc_final: 0.7944 (t0) REVERT: B 959 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8418 (pp) REVERT: B 964 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8286 (tmtt) REVERT: B 979 ASP cc_start: 0.7818 (t0) cc_final: 0.7595 (t0) REVERT: B 1003 SER cc_start: 0.8982 (m) cc_final: 0.8617 (p) REVERT: B 1018 ILE cc_start: 0.8916 (mm) cc_final: 0.8439 (tt) REVERT: B 1019 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7830 (mtp-110) REVERT: B 1021 SER cc_start: 0.8673 (t) cc_final: 0.8410 (p) REVERT: B 1034 LEU cc_start: 0.5367 (mt) cc_final: 0.4979 (mm) REVERT: B 1116 THR cc_start: -0.2698 (OUTLIER) cc_final: -0.3803 (m) REVERT: C 36 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.5944 (p) REVERT: C 65 PHE cc_start: 0.8253 (m-80) cc_final: 0.7970 (m-80) REVERT: C 87 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.7568 (m-40) REVERT: C 128 ILE cc_start: 0.7083 (mt) cc_final: 0.6655 (mt) REVERT: C 170 TYR cc_start: 0.7896 (t80) cc_final: 0.6843 (t80) REVERT: C 177 MET cc_start: 0.5838 (mtp) cc_final: 0.5169 (mmm) REVERT: C 206 LYS cc_start: 0.6998 (tptm) cc_final: 0.6660 (tttt) REVERT: C 220 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7056 (t80) REVERT: C 223 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5059 (mp) REVERT: C 229 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7631 (mt) REVERT: C 269 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.3009 (m-80) REVERT: C 276 LEU cc_start: 0.8372 (tp) cc_final: 0.7996 (tp) REVERT: C 281 GLU cc_start: 0.7824 (tp30) cc_final: 0.7458 (tp30) REVERT: C 300 LYS cc_start: 0.8609 (mttt) cc_final: 0.8074 (mmmt) REVERT: C 310 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8078 (ttmm) REVERT: C 317 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7937 (p0) REVERT: C 324 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7810 (mp0) REVERT: C 338 PHE cc_start: 0.8870 (m-80) cc_final: 0.8351 (m-10) REVERT: C 342 PHE cc_start: 0.8848 (m-80) cc_final: 0.8550 (m-10) REVERT: C 365 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: C 385 THR cc_start: 0.7988 (t) cc_final: 0.7699 (p) REVERT: C 386 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8316 (mttp) REVERT: C 388 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.6487 (m-40) REVERT: C 409 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: C 462 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6590 (ttpp) REVERT: C 508 TYR cc_start: 0.8493 (m-80) cc_final: 0.8152 (m-10) REVERT: C 531 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7855 (m) REVERT: C 535 LYS cc_start: 0.8944 (mttt) cc_final: 0.8299 (mtpp) REVERT: C 562 PHE cc_start: 0.8369 (p90) cc_final: 0.7749 (p90) REVERT: C 563 GLN cc_start: 0.7986 (mt0) cc_final: 0.7640 (pt0) REVERT: C 585 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7221 (mt) REVERT: C 655 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6870 (p90) REVERT: C 699 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.5760 (mt) REVERT: C 765 ARG cc_start: 0.8417 (mtm180) cc_final: 0.8176 (ptp-170) REVERT: C 773 GLU cc_start: 0.8318 (tt0) cc_final: 0.7967 (tt0) REVERT: C 776 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8453 (tptp) REVERT: C 795 LYS cc_start: 0.8207 (mttt) cc_final: 0.7978 (mptt) REVERT: C 873 TYR cc_start: 0.7284 (m-80) cc_final: 0.7010 (m-80) REVERT: C 886 TRP cc_start: 0.4492 (p90) cc_final: 0.4186 (p90) REVERT: C 895 GLN cc_start: -0.0323 (OUTLIER) cc_final: -0.2483 (tm-30) REVERT: C 931 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8845 (pt) REVERT: C 934 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.6982 (mt) REVERT: C 957 GLN cc_start: 0.8594 (tt0) cc_final: 0.8353 (pp30) REVERT: C 964 LYS cc_start: 0.8886 (tttt) cc_final: 0.8475 (tptp) REVERT: C 973 ILE cc_start: 0.8048 (pt) cc_final: 0.7691 (pt) REVERT: C 981 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7837 (mt) REVERT: C 988 GLU cc_start: 0.6844 (tp30) cc_final: 0.6286 (tp30) REVERT: C 1008 VAL cc_start: 0.8485 (t) cc_final: 0.8117 (m) REVERT: C 1013 ILE cc_start: 0.8867 (mt) cc_final: 0.8665 (mm) outliers start: 215 outliers final: 49 residues processed: 845 average time/residue: 0.3977 time to fit residues: 515.7911 Evaluate side-chains 616 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 534 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN A 146 HIS A 164 ASN A 165 ASN A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 774 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A1108 ASN B 165 ASN B 207 HIS B 211 ASN B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 777 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B1002 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 185 ASN C 207 HIS C 245 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 655 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 949 GLN C 953 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.191252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.141601 restraints weight = 63275.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.146316 restraints weight = 45786.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.149770 restraints weight = 35869.485| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 26386 Z= 0.220 Angle : 0.912 22.214 36017 Z= 0.451 Chirality : 0.055 0.720 4182 Planarity : 0.006 0.108 4587 Dihedral : 9.584 103.159 4373 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 0.50 % Allowed : 5.37 % Favored : 94.13 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.34 (0.14), residues: 3187 helix: 1.40 (0.19), residues: 671 sheet: 0.18 (0.20), residues: 658 loop : -1.02 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 64 HIS 0.014 0.002 HIS B1048 PHE 0.031 0.003 PHE B 559 TYR 0.043 0.002 TYR C 904 ARG 0.031 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00949 ( 32) link_NAG-ASN : angle 5.16131 ( 96) link_BETA1-4 : bond 0.01109 ( 10) link_BETA1-4 : angle 1.98431 ( 30) hydrogen bonds : bond 0.06476 ( 872) hydrogen bonds : angle 7.22323 ( 2433) SS BOND : bond 0.00682 ( 42) SS BOND : angle 2.97052 ( 84) covalent geometry : bond 0.00487 (26300) covalent geometry : angle 0.86101 (35807) Misc. bond : bond 0.00629 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 574 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8527 (mmtt) cc_final: 0.7811 (ttpt) REVERT: A 53 ASP cc_start: 0.8410 (t0) cc_final: 0.8001 (t0) REVERT: A 65 PHE cc_start: 0.7620 (m-80) cc_final: 0.7129 (m-80) REVERT: A 133 PHE cc_start: 0.5539 (m-80) cc_final: 0.4947 (m-80) REVERT: A 189 LEU cc_start: 0.8235 (tp) cc_final: 0.7737 (tp) REVERT: A 192 PHE cc_start: 0.7810 (m-80) cc_final: 0.7497 (m-80) REVERT: A 194 PHE cc_start: 0.8987 (m-80) cc_final: 0.8028 (m-80) REVERT: A 195 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8560 (ttpp) REVERT: A 275 PHE cc_start: 0.6666 (m-10) cc_final: 0.5746 (m-10) REVERT: A 310 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8335 (ttmt) REVERT: A 312 ILE cc_start: 0.8411 (tt) cc_final: 0.8132 (tt) REVERT: A 313 TYR cc_start: 0.8340 (m-10) cc_final: 0.7689 (m-10) REVERT: A 355 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8355 (ttm-80) REVERT: A 380 TYR cc_start: 0.7913 (m-80) cc_final: 0.7426 (m-80) REVERT: A 386 LYS cc_start: 0.8607 (mttp) cc_final: 0.8286 (mmmm) REVERT: A 421 TYR cc_start: 0.8423 (m-10) cc_final: 0.7900 (m-10) REVERT: A 462 LYS cc_start: 0.7950 (mmtm) cc_final: 0.6956 (ttpp) REVERT: A 535 LYS cc_start: 0.8080 (mttm) cc_final: 0.6750 (mmmt) REVERT: A 562 PHE cc_start: 0.7846 (p90) cc_final: 0.7600 (p90) REVERT: A 585 LEU cc_start: 0.8377 (mt) cc_final: 0.7846 (tt) REVERT: A 586 ASP cc_start: 0.7333 (p0) cc_final: 0.7012 (p0) REVERT: A 751 ASN cc_start: 0.8786 (m110) cc_final: 0.8353 (m-40) REVERT: A 752 LEU cc_start: 0.8845 (mt) cc_final: 0.8390 (tt) REVERT: A 759 PHE cc_start: 0.8619 (m-80) cc_final: 0.8396 (m-80) REVERT: A 762 GLN cc_start: 0.8757 (mm110) cc_final: 0.8389 (pt0) REVERT: A 764 ASN cc_start: 0.9343 (m110) cc_final: 0.9112 (m110) REVERT: A 776 LYS cc_start: 0.8925 (tptm) cc_final: 0.8267 (tptp) REVERT: A 796 ASP cc_start: 0.7753 (m-30) cc_final: 0.7306 (p0) REVERT: A 867 ASP cc_start: 0.7677 (m-30) cc_final: 0.7210 (p0) REVERT: A 900 MET cc_start: 0.7495 (tmm) cc_final: 0.7127 (tmm) REVERT: A 917 TYR cc_start: 0.8660 (m-80) cc_final: 0.8177 (m-10) REVERT: A 927 PHE cc_start: 0.7487 (t80) cc_final: 0.7064 (t80) REVERT: A 947 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7434 (pttt) REVERT: A 954 GLN cc_start: 0.9124 (tp40) cc_final: 0.8627 (tm-30) REVERT: A 964 LYS cc_start: 0.9367 (ttmm) cc_final: 0.9070 (ttmm) REVERT: A 965 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 968 SER cc_start: 0.8707 (m) cc_final: 0.8425 (t) REVERT: A 970 PHE cc_start: 0.8579 (m-10) cc_final: 0.8219 (m-80) REVERT: A 983 ARG cc_start: 0.8913 (ptt90) cc_final: 0.8545 (ttp80) REVERT: A 990 GLU cc_start: 0.8760 (tt0) cc_final: 0.8414 (mt-10) REVERT: A 993 ILE cc_start: 0.8846 (mt) cc_final: 0.8514 (pt) REVERT: A 994 ASP cc_start: 0.8718 (m-30) cc_final: 0.8038 (m-30) REVERT: A 1000 ARG cc_start: 0.9303 (mtt-85) cc_final: 0.9062 (mtt180) REVERT: A 1001 LEU cc_start: 0.9355 (mt) cc_final: 0.8925 (mm) REVERT: A 1002 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 1018 ILE cc_start: 0.8768 (mm) cc_final: 0.8412 (tt) REVERT: A 1019 ARG cc_start: 0.8967 (ttt180) cc_final: 0.8189 (ttm110) REVERT: B 44 ARG cc_start: 0.7529 (mtt90) cc_final: 0.6954 (mtm-85) REVERT: B 56 LEU cc_start: 0.8895 (tp) cc_final: 0.7955 (pp) REVERT: B 58 PHE cc_start: 0.8185 (m-80) cc_final: 0.7250 (m-80) REVERT: B 63 THR cc_start: 0.7909 (p) cc_final: 0.6555 (t) REVERT: B 64 TRP cc_start: 0.8670 (t60) cc_final: 0.8443 (t-100) REVERT: B 65 PHE cc_start: 0.8285 (m-80) cc_final: 0.7685 (m-80) REVERT: B 117 LEU cc_start: 0.8633 (tt) cc_final: 0.8379 (pp) REVERT: B 128 ILE cc_start: 0.8477 (mt) cc_final: 0.8256 (mt) REVERT: B 129 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7689 (mmmt) REVERT: B 194 PHE cc_start: 0.7677 (m-80) cc_final: 0.7020 (m-10) REVERT: B 212 LEU cc_start: 0.8561 (tp) cc_final: 0.8207 (tt) REVERT: B 223 LEU cc_start: 0.8439 (mt) cc_final: 0.7965 (mm) REVERT: B 266 TYR cc_start: 0.7027 (m-10) cc_final: 0.6796 (m-10) REVERT: B 276 LEU cc_start: 0.8683 (tt) cc_final: 0.7938 (mp) REVERT: B 300 LYS cc_start: 0.8194 (mttt) cc_final: 0.7664 (mtmt) REVERT: B 304 LYS cc_start: 0.8580 (ptpp) cc_final: 0.8267 (mmtt) REVERT: B 306 PHE cc_start: 0.6759 (m-80) cc_final: 0.6554 (m-80) REVERT: B 313 TYR cc_start: 0.7356 (m-10) cc_final: 0.6882 (m-80) REVERT: B 396 TYR cc_start: 0.8183 (m-80) cc_final: 0.7845 (m-80) REVERT: B 557 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8795 (ttpp) REVERT: B 560 LEU cc_start: 0.8694 (mt) cc_final: 0.8361 (mt) REVERT: B 603 ASN cc_start: 0.9201 (t0) cc_final: 0.8767 (p0) REVERT: B 612 TYR cc_start: 0.7325 (m-10) cc_final: 0.6813 (m-10) REVERT: B 656 VAL cc_start: 0.8175 (m) cc_final: 0.7956 (m) REVERT: B 748 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8717 (pp20) REVERT: B 753 LEU cc_start: 0.9138 (tp) cc_final: 0.8850 (tp) REVERT: B 755 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8540 (tm-30) REVERT: B 763 LEU cc_start: 0.9521 (mt) cc_final: 0.9042 (mt) REVERT: B 765 ARG cc_start: 0.9030 (ttm110) cc_final: 0.8696 (ttm110) REVERT: B 775 ASP cc_start: 0.8268 (m-30) cc_final: 0.7258 (m-30) REVERT: B 819 GLU cc_start: 0.8888 (pt0) cc_final: 0.8403 (pt0) REVERT: B 822 LEU cc_start: 0.9115 (tp) cc_final: 0.8673 (mt) REVERT: B 869 MET cc_start: 0.8566 (mtt) cc_final: 0.8310 (mtt) REVERT: B 917 TYR cc_start: 0.8139 (m-10) cc_final: 0.7914 (m-10) REVERT: B 927 PHE cc_start: 0.8460 (t80) cc_final: 0.7870 (t80) REVERT: B 937 SER cc_start: 0.8685 (t) cc_final: 0.8386 (p) REVERT: B 954 GLN cc_start: 0.9050 (mt0) cc_final: 0.8342 (tm-30) REVERT: B 955 ASN cc_start: 0.8759 (m110) cc_final: 0.8405 (t0) REVERT: B 957 GLN cc_start: 0.9183 (pt0) cc_final: 0.8635 (pp30) REVERT: B 960 ASN cc_start: 0.9045 (m-40) cc_final: 0.8697 (m-40) REVERT: B 964 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8478 (tmtt) REVERT: B 965 GLN cc_start: 0.9310 (mm110) cc_final: 0.7872 (mm110) REVERT: B 979 ASP cc_start: 0.8573 (t0) cc_final: 0.8299 (t0) REVERT: B 983 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7475 (tmm-80) REVERT: B 998 THR cc_start: 0.8958 (p) cc_final: 0.8747 (p) REVERT: B 1010 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8619 (mm-40) REVERT: B 1011 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8016 (mp10) REVERT: B 1012 LEU cc_start: 0.9332 (mt) cc_final: 0.9087 (mt) REVERT: B 1017 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8596 (tm-30) REVERT: B 1019 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8295 (ptm160) REVERT: B 1021 SER cc_start: 0.8754 (t) cc_final: 0.8413 (p) REVERT: B 1028 LYS cc_start: 0.7234 (tptt) cc_final: 0.7006 (tptt) REVERT: B 1050 MET cc_start: 0.7188 (tpt) cc_final: 0.6462 (mtp) REVERT: C 91 TYR cc_start: 0.7520 (t80) cc_final: 0.6482 (t80) REVERT: C 117 LEU cc_start: 0.8673 (tt) cc_final: 0.8018 (pt) REVERT: C 128 ILE cc_start: 0.7697 (mt) cc_final: 0.7492 (mp) REVERT: C 133 PHE cc_start: 0.7809 (m-80) cc_final: 0.7309 (m-80) REVERT: C 135 PHE cc_start: 0.8974 (m-10) cc_final: 0.8425 (t80) REVERT: C 192 PHE cc_start: 0.8470 (m-80) cc_final: 0.8190 (m-80) REVERT: C 194 PHE cc_start: 0.7907 (m-80) cc_final: 0.7600 (m-80) REVERT: C 235 ILE cc_start: 0.7081 (mt) cc_final: 0.6744 (mm) REVERT: C 237 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8107 (mtp85) REVERT: C 281 GLU cc_start: 0.8178 (tp30) cc_final: 0.7922 (tp30) REVERT: C 324 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8039 (mp0) REVERT: C 338 PHE cc_start: 0.8837 (m-80) cc_final: 0.8452 (m-10) REVERT: C 342 PHE cc_start: 0.8785 (m-80) cc_final: 0.8426 (m-10) REVERT: C 354 ASN cc_start: 0.8851 (t0) cc_final: 0.8574 (t0) REVERT: C 380 TYR cc_start: 0.8244 (m-10) cc_final: 0.8002 (m-10) REVERT: C 386 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8083 (mttt) REVERT: C 417 LYS cc_start: 0.9069 (tppp) cc_final: 0.8832 (tppt) REVERT: C 425 LEU cc_start: 0.8263 (mt) cc_final: 0.8033 (tp) REVERT: C 517 LEU cc_start: 0.6569 (pp) cc_final: 0.5877 (pp) REVERT: C 562 PHE cc_start: 0.8724 (p90) cc_final: 0.8186 (p90) REVERT: C 583 GLU cc_start: 0.8362 (tp30) cc_final: 0.7884 (tm-30) REVERT: C 588 THR cc_start: 0.8320 (m) cc_final: 0.8088 (p) REVERT: C 737 ASP cc_start: 0.8870 (t0) cc_final: 0.8590 (t0) REVERT: C 738 CYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6574 (p) REVERT: C 748 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8571 (mt-10) REVERT: C 756 TYR cc_start: 0.8258 (m-10) cc_final: 0.7818 (m-10) REVERT: C 759 PHE cc_start: 0.8594 (m-80) cc_final: 0.7981 (m-10) REVERT: C 765 ARG cc_start: 0.9299 (mtm180) cc_final: 0.8854 (ptp-110) REVERT: C 776 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8276 (tmtt) REVERT: C 869 MET cc_start: 0.8984 (mtm) cc_final: 0.8042 (tmm) REVERT: C 917 TYR cc_start: 0.7859 (m-80) cc_final: 0.7536 (m-10) REVERT: C 954 GLN cc_start: 0.9133 (mt0) cc_final: 0.8428 (pp30) REVERT: C 955 ASN cc_start: 0.8004 (p0) cc_final: 0.7539 (p0) REVERT: C 957 GLN cc_start: 0.8891 (tt0) cc_final: 0.8515 (pp30) REVERT: C 959 LEU cc_start: 0.9352 (mp) cc_final: 0.9130 (pp) REVERT: C 964 LYS cc_start: 0.9339 (tttt) cc_final: 0.9042 (tmtt) REVERT: C 965 GLN cc_start: 0.9239 (mm110) cc_final: 0.8269 (mm-40) REVERT: C 979 ASP cc_start: 0.9027 (m-30) cc_final: 0.8721 (m-30) REVERT: C 1010 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8477 (tm-30) REVERT: C 1012 LEU cc_start: 0.9190 (mt) cc_final: 0.8952 (mt) REVERT: C 1017 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8133 (mp0) REVERT: C 1019 ARG cc_start: 0.8536 (ptp-170) cc_final: 0.8073 (ptp90) outliers start: 14 outliers final: 1 residues processed: 586 average time/residue: 0.4009 time to fit residues: 358.7042 Evaluate side-chains 483 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 480 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 174 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 250 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 563 GLN A 564 GLN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 388 ASN C 394 ASN C 544 ASN C 655 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1083 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.182359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.136106 restraints weight = 66794.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.141211 restraints weight = 46825.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.144947 restraints weight = 35711.548| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26386 Z= 0.164 Angle : 0.779 16.174 36017 Z= 0.384 Chirality : 0.051 0.582 4182 Planarity : 0.005 0.064 4587 Dihedral : 8.815 103.166 4373 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 3187 helix: 0.93 (0.19), residues: 695 sheet: 0.13 (0.20), residues: 636 loop : -1.11 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.010 0.002 HIS C 66 PHE 0.027 0.002 PHE B 275 TYR 0.019 0.002 TYR A 674 ARG 0.013 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00807 ( 32) link_NAG-ASN : angle 4.56960 ( 96) link_BETA1-4 : bond 0.00479 ( 10) link_BETA1-4 : angle 1.17500 ( 30) hydrogen bonds : bond 0.05316 ( 872) hydrogen bonds : angle 6.57916 ( 2433) SS BOND : bond 0.00384 ( 42) SS BOND : angle 2.08814 ( 84) covalent geometry : bond 0.00348 (26300) covalent geometry : angle 0.73715 (35807) Misc. bond : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 536 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8653 (mmtt) cc_final: 0.7773 (ttpt) REVERT: A 50 SER cc_start: 0.8198 (p) cc_final: 0.7477 (p) REVERT: A 53 ASP cc_start: 0.8240 (t0) cc_final: 0.7985 (t0) REVERT: A 65 PHE cc_start: 0.7770 (m-80) cc_final: 0.6985 (m-80) REVERT: A 84 LEU cc_start: 0.9327 (mp) cc_final: 0.9062 (mm) REVERT: A 104 TRP cc_start: 0.6154 (m-90) cc_final: 0.5588 (m-10) REVERT: A 106 PHE cc_start: 0.8443 (m-10) cc_final: 0.7876 (m-10) REVERT: A 133 PHE cc_start: 0.5554 (m-80) cc_final: 0.5000 (m-80) REVERT: A 177 MET cc_start: -0.0359 (mmp) cc_final: -0.0634 (mmt) REVERT: A 192 PHE cc_start: 0.7836 (m-80) cc_final: 0.7608 (m-10) REVERT: A 194 PHE cc_start: 0.8528 (m-80) cc_final: 0.7846 (m-80) REVERT: A 202 LYS cc_start: 0.7377 (mttt) cc_final: 0.6838 (mttt) REVERT: A 275 PHE cc_start: 0.6722 (m-10) cc_final: 0.6127 (m-10) REVERT: A 303 LEU cc_start: 0.8684 (mt) cc_final: 0.8471 (mt) REVERT: A 304 LYS cc_start: 0.9171 (ptpp) cc_final: 0.8901 (tptt) REVERT: A 310 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8114 (tptp) REVERT: A 380 TYR cc_start: 0.7981 (m-80) cc_final: 0.7447 (m-80) REVERT: A 386 LYS cc_start: 0.8696 (mttp) cc_final: 0.8357 (mmmm) REVERT: A 421 TYR cc_start: 0.8133 (m-10) cc_final: 0.7905 (m-10) REVERT: A 529 LYS cc_start: 0.8858 (tttm) cc_final: 0.8511 (tmtt) REVERT: A 557 LYS cc_start: 0.7975 (mttt) cc_final: 0.7330 (tmtt) REVERT: A 755 GLN cc_start: 0.8240 (mp10) cc_final: 0.7634 (tt0) REVERT: A 759 PHE cc_start: 0.8961 (m-80) cc_final: 0.8316 (m-80) REVERT: A 763 LEU cc_start: 0.9517 (mt) cc_final: 0.9273 (pp) REVERT: A 776 LYS cc_start: 0.8960 (tptm) cc_final: 0.8502 (tptp) REVERT: A 796 ASP cc_start: 0.7687 (m-30) cc_final: 0.7209 (p0) REVERT: A 867 ASP cc_start: 0.7577 (m-30) cc_final: 0.7109 (p0) REVERT: A 917 TYR cc_start: 0.8547 (m-80) cc_final: 0.8037 (m-10) REVERT: A 927 PHE cc_start: 0.7589 (t80) cc_final: 0.7152 (t80) REVERT: A 949 GLN cc_start: 0.8139 (pp30) cc_final: 0.7866 (pp30) REVERT: A 954 GLN cc_start: 0.9044 (tp40) cc_final: 0.8536 (tm-30) REVERT: A 964 LYS cc_start: 0.9326 (ttmm) cc_final: 0.8566 (tptp) REVERT: A 965 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 968 SER cc_start: 0.8607 (m) cc_final: 0.8186 (t) REVERT: A 970 PHE cc_start: 0.8575 (m-10) cc_final: 0.8340 (m-80) REVERT: A 979 ASP cc_start: 0.9124 (m-30) cc_final: 0.8559 (t0) REVERT: A 983 ARG cc_start: 0.8892 (ptt90) cc_final: 0.8090 (ptt90) REVERT: A 990 GLU cc_start: 0.8777 (tt0) cc_final: 0.8460 (mt-10) REVERT: A 993 ILE cc_start: 0.8853 (mt) cc_final: 0.8090 (tp) REVERT: A 994 ASP cc_start: 0.8738 (m-30) cc_final: 0.8099 (m-30) REVERT: A 1001 LEU cc_start: 0.9374 (mt) cc_final: 0.9137 (mm) REVERT: A 1002 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 1011 GLN cc_start: 0.8407 (tp40) cc_final: 0.7801 (tp40) REVERT: A 1014 ARG cc_start: 0.8745 (mmp-170) cc_final: 0.8354 (mmm160) REVERT: B 37 TYR cc_start: 0.8495 (p90) cc_final: 0.8196 (p90) REVERT: B 44 ARG cc_start: 0.7747 (mtt90) cc_final: 0.6674 (ptp90) REVERT: B 58 PHE cc_start: 0.8077 (m-80) cc_final: 0.7219 (m-80) REVERT: B 63 THR cc_start: 0.7895 (p) cc_final: 0.6903 (t) REVERT: B 64 TRP cc_start: 0.8684 (t60) cc_final: 0.8459 (t60) REVERT: B 65 PHE cc_start: 0.8188 (m-80) cc_final: 0.7448 (m-10) REVERT: B 117 LEU cc_start: 0.8724 (tt) cc_final: 0.8434 (pp) REVERT: B 128 ILE cc_start: 0.8541 (mt) cc_final: 0.8039 (mm) REVERT: B 129 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7703 (mmmt) REVERT: B 194 PHE cc_start: 0.7665 (m-80) cc_final: 0.7141 (m-10) REVERT: B 212 LEU cc_start: 0.8567 (tp) cc_final: 0.8197 (tt) REVERT: B 266 TYR cc_start: 0.7157 (m-10) cc_final: 0.6806 (m-10) REVERT: B 287 ASP cc_start: 0.8087 (m-30) cc_final: 0.7463 (t70) REVERT: B 304 LYS cc_start: 0.8387 (ptpp) cc_final: 0.8167 (mmtt) REVERT: B 313 TYR cc_start: 0.7746 (m-10) cc_final: 0.7202 (m-10) REVERT: B 396 TYR cc_start: 0.8153 (m-80) cc_final: 0.7840 (m-80) REVERT: B 537 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8282 (tppt) REVERT: B 562 PHE cc_start: 0.8391 (p90) cc_final: 0.7686 (p90) REVERT: B 571 ASP cc_start: 0.8918 (m-30) cc_final: 0.8574 (m-30) REVERT: B 603 ASN cc_start: 0.9260 (t0) cc_final: 0.8839 (p0) REVERT: B 755 GLN cc_start: 0.9019 (pt0) cc_final: 0.8518 (pt0) REVERT: B 819 GLU cc_start: 0.8892 (pt0) cc_final: 0.8295 (pt0) REVERT: B 822 LEU cc_start: 0.9046 (tp) cc_final: 0.8585 (mt) REVERT: B 824 ASN cc_start: 0.8634 (m110) cc_final: 0.8357 (m110) REVERT: B 869 MET cc_start: 0.8502 (mtt) cc_final: 0.8118 (mmp) REVERT: B 927 PHE cc_start: 0.8394 (t80) cc_final: 0.7752 (t80) REVERT: B 954 GLN cc_start: 0.9040 (mt0) cc_final: 0.8485 (tm-30) REVERT: B 955 ASN cc_start: 0.8753 (m110) cc_final: 0.8450 (t0) REVERT: B 957 GLN cc_start: 0.9137 (pt0) cc_final: 0.8701 (pp30) REVERT: B 960 ASN cc_start: 0.8785 (m-40) cc_final: 0.8398 (t0) REVERT: B 964 LYS cc_start: 0.9016 (ttmm) cc_final: 0.7898 (tptp) REVERT: B 965 GLN cc_start: 0.9182 (mm110) cc_final: 0.8594 (mm110) REVERT: B 979 ASP cc_start: 0.8609 (t0) cc_final: 0.8399 (t0) REVERT: B 1002 GLN cc_start: 0.8850 (mp10) cc_final: 0.8627 (mp10) REVERT: B 1011 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8081 (mp10) REVERT: B 1017 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8567 (tm-30) REVERT: B 1019 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8114 (ptm160) REVERT: B 1021 SER cc_start: 0.8693 (t) cc_final: 0.8415 (p) REVERT: B 1028 LYS cc_start: 0.7200 (tptm) cc_final: 0.6958 (tptt) REVERT: B 1050 MET cc_start: 0.6100 (tpt) cc_final: 0.5848 (mtp) REVERT: C 59 PHE cc_start: 0.7748 (m-80) cc_final: 0.7254 (m-10) REVERT: C 65 PHE cc_start: 0.7595 (m-80) cc_final: 0.7092 (m-80) REVERT: C 117 LEU cc_start: 0.8790 (tt) cc_final: 0.8208 (pt) REVERT: C 135 PHE cc_start: 0.9069 (m-10) cc_final: 0.8777 (m-10) REVERT: C 160 TYR cc_start: 0.8332 (p90) cc_final: 0.7245 (p90) REVERT: C 194 PHE cc_start: 0.7840 (m-80) cc_final: 0.7595 (m-80) REVERT: C 235 ILE cc_start: 0.6921 (mt) cc_final: 0.6614 (mm) REVERT: C 237 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8609 (mmm-85) REVERT: C 276 LEU cc_start: 0.7931 (tp) cc_final: 0.7721 (tp) REVERT: C 281 GLU cc_start: 0.8310 (tp30) cc_final: 0.7799 (tp30) REVERT: C 289 VAL cc_start: 0.8663 (t) cc_final: 0.8327 (p) REVERT: C 300 LYS cc_start: 0.8180 (mttt) cc_final: 0.7700 (mmtt) REVERT: C 313 TYR cc_start: 0.7314 (m-80) cc_final: 0.6971 (m-80) REVERT: C 324 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8047 (pm20) REVERT: C 338 PHE cc_start: 0.9042 (m-80) cc_final: 0.8514 (m-10) REVERT: C 342 PHE cc_start: 0.8759 (m-80) cc_final: 0.8418 (m-10) REVERT: C 365 TYR cc_start: 0.8558 (m-80) cc_final: 0.8233 (m-80) REVERT: C 417 LYS cc_start: 0.9078 (tppp) cc_final: 0.8873 (tppt) REVERT: C 425 LEU cc_start: 0.8199 (mt) cc_final: 0.7924 (tp) REVERT: C 516 GLU cc_start: 0.6186 (mp0) cc_final: 0.5796 (mp0) REVERT: C 562 PHE cc_start: 0.8829 (p90) cc_final: 0.8450 (p90) REVERT: C 563 GLN cc_start: 0.8293 (mt0) cc_final: 0.7860 (mm-40) REVERT: C 583 GLU cc_start: 0.8485 (tp30) cc_final: 0.8150 (tm-30) REVERT: C 756 TYR cc_start: 0.8345 (m-10) cc_final: 0.8126 (m-10) REVERT: C 759 PHE cc_start: 0.8555 (m-80) cc_final: 0.8095 (m-10) REVERT: C 761 THR cc_start: 0.9375 (m) cc_final: 0.9078 (p) REVERT: C 762 GLN cc_start: 0.9149 (mt0) cc_final: 0.8821 (mt0) REVERT: C 763 LEU cc_start: 0.9167 (mt) cc_final: 0.8927 (mt) REVERT: C 765 ARG cc_start: 0.9197 (mtm180) cc_final: 0.8642 (ptp-110) REVERT: C 776 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8323 (tmtt) REVERT: C 869 MET cc_start: 0.8952 (mtm) cc_final: 0.8149 (tmm) REVERT: C 934 ILE cc_start: 0.7397 (tp) cc_final: 0.6884 (mm) REVERT: C 936 ASP cc_start: 0.8419 (m-30) cc_final: 0.8159 (m-30) REVERT: C 955 ASN cc_start: 0.8042 (p0) cc_final: 0.7395 (p0) REVERT: C 957 GLN cc_start: 0.8854 (tt0) cc_final: 0.8567 (pp30) REVERT: C 959 LEU cc_start: 0.9207 (mp) cc_final: 0.8936 (pp) REVERT: C 964 LYS cc_start: 0.9336 (tttt) cc_final: 0.8992 (tmtt) REVERT: C 965 GLN cc_start: 0.9189 (mm110) cc_final: 0.8253 (mm110) REVERT: C 969 ASN cc_start: 0.7728 (p0) cc_final: 0.6901 (p0) REVERT: C 970 PHE cc_start: 0.8000 (m-80) cc_final: 0.7458 (m-10) REVERT: C 979 ASP cc_start: 0.9025 (m-30) cc_final: 0.8765 (m-30) REVERT: C 983 ARG cc_start: 0.9006 (tmt-80) cc_final: 0.8664 (tpt90) REVERT: C 994 ASP cc_start: 0.8511 (m-30) cc_final: 0.8265 (m-30) REVERT: C 998 THR cc_start: 0.9056 (m) cc_final: 0.8347 (p) REVERT: C 1000 ARG cc_start: 0.9103 (mmm160) cc_final: 0.8746 (mmm160) REVERT: C 1001 LEU cc_start: 0.9379 (tp) cc_final: 0.9098 (tp) REVERT: C 1002 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8529 (mm110) REVERT: C 1010 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8385 (tm-30) REVERT: C 1017 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8261 (pp20) REVERT: C 1018 ILE cc_start: 0.8749 (pt) cc_final: 0.7986 (pt) outliers start: 1 outliers final: 0 residues processed: 537 average time/residue: 0.4234 time to fit residues: 348.5150 Evaluate side-chains 476 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 270 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 139 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 232 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 chunk 214 optimal weight: 40.0000 chunk 28 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.179443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.135360 restraints weight = 68029.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.140631 restraints weight = 46787.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.144436 restraints weight = 35078.870| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26386 Z= 0.151 Angle : 0.737 14.031 36017 Z= 0.364 Chirality : 0.049 0.535 4182 Planarity : 0.005 0.081 4587 Dihedral : 8.328 102.994 4373 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.75 (0.14), residues: 3187 helix: 0.75 (0.19), residues: 697 sheet: -0.08 (0.20), residues: 606 loop : -1.16 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 64 HIS 0.007 0.001 HIS C 49 PHE 0.031 0.002 PHE C 592 TYR 0.018 0.002 TYR C 380 ARG 0.008 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 32) link_NAG-ASN : angle 3.95086 ( 96) link_BETA1-4 : bond 0.00544 ( 10) link_BETA1-4 : angle 1.21276 ( 30) hydrogen bonds : bond 0.04931 ( 872) hydrogen bonds : angle 6.27816 ( 2433) SS BOND : bond 0.00362 ( 42) SS BOND : angle 2.00988 ( 84) covalent geometry : bond 0.00321 (26300) covalent geometry : angle 0.70221 (35807) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 522 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8643 (mmtt) cc_final: 0.7596 (ttpt) REVERT: A 53 ASP cc_start: 0.8305 (t0) cc_final: 0.7873 (t0) REVERT: A 65 PHE cc_start: 0.7812 (m-80) cc_final: 0.7327 (m-80) REVERT: A 84 LEU cc_start: 0.9101 (mp) cc_final: 0.8872 (mm) REVERT: A 104 TRP cc_start: 0.6660 (m-90) cc_final: 0.6017 (m-90) REVERT: A 128 ILE cc_start: 0.8762 (mt) cc_final: 0.7892 (mt) REVERT: A 170 TYR cc_start: 0.7410 (t80) cc_final: 0.6800 (t80) REVERT: A 192 PHE cc_start: 0.7861 (m-80) cc_final: 0.7647 (m-80) REVERT: A 194 PHE cc_start: 0.8385 (m-80) cc_final: 0.7793 (m-80) REVERT: A 228 ASP cc_start: 0.8331 (m-30) cc_final: 0.8015 (m-30) REVERT: A 275 PHE cc_start: 0.6778 (m-10) cc_final: 0.6185 (m-10) REVERT: A 304 LYS cc_start: 0.9183 (ptpp) cc_final: 0.8896 (mptt) REVERT: A 310 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8209 (tppt) REVERT: A 380 TYR cc_start: 0.8069 (m-80) cc_final: 0.7502 (m-80) REVERT: A 386 LYS cc_start: 0.8752 (mttp) cc_final: 0.8527 (mmmm) REVERT: A 461 LEU cc_start: 0.8201 (mt) cc_final: 0.7794 (mt) REVERT: A 529 LYS cc_start: 0.8695 (tttm) cc_final: 0.8297 (tmtt) REVERT: A 557 LYS cc_start: 0.8100 (mttt) cc_final: 0.7337 (tptp) REVERT: A 562 PHE cc_start: 0.8399 (p90) cc_final: 0.8137 (p90) REVERT: A 585 LEU cc_start: 0.8697 (mp) cc_final: 0.8403 (mp) REVERT: A 654 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7039 (tm-30) REVERT: A 751 ASN cc_start: 0.8854 (m110) cc_final: 0.8426 (p0) REVERT: A 752 LEU cc_start: 0.8764 (tt) cc_final: 0.8481 (tt) REVERT: A 759 PHE cc_start: 0.8740 (m-80) cc_final: 0.8258 (m-80) REVERT: A 764 ASN cc_start: 0.9091 (m110) cc_final: 0.8632 (m-40) REVERT: A 776 LYS cc_start: 0.8963 (tptm) cc_final: 0.8441 (tptp) REVERT: A 796 ASP cc_start: 0.7691 (m-30) cc_final: 0.7182 (p0) REVERT: A 867 ASP cc_start: 0.7554 (m-30) cc_final: 0.7312 (p0) REVERT: A 917 TYR cc_start: 0.8452 (m-80) cc_final: 0.7919 (m-10) REVERT: A 927 PHE cc_start: 0.7828 (t80) cc_final: 0.7366 (t80) REVERT: A 947 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7562 (pttt) REVERT: A 949 GLN cc_start: 0.8132 (pp30) cc_final: 0.7923 (pp30) REVERT: A 954 GLN cc_start: 0.9011 (tp40) cc_final: 0.8471 (tm-30) REVERT: A 964 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8359 (tptp) REVERT: A 965 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8295 (tm-30) REVERT: A 970 PHE cc_start: 0.8479 (m-10) cc_final: 0.8252 (m-80) REVERT: A 979 ASP cc_start: 0.9099 (m-30) cc_final: 0.8535 (t0) REVERT: A 990 GLU cc_start: 0.8781 (tt0) cc_final: 0.8424 (mt-10) REVERT: A 994 ASP cc_start: 0.8544 (m-30) cc_final: 0.8101 (m-30) REVERT: A 1002 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8104 (tm-30) REVERT: A 1011 GLN cc_start: 0.8554 (tp40) cc_final: 0.7914 (tp40) REVERT: A 1014 ARG cc_start: 0.8755 (mmp-170) cc_final: 0.8409 (mmm160) REVERT: A 1018 ILE cc_start: 0.8898 (mm) cc_final: 0.8604 (tt) REVERT: A 1050 MET cc_start: 0.4806 (ttt) cc_final: 0.4581 (ttt) REVERT: B 41 LYS cc_start: 0.8782 (tppt) cc_final: 0.8174 (tppt) REVERT: B 44 ARG cc_start: 0.7852 (mtt90) cc_final: 0.6760 (ptp90) REVERT: B 58 PHE cc_start: 0.8129 (m-80) cc_final: 0.6134 (m-80) REVERT: B 59 PHE cc_start: 0.7319 (t80) cc_final: 0.7099 (t80) REVERT: B 65 PHE cc_start: 0.8145 (m-80) cc_final: 0.7629 (m-80) REVERT: B 127 VAL cc_start: 0.8876 (m) cc_final: 0.8292 (p) REVERT: B 128 ILE cc_start: 0.8801 (mt) cc_final: 0.7814 (mt) REVERT: B 170 TYR cc_start: 0.8342 (t80) cc_final: 0.7573 (t80) REVERT: B 194 PHE cc_start: 0.7907 (m-80) cc_final: 0.7456 (m-10) REVERT: B 212 LEU cc_start: 0.8543 (tp) cc_final: 0.8198 (tt) REVERT: B 265 TYR cc_start: 0.7276 (p90) cc_final: 0.6607 (p90) REVERT: B 266 TYR cc_start: 0.7362 (m-10) cc_final: 0.6961 (m-10) REVERT: B 274 THR cc_start: 0.5705 (m) cc_final: 0.5433 (m) REVERT: B 275 PHE cc_start: 0.6700 (m-10) cc_final: 0.5430 (m-10) REVERT: B 287 ASP cc_start: 0.8118 (m-30) cc_final: 0.7224 (t70) REVERT: B 304 LYS cc_start: 0.8404 (ptpp) cc_final: 0.8199 (mmtt) REVERT: B 313 TYR cc_start: 0.7738 (m-10) cc_final: 0.7251 (m-10) REVERT: B 319 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8128 (ptp90) REVERT: B 396 TYR cc_start: 0.8111 (m-80) cc_final: 0.7812 (m-80) REVERT: B 603 ASN cc_start: 0.9269 (t0) cc_final: 0.8852 (p0) REVERT: B 726 ILE cc_start: 0.3525 (OUTLIER) cc_final: 0.3213 (mt) REVERT: B 755 GLN cc_start: 0.9042 (pt0) cc_final: 0.8528 (pt0) REVERT: B 819 GLU cc_start: 0.8868 (pt0) cc_final: 0.8322 (pt0) REVERT: B 822 LEU cc_start: 0.9017 (tp) cc_final: 0.8532 (mt) REVERT: B 824 ASN cc_start: 0.8694 (m110) cc_final: 0.8460 (m110) REVERT: B 869 MET cc_start: 0.8492 (mtt) cc_final: 0.7670 (mmt) REVERT: B 873 TYR cc_start: 0.7767 (m-10) cc_final: 0.7446 (m-80) REVERT: B 927 PHE cc_start: 0.8488 (t80) cc_final: 0.7813 (t80) REVERT: B 954 GLN cc_start: 0.9020 (mt0) cc_final: 0.8502 (pp30) REVERT: B 955 ASN cc_start: 0.8705 (m110) cc_final: 0.8442 (t0) REVERT: B 957 GLN cc_start: 0.9021 (pt0) cc_final: 0.8672 (pp30) REVERT: B 959 LEU cc_start: 0.8951 (mm) cc_final: 0.8751 (pp) REVERT: B 960 ASN cc_start: 0.8809 (m-40) cc_final: 0.8148 (m-40) REVERT: B 964 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8633 (ptpt) REVERT: B 965 GLN cc_start: 0.9157 (mm110) cc_final: 0.8744 (mm-40) REVERT: B 979 ASP cc_start: 0.8583 (t0) cc_final: 0.8333 (t0) REVERT: B 1002 GLN cc_start: 0.8819 (mp10) cc_final: 0.8464 (mp10) REVERT: B 1009 THR cc_start: 0.9073 (p) cc_final: 0.8817 (p) REVERT: B 1011 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8113 (mp10) REVERT: B 1014 ARG cc_start: 0.8836 (mtt90) cc_final: 0.8441 (ptp-170) REVERT: B 1017 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8456 (tm-30) REVERT: B 1019 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.7971 (ttm-80) REVERT: B 1021 SER cc_start: 0.8688 (t) cc_final: 0.8425 (p) REVERT: B 1028 LYS cc_start: 0.7090 (tptm) cc_final: 0.6785 (tptt) REVERT: B 1050 MET cc_start: 0.5958 (tpt) cc_final: 0.5577 (mtp) REVERT: B 1107 ARG cc_start: 0.5487 (tmt170) cc_final: 0.5176 (tmm160) REVERT: C 41 LYS cc_start: 0.8617 (tppt) cc_final: 0.7853 (tppt) REVERT: C 59 PHE cc_start: 0.8135 (m-80) cc_final: 0.7668 (m-10) REVERT: C 65 PHE cc_start: 0.7732 (m-80) cc_final: 0.7467 (m-80) REVERT: C 91 TYR cc_start: 0.7448 (t80) cc_final: 0.6981 (t80) REVERT: C 117 LEU cc_start: 0.8799 (tt) cc_final: 0.8288 (pt) REVERT: C 129 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8469 (mmmt) REVERT: C 135 PHE cc_start: 0.8958 (m-10) cc_final: 0.8746 (m-10) REVERT: C 160 TYR cc_start: 0.8225 (p90) cc_final: 0.7701 (p90) REVERT: C 177 MET cc_start: 0.4761 (mtm) cc_final: 0.3105 (mmm) REVERT: C 192 PHE cc_start: 0.8558 (m-80) cc_final: 0.8282 (m-80) REVERT: C 194 PHE cc_start: 0.7893 (m-80) cc_final: 0.7570 (m-80) REVERT: C 235 ILE cc_start: 0.6953 (mt) cc_final: 0.6697 (mm) REVERT: C 237 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8517 (mmm-85) REVERT: C 276 LEU cc_start: 0.8019 (tp) cc_final: 0.7732 (tp) REVERT: C 281 GLU cc_start: 0.8290 (tp30) cc_final: 0.7709 (tp30) REVERT: C 289 VAL cc_start: 0.8679 (t) cc_final: 0.8406 (p) REVERT: C 298 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7401 (mp0) REVERT: C 300 LYS cc_start: 0.8288 (mttt) cc_final: 0.7735 (mmtt) REVERT: C 313 TYR cc_start: 0.7324 (m-80) cc_final: 0.6978 (m-80) REVERT: C 324 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8142 (mp0) REVERT: C 338 PHE cc_start: 0.9088 (m-80) cc_final: 0.8505 (m-10) REVERT: C 342 PHE cc_start: 0.8824 (m-80) cc_final: 0.8491 (m-10) REVERT: C 350 VAL cc_start: 0.7894 (p) cc_final: 0.7564 (p) REVERT: C 356 LYS cc_start: 0.7931 (tttm) cc_final: 0.7439 (tmmt) REVERT: C 365 TYR cc_start: 0.8600 (m-80) cc_final: 0.8258 (m-80) REVERT: C 380 TYR cc_start: 0.7810 (m-10) cc_final: 0.7492 (m-80) REVERT: C 386 LYS cc_start: 0.8331 (mttt) cc_final: 0.7947 (mtmm) REVERT: C 408 ARG cc_start: 0.8477 (mpt180) cc_final: 0.8164 (mpp-170) REVERT: C 409 GLN cc_start: 0.8180 (mp10) cc_final: 0.7656 (mp10) REVERT: C 417 LYS cc_start: 0.9085 (tppp) cc_final: 0.8839 (tppt) REVERT: C 418 ILE cc_start: 0.9548 (pt) cc_final: 0.9165 (mm) REVERT: C 425 LEU cc_start: 0.8286 (mt) cc_final: 0.7968 (tp) REVERT: C 490 PHE cc_start: 0.8393 (t80) cc_final: 0.8146 (t80) REVERT: C 516 GLU cc_start: 0.6364 (mp0) cc_final: 0.6012 (mp0) REVERT: C 533 LEU cc_start: 0.8800 (tp) cc_final: 0.8589 (pp) REVERT: C 583 GLU cc_start: 0.8491 (tp30) cc_final: 0.8177 (tm-30) REVERT: C 747 THR cc_start: 0.9085 (p) cc_final: 0.8796 (p) REVERT: C 748 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8618 (pm20) REVERT: C 755 GLN cc_start: 0.9115 (pt0) cc_final: 0.8828 (pt0) REVERT: C 756 TYR cc_start: 0.8385 (m-10) cc_final: 0.8177 (m-10) REVERT: C 759 PHE cc_start: 0.8578 (m-80) cc_final: 0.8050 (m-10) REVERT: C 761 THR cc_start: 0.9382 (m) cc_final: 0.8913 (p) REVERT: C 762 GLN cc_start: 0.9135 (mt0) cc_final: 0.8765 (mt0) REVERT: C 763 LEU cc_start: 0.9177 (mt) cc_final: 0.8968 (mt) REVERT: C 765 ARG cc_start: 0.9140 (mtm180) cc_final: 0.8740 (ptp-110) REVERT: C 770 ILE cc_start: 0.9219 (pt) cc_final: 0.8788 (pt) REVERT: C 773 GLU cc_start: 0.8697 (tt0) cc_final: 0.7993 (pp20) REVERT: C 774 GLN cc_start: 0.8887 (pt0) cc_final: 0.8671 (pp30) REVERT: C 776 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8335 (tmtt) REVERT: C 858 LEU cc_start: 0.8842 (mp) cc_final: 0.8543 (mm) REVERT: C 869 MET cc_start: 0.8994 (mtm) cc_final: 0.8186 (tmm) REVERT: C 917 TYR cc_start: 0.8053 (m-80) cc_final: 0.7712 (m-10) REVERT: C 934 ILE cc_start: 0.7018 (tp) cc_final: 0.6675 (mm) REVERT: C 936 ASP cc_start: 0.8231 (m-30) cc_final: 0.7999 (m-30) REVERT: C 955 ASN cc_start: 0.8058 (p0) cc_final: 0.7425 (p0) REVERT: C 957 GLN cc_start: 0.8898 (tt0) cc_final: 0.8612 (pp30) REVERT: C 959 LEU cc_start: 0.9143 (mp) cc_final: 0.8881 (pp) REVERT: C 964 LYS cc_start: 0.9366 (tttt) cc_final: 0.8753 (ttpp) REVERT: C 979 ASP cc_start: 0.9091 (m-30) cc_final: 0.8807 (m-30) REVERT: C 1000 ARG cc_start: 0.9081 (mmm160) cc_final: 0.8627 (mmt180) REVERT: C 1010 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8235 (tm-30) REVERT: C 1014 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.7756 (mmp80) REVERT: C 1017 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8089 (tm-30) REVERT: C 1018 ILE cc_start: 0.8748 (pt) cc_final: 0.7925 (pt) outliers start: 2 outliers final: 1 residues processed: 524 average time/residue: 0.6344 time to fit residues: 526.3470 Evaluate side-chains 462 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 460 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 3.9990 chunk 312 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B1058 HIS ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.178730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.131037 restraints weight = 62859.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.135407 restraints weight = 46007.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.138560 restraints weight = 36186.602| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 26386 Z= 0.318 Angle : 0.862 12.446 36017 Z= 0.449 Chirality : 0.052 0.477 4182 Planarity : 0.007 0.132 4587 Dihedral : 8.498 105.601 4373 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.10 % 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: -1.39 (0.14), residues: 3187 helix: -0.02 (0.18), residues: 702 sheet: -0.60 (0.20), residues: 630 loop : -1.42 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 64 HIS 0.018 0.003 HIS C 66 PHE 0.029 0.003 PHE A 800 TYR 0.041 0.003 TYR B 266 ARG 0.009 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 32) link_NAG-ASN : angle 3.96514 ( 96) link_BETA1-4 : bond 0.00493 ( 10) link_BETA1-4 : angle 1.57060 ( 30) hydrogen bonds : bond 0.05984 ( 872) hydrogen bonds : angle 6.72269 ( 2433) SS BOND : bond 0.00696 ( 42) SS BOND : angle 2.03426 ( 84) covalent geometry : bond 0.00617 (26300) covalent geometry : angle 0.83263 (35807) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 525 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7537 (ttpp) REVERT: A 53 ASP cc_start: 0.8530 (t0) cc_final: 0.8156 (t0) REVERT: A 65 PHE cc_start: 0.7975 (m-80) cc_final: 0.7307 (m-80) REVERT: A 84 LEU cc_start: 0.9246 (mp) cc_final: 0.9026 (mm) REVERT: A 91 TYR cc_start: 0.7420 (t80) cc_final: 0.7163 (t80) REVERT: A 99 ASN cc_start: 0.9376 (t0) cc_final: 0.9023 (t0) REVERT: A 104 TRP cc_start: 0.6725 (m-90) cc_final: 0.6385 (m-10) REVERT: A 106 PHE cc_start: 0.7534 (m-10) cc_final: 0.6749 (m-10) REVERT: A 118 LEU cc_start: 0.8731 (tp) cc_final: 0.8455 (mm) REVERT: A 192 PHE cc_start: 0.8057 (m-80) cc_final: 0.7757 (m-80) REVERT: A 194 PHE cc_start: 0.8359 (m-80) cc_final: 0.7177 (m-80) REVERT: A 202 LYS cc_start: 0.7385 (mmtt) cc_final: 0.7059 (mmtt) REVERT: A 223 LEU cc_start: 0.8916 (mm) cc_final: 0.8656 (mm) REVERT: A 228 ASP cc_start: 0.8143 (m-30) cc_final: 0.7897 (m-30) REVERT: A 275 PHE cc_start: 0.7000 (m-10) cc_final: 0.6140 (m-10) REVERT: A 304 LYS cc_start: 0.9262 (ptpp) cc_final: 0.8954 (mptt) REVERT: A 309 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8485 (tm-30) REVERT: A 310 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8667 (tptp) REVERT: A 357 ARG cc_start: 0.7480 (tmm160) cc_final: 0.7133 (tmm160) REVERT: A 380 TYR cc_start: 0.8195 (m-80) cc_final: 0.7657 (m-80) REVERT: A 389 ASP cc_start: 0.8926 (m-30) cc_final: 0.8405 (p0) REVERT: A 505 TYR cc_start: 0.8447 (t80) cc_final: 0.8217 (t80) REVERT: A 529 LYS cc_start: 0.9039 (tttm) cc_final: 0.8778 (mmtm) REVERT: A 562 PHE cc_start: 0.8444 (p90) cc_final: 0.8178 (p90) REVERT: A 751 ASN cc_start: 0.8956 (m110) cc_final: 0.8637 (m110) REVERT: A 756 TYR cc_start: 0.8799 (m-80) cc_final: 0.8384 (m-10) REVERT: A 759 PHE cc_start: 0.8848 (m-80) cc_final: 0.8034 (m-10) REVERT: A 762 GLN cc_start: 0.9025 (mt0) cc_final: 0.8757 (mt0) REVERT: A 776 LYS cc_start: 0.9016 (tptm) cc_final: 0.8485 (tptp) REVERT: A 867 ASP cc_start: 0.7974 (m-30) cc_final: 0.7639 (p0) REVERT: A 873 TYR cc_start: 0.8626 (m-10) cc_final: 0.8316 (m-80) REVERT: A 917 TYR cc_start: 0.8254 (m-80) cc_final: 0.7639 (m-10) REVERT: A 927 PHE cc_start: 0.7930 (t80) cc_final: 0.7453 (t80) REVERT: A 947 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7762 (pttt) REVERT: A 954 GLN cc_start: 0.9039 (tp40) cc_final: 0.8567 (tm-30) REVERT: A 964 LYS cc_start: 0.9277 (ttmm) cc_final: 0.8827 (mmtt) REVERT: A 979 ASP cc_start: 0.9216 (m-30) cc_final: 0.8633 (t0) REVERT: A 983 ARG cc_start: 0.8769 (ptt90) cc_final: 0.7676 (ttp80) REVERT: A 990 GLU cc_start: 0.8902 (tt0) cc_final: 0.8488 (mt-10) REVERT: A 994 ASP cc_start: 0.8874 (m-30) cc_final: 0.8387 (m-30) REVERT: A 1002 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 1014 ARG cc_start: 0.8923 (mmp-170) cc_final: 0.8517 (mmm160) REVERT: A 1050 MET cc_start: 0.5905 (ttt) cc_final: 0.5437 (ttt) REVERT: A 1053 PRO cc_start: 0.8362 (Cg_endo) cc_final: 0.7817 (Cg_exo) REVERT: B 37 TYR cc_start: 0.8848 (p90) cc_final: 0.8068 (p90) REVERT: B 41 LYS cc_start: 0.8754 (tppt) cc_final: 0.8325 (tppt) REVERT: B 56 LEU cc_start: 0.8918 (tt) cc_final: 0.8216 (pp) REVERT: B 58 PHE cc_start: 0.8130 (m-80) cc_final: 0.7292 (m-80) REVERT: B 65 PHE cc_start: 0.8486 (m-80) cc_final: 0.7920 (m-80) REVERT: B 86 PHE cc_start: 0.8179 (t80) cc_final: 0.7794 (t80) REVERT: B 129 LYS cc_start: 0.8342 (mppt) cc_final: 0.7922 (mmtm) REVERT: B 170 TYR cc_start: 0.8545 (t80) cc_final: 0.7898 (t80) REVERT: B 194 PHE cc_start: 0.7868 (m-80) cc_final: 0.7331 (m-10) REVERT: B 276 LEU cc_start: 0.8780 (tt) cc_final: 0.8080 (mt) REVERT: B 298 GLU cc_start: 0.8524 (tt0) cc_final: 0.8114 (tt0) REVERT: B 313 TYR cc_start: 0.7731 (m-80) cc_final: 0.7120 (m-80) REVERT: B 319 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8070 (mtm110) REVERT: B 365 TYR cc_start: 0.8588 (t80) cc_final: 0.8284 (t80) REVERT: B 396 TYR cc_start: 0.8140 (m-80) cc_final: 0.7892 (m-80) REVERT: B 562 PHE cc_start: 0.8869 (p90) cc_final: 0.8235 (p90) REVERT: B 586 ASP cc_start: 0.8180 (t0) cc_final: 0.7600 (p0) REVERT: B 587 ILE cc_start: 0.8799 (tp) cc_final: 0.8575 (tp) REVERT: B 603 ASN cc_start: 0.9389 (t0) cc_final: 0.8982 (p0) REVERT: B 731 MET cc_start: 0.7920 (tmm) cc_final: 0.7667 (tmm) REVERT: B 755 GLN cc_start: 0.9050 (pt0) cc_final: 0.8832 (pt0) REVERT: B 759 PHE cc_start: 0.8285 (m-80) cc_final: 0.7880 (m-80) REVERT: B 819 GLU cc_start: 0.8900 (pt0) cc_final: 0.8493 (pt0) REVERT: B 822 LEU cc_start: 0.9107 (tp) cc_final: 0.8719 (mt) REVERT: B 824 ASN cc_start: 0.8890 (m110) cc_final: 0.8621 (m-40) REVERT: B 869 MET cc_start: 0.8588 (mtt) cc_final: 0.8347 (mmt) REVERT: B 917 TYR cc_start: 0.8555 (m-80) cc_final: 0.8023 (m-80) REVERT: B 927 PHE cc_start: 0.8535 (t80) cc_final: 0.7924 (t80) REVERT: B 954 GLN cc_start: 0.9161 (mt0) cc_final: 0.8544 (tm-30) REVERT: B 955 ASN cc_start: 0.8882 (m110) cc_final: 0.8628 (t0) REVERT: B 959 LEU cc_start: 0.9092 (mm) cc_final: 0.8841 (pp) REVERT: B 960 ASN cc_start: 0.8815 (m-40) cc_final: 0.8030 (m-40) REVERT: B 984 LEU cc_start: 0.8724 (mt) cc_final: 0.8520 (mt) REVERT: B 1010 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8537 (mm-40) REVERT: B 1011 GLN cc_start: 0.8611 (mm-40) cc_final: 0.7982 (mm-40) REVERT: B 1017 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 1019 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8223 (ttm-80) REVERT: B 1021 SER cc_start: 0.8880 (t) cc_final: 0.8654 (p) REVERT: B 1028 LYS cc_start: 0.7567 (tptm) cc_final: 0.7181 (tptt) REVERT: B 1048 HIS cc_start: 0.6999 (p-80) cc_final: 0.6719 (p-80) REVERT: C 41 LYS cc_start: 0.8476 (tppt) cc_final: 0.7901 (tppt) REVERT: C 42 VAL cc_start: 0.9064 (m) cc_final: 0.8856 (p) REVERT: C 65 PHE cc_start: 0.8039 (m-80) cc_final: 0.7356 (m-80) REVERT: C 66 HIS cc_start: 0.5681 (OUTLIER) cc_final: 0.3341 (t70) REVERT: C 88 ASP cc_start: 0.9167 (p0) cc_final: 0.8837 (p0) REVERT: C 91 TYR cc_start: 0.7455 (t80) cc_final: 0.6686 (t80) REVERT: C 117 LEU cc_start: 0.8798 (tt) cc_final: 0.8469 (pp) REVERT: C 129 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8541 (mmmt) REVERT: C 133 PHE cc_start: 0.8190 (m-80) cc_final: 0.7605 (m-80) REVERT: C 160 TYR cc_start: 0.8742 (p90) cc_final: 0.8465 (p90) REVERT: C 192 PHE cc_start: 0.8672 (m-80) cc_final: 0.8138 (m-80) REVERT: C 201 PHE cc_start: 0.8647 (t80) cc_final: 0.8437 (t80) REVERT: C 223 LEU cc_start: 0.8555 (pt) cc_final: 0.8144 (pt) REVERT: C 235 ILE cc_start: 0.7219 (mt) cc_final: 0.6989 (mm) REVERT: C 281 GLU cc_start: 0.8368 (tp30) cc_final: 0.7990 (tp30) REVERT: C 298 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7571 (mp0) REVERT: C 300 LYS cc_start: 0.8508 (mttt) cc_final: 0.7997 (mmtp) REVERT: C 313 TYR cc_start: 0.7341 (m-80) cc_final: 0.6955 (m-80) REVERT: C 324 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8371 (mp0) REVERT: C 338 PHE cc_start: 0.9105 (m-80) cc_final: 0.8556 (m-10) REVERT: C 342 PHE cc_start: 0.8795 (m-80) cc_final: 0.8481 (m-80) REVERT: C 365 TYR cc_start: 0.8660 (m-80) cc_final: 0.8255 (m-80) REVERT: C 377 PHE cc_start: 0.7906 (t80) cc_final: 0.7688 (t80) REVERT: C 417 LYS cc_start: 0.8964 (tppp) cc_final: 0.8540 (tppt) REVERT: C 421 TYR cc_start: 0.8712 (m-10) cc_final: 0.8409 (m-10) REVERT: C 425 LEU cc_start: 0.8267 (mt) cc_final: 0.7949 (tp) REVERT: C 451 TYR cc_start: 0.6719 (m-80) cc_final: 0.6382 (m-80) REVERT: C 490 PHE cc_start: 0.8588 (t80) cc_final: 0.8382 (t80) REVERT: C 505 TYR cc_start: 0.8559 (t80) cc_final: 0.8254 (t80) REVERT: C 543 PHE cc_start: 0.8403 (m-80) cc_final: 0.8200 (m-80) REVERT: C 563 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7389 (mm-40) REVERT: C 571 ASP cc_start: 0.9254 (t0) cc_final: 0.8908 (t0) REVERT: C 737 ASP cc_start: 0.8747 (t0) cc_final: 0.8506 (t0) REVERT: C 748 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8923 (mp0) REVERT: C 755 GLN cc_start: 0.9196 (pt0) cc_final: 0.8750 (pp30) REVERT: C 756 TYR cc_start: 0.8502 (m-10) cc_final: 0.7801 (m-10) REVERT: C 759 PHE cc_start: 0.8577 (m-80) cc_final: 0.7987 (m-10) REVERT: C 762 GLN cc_start: 0.9169 (mt0) cc_final: 0.8766 (mt0) REVERT: C 765 ARG cc_start: 0.9303 (mtm180) cc_final: 0.8968 (ptp-110) REVERT: C 770 ILE cc_start: 0.9245 (pt) cc_final: 0.8838 (pt) REVERT: C 773 GLU cc_start: 0.8845 (tt0) cc_final: 0.8236 (pp20) REVERT: C 774 GLN cc_start: 0.9148 (pt0) cc_final: 0.8800 (pp30) REVERT: C 776 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8413 (tmtt) REVERT: C 858 LEU cc_start: 0.8821 (mp) cc_final: 0.8486 (mm) REVERT: C 869 MET cc_start: 0.9180 (mtm) cc_final: 0.8234 (tmm) REVERT: C 902 MET cc_start: 0.5437 (tmm) cc_final: 0.5177 (ptm) REVERT: C 934 ILE cc_start: 0.8002 (tp) cc_final: 0.7748 (tp) REVERT: C 935 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8904 (mm110) REVERT: C 955 ASN cc_start: 0.8188 (p0) cc_final: 0.7243 (p0) REVERT: C 957 GLN cc_start: 0.9008 (tt0) cc_final: 0.8629 (pp30) REVERT: C 959 LEU cc_start: 0.9260 (mp) cc_final: 0.9023 (pp) REVERT: C 964 LYS cc_start: 0.9457 (tttt) cc_final: 0.9111 (tmtt) REVERT: C 970 PHE cc_start: 0.8284 (m-80) cc_final: 0.8050 (m-10) REVERT: C 979 ASP cc_start: 0.9200 (m-30) cc_final: 0.8902 (m-30) REVERT: C 994 ASP cc_start: 0.8679 (m-30) cc_final: 0.8413 (m-30) REVERT: C 1001 LEU cc_start: 0.9439 (tp) cc_final: 0.9074 (tp) REVERT: C 1002 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8722 (mm110) REVERT: C 1010 GLN cc_start: 0.8954 (tp-100) cc_final: 0.7634 (tm-30) REVERT: C 1014 ARG cc_start: 0.8716 (mmt-90) cc_final: 0.7882 (mmp80) REVERT: C 1017 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8604 (tm-30) REVERT: C 1018 ILE cc_start: 0.8802 (pt) cc_final: 0.8202 (pt) outliers start: 3 outliers final: 1 residues processed: 528 average time/residue: 0.4524 time to fit residues: 371.6956 Evaluate side-chains 473 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 470 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 145 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 241 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 100 optimal weight: 0.0070 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 935 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 779 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.176771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.130008 restraints weight = 64535.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134855 restraints weight = 45603.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.138432 restraints weight = 34986.390| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26386 Z= 0.155 Angle : 0.728 12.640 36017 Z= 0.364 Chirality : 0.049 0.434 4182 Planarity : 0.005 0.077 4587 Dihedral : 8.186 106.439 4373 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3187 helix: 0.45 (0.19), residues: 690 sheet: -0.56 (0.21), residues: 613 loop : -1.34 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 436 HIS 0.024 0.002 HIS B 66 PHE 0.045 0.002 PHE A 238 TYR 0.023 0.002 TYR A 495 ARG 0.007 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 32) link_NAG-ASN : angle 3.57340 ( 96) link_BETA1-4 : bond 0.00365 ( 10) link_BETA1-4 : angle 1.50548 ( 30) hydrogen bonds : bond 0.04752 ( 872) hydrogen bonds : angle 6.26976 ( 2433) SS BOND : bond 0.00505 ( 42) SS BOND : angle 1.99401 ( 84) covalent geometry : bond 0.00339 (26300) covalent geometry : angle 0.69834 (35807) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7520 (ttpt) REVERT: A 53 ASP cc_start: 0.8423 (t0) cc_final: 0.8022 (t0) REVERT: A 65 PHE cc_start: 0.7888 (m-80) cc_final: 0.7224 (m-80) REVERT: A 84 LEU cc_start: 0.9189 (mp) cc_final: 0.8949 (mm) REVERT: A 99 ASN cc_start: 0.9322 (t0) cc_final: 0.9044 (t0) REVERT: A 104 TRP cc_start: 0.6727 (m-90) cc_final: 0.6335 (m-10) REVERT: A 106 PHE cc_start: 0.8022 (m-10) cc_final: 0.7711 (m-10) REVERT: A 117 LEU cc_start: 0.7879 (tp) cc_final: 0.7672 (tp) REVERT: A 118 LEU cc_start: 0.8681 (tp) cc_final: 0.8396 (mm) REVERT: A 128 ILE cc_start: 0.8629 (mt) cc_final: 0.7590 (mm) REVERT: A 135 PHE cc_start: 0.8433 (m-10) cc_final: 0.8013 (m-10) REVERT: A 170 TYR cc_start: 0.7394 (t80) cc_final: 0.7055 (t80) REVERT: A 192 PHE cc_start: 0.8041 (m-80) cc_final: 0.7728 (m-80) REVERT: A 194 PHE cc_start: 0.8300 (m-80) cc_final: 0.7386 (m-80) REVERT: A 201 PHE cc_start: 0.7820 (m-80) cc_final: 0.7450 (m-80) REVERT: A 207 HIS cc_start: 0.9284 (p-80) cc_final: 0.8915 (p-80) REVERT: A 223 LEU cc_start: 0.8857 (mm) cc_final: 0.8552 (mm) REVERT: A 275 PHE cc_start: 0.6557 (m-10) cc_final: 0.5988 (m-10) REVERT: A 304 LYS cc_start: 0.9272 (ptpp) cc_final: 0.8952 (mmtt) REVERT: A 309 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8383 (tm-30) REVERT: A 310 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8359 (tppt) REVERT: A 357 ARG cc_start: 0.7692 (tmm160) cc_final: 0.7376 (tmm160) REVERT: A 365 TYR cc_start: 0.8137 (m-80) cc_final: 0.7829 (m-80) REVERT: A 380 TYR cc_start: 0.8268 (m-80) cc_final: 0.7650 (m-80) REVERT: A 389 ASP cc_start: 0.8625 (m-30) cc_final: 0.8276 (p0) REVERT: A 400 PHE cc_start: 0.6921 (p90) cc_final: 0.6281 (p90) REVERT: A 529 LYS cc_start: 0.8836 (tttm) cc_final: 0.8627 (mmtm) REVERT: A 557 LYS cc_start: 0.8314 (mttt) cc_final: 0.7501 (tptm) REVERT: A 562 PHE cc_start: 0.8280 (p90) cc_final: 0.7677 (p90) REVERT: A 751 ASN cc_start: 0.8988 (m110) cc_final: 0.8709 (p0) REVERT: A 752 LEU cc_start: 0.9161 (tt) cc_final: 0.8870 (tt) REVERT: A 759 PHE cc_start: 0.8882 (m-80) cc_final: 0.8209 (m-80) REVERT: A 762 GLN cc_start: 0.9046 (mt0) cc_final: 0.8125 (mp10) REVERT: A 763 LEU cc_start: 0.9475 (mt) cc_final: 0.9181 (mt) REVERT: A 764 ASN cc_start: 0.9061 (m110) cc_final: 0.8820 (m-40) REVERT: A 774 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8355 (mm-40) REVERT: A 776 LYS cc_start: 0.8972 (tptm) cc_final: 0.8408 (tptp) REVERT: A 856 ASN cc_start: 0.8291 (t0) cc_final: 0.7987 (p0) REVERT: A 867 ASP cc_start: 0.7883 (m-30) cc_final: 0.7534 (p0) REVERT: A 869 MET cc_start: 0.8231 (ptp) cc_final: 0.7682 (ptp) REVERT: A 873 TYR cc_start: 0.8397 (m-10) cc_final: 0.8093 (m-80) REVERT: A 917 TYR cc_start: 0.8015 (m-80) cc_final: 0.7423 (m-10) REVERT: A 927 PHE cc_start: 0.8079 (t80) cc_final: 0.7525 (t80) REVERT: A 954 GLN cc_start: 0.8977 (tp40) cc_final: 0.8516 (tm-30) REVERT: A 964 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8254 (tptp) REVERT: A 969 ASN cc_start: 0.9293 (p0) cc_final: 0.9042 (p0) REVERT: A 979 ASP cc_start: 0.9033 (m-30) cc_final: 0.8409 (t0) REVERT: A 983 ARG cc_start: 0.8720 (ptt90) cc_final: 0.7478 (ttp80) REVERT: A 990 GLU cc_start: 0.8806 (tt0) cc_final: 0.8421 (mt-10) REVERT: A 994 ASP cc_start: 0.8702 (m-30) cc_final: 0.8178 (m-30) REVERT: A 1002 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 1005 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8978 (mm-40) REVERT: A 1010 GLN cc_start: 0.8718 (pp30) cc_final: 0.8451 (pp30) REVERT: A 1014 ARG cc_start: 0.8808 (mmp-170) cc_final: 0.8589 (mmp-170) REVERT: A 1019 ARG cc_start: 0.8886 (ttt180) cc_final: 0.8085 (ttm110) REVERT: A 1023 ASN cc_start: 0.8726 (m-40) cc_final: 0.8509 (m-40) REVERT: A 1050 MET cc_start: 0.5378 (ttt) cc_final: 0.4802 (ttt) REVERT: A 1062 PHE cc_start: 0.6779 (m-10) cc_final: 0.6216 (m-80) REVERT: B 37 TYR cc_start: 0.8586 (p90) cc_final: 0.7948 (p90) REVERT: B 41 LYS cc_start: 0.8745 (tppt) cc_final: 0.8393 (tppt) REVERT: B 58 PHE cc_start: 0.8168 (m-80) cc_final: 0.6400 (m-80) REVERT: B 65 PHE cc_start: 0.8316 (m-80) cc_final: 0.7942 (m-80) REVERT: B 86 PHE cc_start: 0.8051 (t80) cc_final: 0.7768 (t80) REVERT: B 129 LYS cc_start: 0.8279 (mppt) cc_final: 0.7943 (mmtm) REVERT: B 153 MET cc_start: 0.4270 (ptp) cc_final: 0.4018 (ptp) REVERT: B 194 PHE cc_start: 0.7934 (m-80) cc_final: 0.7331 (m-10) REVERT: B 265 TYR cc_start: 0.6512 (p90) cc_final: 0.6276 (p90) REVERT: B 275 PHE cc_start: 0.7462 (m-10) cc_final: 0.5987 (m-10) REVERT: B 276 LEU cc_start: 0.8759 (tt) cc_final: 0.7956 (mt) REVERT: B 298 GLU cc_start: 0.8496 (tt0) cc_final: 0.8113 (tt0) REVERT: B 300 LYS cc_start: 0.8018 (mttt) cc_final: 0.7495 (mtmm) REVERT: B 313 TYR cc_start: 0.7630 (m-80) cc_final: 0.7064 (m-10) REVERT: B 553 THR cc_start: 0.7892 (m) cc_final: 0.6798 (m) REVERT: B 562 PHE cc_start: 0.8846 (p90) cc_final: 0.8149 (p90) REVERT: B 571 ASP cc_start: 0.9105 (m-30) cc_final: 0.8561 (m-30) REVERT: B 578 ASP cc_start: 0.8487 (p0) cc_final: 0.8253 (p0) REVERT: B 586 ASP cc_start: 0.8153 (t0) cc_final: 0.7549 (p0) REVERT: B 603 ASN cc_start: 0.9308 (t0) cc_final: 0.8978 (p0) REVERT: B 697 MET cc_start: 0.7713 (pmm) cc_final: 0.7487 (pmm) REVERT: B 731 MET cc_start: 0.7679 (tmm) cc_final: 0.7443 (tmm) REVERT: B 759 PHE cc_start: 0.8249 (m-80) cc_final: 0.7969 (m-80) REVERT: B 819 GLU cc_start: 0.8846 (pt0) cc_final: 0.8293 (pt0) REVERT: B 822 LEU cc_start: 0.9097 (tp) cc_final: 0.8632 (mt) REVERT: B 824 ASN cc_start: 0.8733 (m110) cc_final: 0.8443 (m110) REVERT: B 869 MET cc_start: 0.8474 (mtt) cc_final: 0.7682 (mmt) REVERT: B 873 TYR cc_start: 0.7920 (m-10) cc_final: 0.7184 (m-80) REVERT: B 917 TYR cc_start: 0.8305 (m-80) cc_final: 0.7882 (m-80) REVERT: B 927 PHE cc_start: 0.8474 (t80) cc_final: 0.7802 (t80) REVERT: B 937 SER cc_start: 0.8640 (t) cc_final: 0.8327 (p) REVERT: B 954 GLN cc_start: 0.9059 (mt0) cc_final: 0.8503 (tm-30) REVERT: B 955 ASN cc_start: 0.8884 (m110) cc_final: 0.8579 (t0) REVERT: B 960 ASN cc_start: 0.8761 (m-40) cc_final: 0.7920 (t0) REVERT: B 964 LYS cc_start: 0.9088 (ptpp) cc_final: 0.7942 (pttt) REVERT: B 965 GLN cc_start: 0.9022 (mm110) cc_final: 0.8749 (mm-40) REVERT: B 983 ARG cc_start: 0.8089 (tmm-80) cc_final: 0.7454 (tmm-80) REVERT: B 995 ARG cc_start: 0.8538 (ptt180) cc_final: 0.8290 (ptt180) REVERT: B 1011 GLN cc_start: 0.8620 (mm-40) cc_final: 0.7961 (mm-40) REVERT: B 1017 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 1019 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8103 (ttm-80) REVERT: B 1021 SER cc_start: 0.8801 (t) cc_final: 0.8582 (p) REVERT: B 1028 LYS cc_start: 0.7486 (tptm) cc_final: 0.7088 (tptt) REVERT: B 1107 ARG cc_start: 0.6083 (tmt170) cc_final: 0.5829 (tmt170) REVERT: C 41 LYS cc_start: 0.8514 (tppt) cc_final: 0.7832 (tppt) REVERT: C 42 VAL cc_start: 0.9003 (m) cc_final: 0.8801 (p) REVERT: C 65 PHE cc_start: 0.7943 (m-80) cc_final: 0.7516 (m-80) REVERT: C 88 ASP cc_start: 0.9120 (p0) cc_final: 0.8869 (p0) REVERT: C 91 TYR cc_start: 0.7316 (t80) cc_final: 0.6629 (t80) REVERT: C 117 LEU cc_start: 0.8826 (tt) cc_final: 0.8441 (pp) REVERT: C 129 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8459 (mmmt) REVERT: C 133 PHE cc_start: 0.8193 (m-80) cc_final: 0.7485 (m-80) REVERT: C 135 PHE cc_start: 0.9090 (m-80) cc_final: 0.8702 (m-10) REVERT: C 177 MET cc_start: 0.4669 (mtm) cc_final: 0.3440 (mmm) REVERT: C 192 PHE cc_start: 0.8672 (m-80) cc_final: 0.8102 (m-80) REVERT: C 194 PHE cc_start: 0.7817 (m-80) cc_final: 0.7572 (m-80) REVERT: C 223 LEU cc_start: 0.8051 (pt) cc_final: 0.7701 (pt) REVERT: C 235 ILE cc_start: 0.7322 (mt) cc_final: 0.7115 (mm) REVERT: C 237 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8462 (mtp180) REVERT: C 281 GLU cc_start: 0.8297 (tp30) cc_final: 0.7863 (tp30) REVERT: C 298 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 300 LYS cc_start: 0.8249 (mttt) cc_final: 0.7785 (mmtt) REVERT: C 313 TYR cc_start: 0.7302 (m-80) cc_final: 0.6863 (m-80) REVERT: C 314 GLN cc_start: 0.7403 (tm-30) cc_final: 0.7192 (tm-30) REVERT: C 324 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8318 (mp0) REVERT: C 338 PHE cc_start: 0.9058 (m-80) cc_final: 0.8578 (m-10) REVERT: C 342 PHE cc_start: 0.8814 (m-80) cc_final: 0.8425 (m-80) REVERT: C 365 TYR cc_start: 0.8745 (m-80) cc_final: 0.8325 (m-80) REVERT: C 380 TYR cc_start: 0.7697 (m-80) cc_final: 0.7117 (m-80) REVERT: C 386 LYS cc_start: 0.8491 (mttt) cc_final: 0.8043 (mtmm) REVERT: C 409 GLN cc_start: 0.8463 (mp10) cc_final: 0.7963 (mp10) REVERT: C 417 LYS cc_start: 0.8918 (tppp) cc_final: 0.8434 (tppt) REVERT: C 421 TYR cc_start: 0.8687 (m-10) cc_final: 0.8393 (m-10) REVERT: C 424 LYS cc_start: 0.7058 (ttpt) cc_final: 0.6843 (tppt) REVERT: C 425 LEU cc_start: 0.8253 (mt) cc_final: 0.7941 (tp) REVERT: C 451 TYR cc_start: 0.6113 (m-80) cc_final: 0.5638 (m-80) REVERT: C 458 LYS cc_start: 0.6950 (mtmm) cc_final: 0.6728 (mtpp) REVERT: C 543 PHE cc_start: 0.8366 (m-80) cc_final: 0.8142 (m-80) REVERT: C 563 GLN cc_start: 0.7705 (mm-40) cc_final: 0.6932 (mm-40) REVERT: C 565 PHE cc_start: 0.8204 (m-10) cc_final: 0.7893 (m-10) REVERT: C 737 ASP cc_start: 0.8665 (t0) cc_final: 0.8385 (t0) REVERT: C 748 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8940 (pm20) REVERT: C 755 GLN cc_start: 0.9176 (pt0) cc_final: 0.8908 (pt0) REVERT: C 756 TYR cc_start: 0.8500 (m-10) cc_final: 0.8295 (m-10) REVERT: C 759 PHE cc_start: 0.8564 (m-80) cc_final: 0.8002 (m-10) REVERT: C 762 GLN cc_start: 0.9137 (mt0) cc_final: 0.8632 (mt0) REVERT: C 763 LEU cc_start: 0.9048 (mt) cc_final: 0.8724 (mt) REVERT: C 770 ILE cc_start: 0.9209 (pt) cc_final: 0.8716 (pt) REVERT: C 773 GLU cc_start: 0.8720 (tt0) cc_final: 0.8085 (pp20) REVERT: C 774 GLN cc_start: 0.9051 (pt0) cc_final: 0.8681 (pp30) REVERT: C 776 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8092 (tptp) REVERT: C 858 LEU cc_start: 0.8835 (mp) cc_final: 0.8507 (mm) REVERT: C 869 MET cc_start: 0.8997 (mtm) cc_final: 0.7583 (mtt) REVERT: C 873 TYR cc_start: 0.8034 (m-10) cc_final: 0.7557 (m-80) REVERT: C 957 GLN cc_start: 0.9027 (tt0) cc_final: 0.8621 (pp30) REVERT: C 959 LEU cc_start: 0.9099 (mp) cc_final: 0.8873 (pp) REVERT: C 964 LYS cc_start: 0.9401 (tttt) cc_final: 0.8730 (tppt) REVERT: C 970 PHE cc_start: 0.8095 (m-80) cc_final: 0.7609 (m-10) REVERT: C 979 ASP cc_start: 0.9116 (m-30) cc_final: 0.8875 (m-30) REVERT: C 1001 LEU cc_start: 0.9359 (tp) cc_final: 0.9004 (tp) REVERT: C 1002 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8557 (mm110) REVERT: C 1010 GLN cc_start: 0.8913 (tp-100) cc_final: 0.7582 (tm-30) REVERT: C 1014 ARG cc_start: 0.8920 (mmt-90) cc_final: 0.7781 (mmp80) REVERT: C 1017 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8479 (tm-30) REVERT: C 1018 ILE cc_start: 0.8793 (pt) cc_final: 0.7999 (pt) REVERT: C 1050 MET cc_start: 0.2580 (ttt) cc_final: 0.2022 (ttt) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.4023 time to fit residues: 324.1617 Evaluate side-chains 470 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 61 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 306 optimal weight: 0.5980 chunk 300 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 296 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 764 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.174311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.128617 restraints weight = 66338.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.133498 restraints weight = 46514.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.137130 restraints weight = 35454.310| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26386 Z= 0.151 Angle : 0.716 11.874 36017 Z= 0.357 Chirality : 0.048 0.404 4182 Planarity : 0.005 0.074 4587 Dihedral : 8.002 105.689 4373 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3187 helix: 0.46 (0.19), residues: 686 sheet: -0.51 (0.20), residues: 601 loop : -1.35 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 64 HIS 0.015 0.002 HIS B 66 PHE 0.029 0.002 PHE B 175 TYR 0.018 0.002 TYR A 495 ARG 0.007 0.001 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 32) link_NAG-ASN : angle 3.40333 ( 96) link_BETA1-4 : bond 0.00415 ( 10) link_BETA1-4 : angle 1.40689 ( 30) hydrogen bonds : bond 0.04522 ( 872) hydrogen bonds : angle 6.11607 ( 2433) SS BOND : bond 0.00335 ( 42) SS BOND : angle 2.03267 ( 84) covalent geometry : bond 0.00326 (26300) covalent geometry : angle 0.68742 (35807) Misc. bond : bond 0.00877 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7440 (ttpp) REVERT: A 43 PHE cc_start: 0.8403 (t80) cc_final: 0.8128 (t80) REVERT: A 53 ASP cc_start: 0.8427 (t0) cc_final: 0.8022 (t0) REVERT: A 54 LEU cc_start: 0.8633 (tp) cc_final: 0.8212 (tp) REVERT: A 65 PHE cc_start: 0.7923 (m-80) cc_final: 0.7371 (m-80) REVERT: A 84 LEU cc_start: 0.9177 (mp) cc_final: 0.8932 (mm) REVERT: A 99 ASN cc_start: 0.9347 (t0) cc_final: 0.9117 (t0) REVERT: A 104 TRP cc_start: 0.6597 (m-90) cc_final: 0.6252 (m-10) REVERT: A 106 PHE cc_start: 0.7748 (m-10) cc_final: 0.7485 (m-10) REVERT: A 128 ILE cc_start: 0.8466 (mt) cc_final: 0.7811 (mm) REVERT: A 129 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8821 (mmmt) REVERT: A 192 PHE cc_start: 0.7990 (m-80) cc_final: 0.7667 (m-80) REVERT: A 194 PHE cc_start: 0.8206 (m-80) cc_final: 0.7311 (m-80) REVERT: A 201 PHE cc_start: 0.7780 (m-80) cc_final: 0.7383 (m-80) REVERT: A 207 HIS cc_start: 0.9282 (p-80) cc_final: 0.8922 (p-80) REVERT: A 223 LEU cc_start: 0.8894 (mm) cc_final: 0.8574 (mm) REVERT: A 275 PHE cc_start: 0.6686 (m-10) cc_final: 0.6010 (m-10) REVERT: A 304 LYS cc_start: 0.9275 (ptpp) cc_final: 0.8986 (mmtt) REVERT: A 309 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 310 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8293 (tppt) REVERT: A 357 ARG cc_start: 0.7654 (tmm160) cc_final: 0.7315 (tmm160) REVERT: A 365 TYR cc_start: 0.8215 (m-80) cc_final: 0.7831 (m-80) REVERT: A 380 TYR cc_start: 0.8265 (m-80) cc_final: 0.7642 (m-80) REVERT: A 389 ASP cc_start: 0.8596 (m-30) cc_final: 0.8269 (p0) REVERT: A 532 ASN cc_start: 0.8572 (p0) cc_final: 0.8366 (t0) REVERT: A 557 LYS cc_start: 0.8272 (mttt) cc_final: 0.7469 (tptm) REVERT: A 562 PHE cc_start: 0.8321 (p90) cc_final: 0.7677 (p90) REVERT: A 751 ASN cc_start: 0.8941 (m110) cc_final: 0.8735 (p0) REVERT: A 752 LEU cc_start: 0.9191 (tt) cc_final: 0.8913 (tt) REVERT: A 759 PHE cc_start: 0.8806 (m-80) cc_final: 0.8126 (m-80) REVERT: A 762 GLN cc_start: 0.8947 (mt0) cc_final: 0.8698 (mt0) REVERT: A 763 LEU cc_start: 0.9442 (mt) cc_final: 0.9192 (mt) REVERT: A 764 ASN cc_start: 0.8961 (m110) cc_final: 0.8738 (m-40) REVERT: A 776 LYS cc_start: 0.8964 (tptm) cc_final: 0.8385 (tptp) REVERT: A 856 ASN cc_start: 0.8210 (t0) cc_final: 0.7987 (p0) REVERT: A 867 ASP cc_start: 0.7831 (m-30) cc_final: 0.7523 (p0) REVERT: A 869 MET cc_start: 0.8407 (ptp) cc_final: 0.7815 (ptp) REVERT: A 873 TYR cc_start: 0.8405 (m-10) cc_final: 0.8125 (m-80) REVERT: A 917 TYR cc_start: 0.8012 (m-80) cc_final: 0.7432 (m-10) REVERT: A 927 PHE cc_start: 0.8171 (t80) cc_final: 0.7576 (t80) REVERT: A 947 LYS cc_start: 0.7026 (pttt) cc_final: 0.6797 (pttm) REVERT: A 954 GLN cc_start: 0.8884 (tp40) cc_final: 0.8464 (tm-30) REVERT: A 964 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8205 (tppt) REVERT: A 979 ASP cc_start: 0.9191 (m-30) cc_final: 0.8623 (t0) REVERT: A 983 ARG cc_start: 0.8701 (ptt90) cc_final: 0.7616 (ttp80) REVERT: A 990 GLU cc_start: 0.8807 (tt0) cc_final: 0.8417 (mt-10) REVERT: A 994 ASP cc_start: 0.8678 (m-30) cc_final: 0.8188 (m-30) REVERT: A 998 THR cc_start: 0.9148 (m) cc_final: 0.8932 (p) REVERT: A 1000 ARG cc_start: 0.9101 (mmt180) cc_final: 0.8814 (mmt180) REVERT: A 1002 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 1005 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8769 (mm-40) REVERT: A 1014 ARG cc_start: 0.8811 (mmp-170) cc_final: 0.8375 (mmp80) REVERT: A 1019 ARG cc_start: 0.8887 (ttt180) cc_final: 0.8095 (ttm110) REVERT: A 1050 MET cc_start: 0.5267 (ttt) cc_final: 0.4746 (ttt) REVERT: B 37 TYR cc_start: 0.8623 (p90) cc_final: 0.8111 (p90) REVERT: B 41 LYS cc_start: 0.8739 (tppt) cc_final: 0.8360 (tppt) REVERT: B 58 PHE cc_start: 0.8105 (m-80) cc_final: 0.7216 (m-80) REVERT: B 86 PHE cc_start: 0.7965 (t80) cc_final: 0.7650 (t80) REVERT: B 129 LYS cc_start: 0.8252 (mppt) cc_final: 0.7940 (mmtm) REVERT: B 177 MET cc_start: -0.0040 (mmp) cc_final: -0.0722 (mpp) REVERT: B 194 PHE cc_start: 0.7915 (m-80) cc_final: 0.7459 (m-10) REVERT: B 265 TYR cc_start: 0.6659 (p90) cc_final: 0.6413 (p90) REVERT: B 276 LEU cc_start: 0.8733 (tt) cc_final: 0.8031 (mt) REVERT: B 298 GLU cc_start: 0.8569 (tt0) cc_final: 0.8175 (tt0) REVERT: B 300 LYS cc_start: 0.8061 (mttt) cc_final: 0.7479 (mtmm) REVERT: B 313 TYR cc_start: 0.7627 (m-80) cc_final: 0.7046 (m-10) REVERT: B 319 ARG cc_start: 0.8579 (ptp90) cc_final: 0.8076 (ptp90) REVERT: B 321 GLN cc_start: 0.8257 (mp10) cc_final: 0.7916 (mp10) REVERT: B 562 PHE cc_start: 0.8803 (p90) cc_final: 0.8058 (p90) REVERT: B 586 ASP cc_start: 0.8157 (t0) cc_final: 0.7625 (p0) REVERT: B 587 ILE cc_start: 0.8691 (tp) cc_final: 0.8486 (tp) REVERT: B 603 ASN cc_start: 0.9292 (t0) cc_final: 0.8993 (p0) REVERT: B 731 MET cc_start: 0.7611 (tmm) cc_final: 0.7410 (tmm) REVERT: B 753 LEU cc_start: 0.8966 (mm) cc_final: 0.8624 (mt) REVERT: B 754 LEU cc_start: 0.8965 (mt) cc_final: 0.8763 (mt) REVERT: B 759 PHE cc_start: 0.8244 (m-80) cc_final: 0.7964 (m-80) REVERT: B 819 GLU cc_start: 0.8832 (pt0) cc_final: 0.8291 (pt0) REVERT: B 822 LEU cc_start: 0.9073 (tp) cc_final: 0.8604 (mt) REVERT: B 824 ASN cc_start: 0.8815 (m110) cc_final: 0.8450 (m110) REVERT: B 869 MET cc_start: 0.8720 (mtt) cc_final: 0.7686 (mmp) REVERT: B 873 TYR cc_start: 0.7447 (m-10) cc_final: 0.7119 (m-80) REVERT: B 917 TYR cc_start: 0.8254 (m-80) cc_final: 0.8024 (m-80) REVERT: B 927 PHE cc_start: 0.8515 (t80) cc_final: 0.7811 (t80) REVERT: B 937 SER cc_start: 0.8611 (t) cc_final: 0.8303 (p) REVERT: B 954 GLN cc_start: 0.9127 (mt0) cc_final: 0.8576 (tm-30) REVERT: B 960 ASN cc_start: 0.8647 (m-40) cc_final: 0.7854 (t0) REVERT: B 964 LYS cc_start: 0.9033 (ptpp) cc_final: 0.7744 (pttt) REVERT: B 965 GLN cc_start: 0.8925 (mm110) cc_final: 0.8626 (mm-40) REVERT: B 995 ARG cc_start: 0.8412 (ptt180) cc_final: 0.8019 (ttp-170) REVERT: B 1011 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8071 (mp10) REVERT: B 1014 ARG cc_start: 0.8961 (mtt90) cc_final: 0.7994 (ptp-110) REVERT: B 1017 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8469 (tm-30) REVERT: B 1021 SER cc_start: 0.8880 (t) cc_final: 0.8655 (p) REVERT: B 1028 LYS cc_start: 0.7209 (tptm) cc_final: 0.6936 (tptt) REVERT: B 1107 ARG cc_start: 0.6235 (tmt170) cc_final: 0.6030 (tmt170) REVERT: C 41 LYS cc_start: 0.8553 (tppt) cc_final: 0.7893 (tppt) REVERT: C 65 PHE cc_start: 0.7955 (m-80) cc_final: 0.7572 (m-80) REVERT: C 88 ASP cc_start: 0.9101 (p0) cc_final: 0.8828 (p0) REVERT: C 117 LEU cc_start: 0.8776 (tt) cc_final: 0.8222 (pt) REVERT: C 129 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8450 (mmmt) REVERT: C 133 PHE cc_start: 0.8166 (m-80) cc_final: 0.7470 (m-80) REVERT: C 135 PHE cc_start: 0.9081 (m-80) cc_final: 0.8774 (m-80) REVERT: C 192 PHE cc_start: 0.8689 (m-80) cc_final: 0.8129 (m-80) REVERT: C 194 PHE cc_start: 0.7864 (m-80) cc_final: 0.7598 (m-80) REVERT: C 223 LEU cc_start: 0.7978 (pt) cc_final: 0.7672 (pt) REVERT: C 235 ILE cc_start: 0.7312 (mt) cc_final: 0.7025 (mm) REVERT: C 237 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8478 (mtp180) REVERT: C 281 GLU cc_start: 0.8338 (tp30) cc_final: 0.7920 (tp30) REVERT: C 298 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7447 (mp0) REVERT: C 300 LYS cc_start: 0.8279 (mttt) cc_final: 0.7802 (mmtt) REVERT: C 313 TYR cc_start: 0.7323 (m-80) cc_final: 0.6938 (m-80) REVERT: C 324 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8338 (mp0) REVERT: C 338 PHE cc_start: 0.9181 (m-80) cc_final: 0.8587 (m-10) REVERT: C 342 PHE cc_start: 0.8734 (m-80) cc_final: 0.8390 (m-80) REVERT: C 365 TYR cc_start: 0.8760 (m-80) cc_final: 0.8306 (m-80) REVERT: C 380 TYR cc_start: 0.7369 (m-80) cc_final: 0.7078 (m-80) REVERT: C 386 LYS cc_start: 0.8559 (mttt) cc_final: 0.8165 (mtmm) REVERT: C 409 GLN cc_start: 0.8503 (mp10) cc_final: 0.8097 (mp10) REVERT: C 417 LYS cc_start: 0.8971 (tppp) cc_final: 0.8529 (tppt) REVERT: C 418 ILE cc_start: 0.9479 (pt) cc_final: 0.9010 (mt) REVERT: C 421 TYR cc_start: 0.8730 (m-10) cc_final: 0.8438 (m-10) REVERT: C 424 LYS cc_start: 0.7067 (ttpt) cc_final: 0.6631 (mtpt) REVERT: C 425 LEU cc_start: 0.8236 (mt) cc_final: 0.7800 (tp) REVERT: C 451 TYR cc_start: 0.6212 (m-80) cc_final: 0.5827 (m-80) REVERT: C 460 ASN cc_start: 0.7798 (t0) cc_final: 0.7167 (t0) REVERT: C 490 PHE cc_start: 0.8535 (t80) cc_final: 0.8291 (t80) REVERT: C 535 LYS cc_start: 0.9055 (mmpt) cc_final: 0.8841 (mmmt) REVERT: C 543 PHE cc_start: 0.8431 (m-80) cc_final: 0.8219 (m-80) REVERT: C 563 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7009 (mm-40) REVERT: C 571 ASP cc_start: 0.9194 (t0) cc_final: 0.8572 (t0) REVERT: C 737 ASP cc_start: 0.8562 (t0) cc_final: 0.8272 (t0) REVERT: C 748 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8972 (pm20) REVERT: C 755 GLN cc_start: 0.9212 (pt0) cc_final: 0.8888 (pp30) REVERT: C 756 TYR cc_start: 0.8359 (m-10) cc_final: 0.7737 (m-10) REVERT: C 759 PHE cc_start: 0.8547 (m-80) cc_final: 0.8330 (m-10) REVERT: C 762 GLN cc_start: 0.8966 (mt0) cc_final: 0.8500 (mt0) REVERT: C 763 LEU cc_start: 0.9005 (mt) cc_final: 0.8695 (mt) REVERT: C 764 ASN cc_start: 0.9048 (m110) cc_final: 0.8627 (m110) REVERT: C 765 ARG cc_start: 0.8839 (ptp-110) cc_final: 0.8590 (ptp90) REVERT: C 770 ILE cc_start: 0.9171 (pt) cc_final: 0.8687 (pt) REVERT: C 773 GLU cc_start: 0.8660 (tt0) cc_final: 0.7962 (pp20) REVERT: C 774 GLN cc_start: 0.8942 (pt0) cc_final: 0.8625 (pp30) REVERT: C 776 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8274 (tmtt) REVERT: C 858 LEU cc_start: 0.8822 (mp) cc_final: 0.8526 (mm) REVERT: C 869 MET cc_start: 0.9136 (mtm) cc_final: 0.8299 (mmt) REVERT: C 873 TYR cc_start: 0.8078 (m-10) cc_final: 0.7605 (m-80) REVERT: C 936 ASP cc_start: 0.8399 (m-30) cc_final: 0.8147 (m-30) REVERT: C 955 ASN cc_start: 0.8004 (p0) cc_final: 0.7678 (p0) REVERT: C 957 GLN cc_start: 0.8994 (tt0) cc_final: 0.8665 (pp30) REVERT: C 959 LEU cc_start: 0.9148 (mp) cc_final: 0.8890 (pp) REVERT: C 964 LYS cc_start: 0.9375 (tttt) cc_final: 0.8996 (tmtt) REVERT: C 970 PHE cc_start: 0.8149 (m-80) cc_final: 0.7539 (m-10) REVERT: C 979 ASP cc_start: 0.9172 (m-30) cc_final: 0.8846 (m-30) REVERT: C 981 LEU cc_start: 0.9217 (mt) cc_final: 0.8968 (mt) REVERT: C 994 ASP cc_start: 0.8808 (m-30) cc_final: 0.8557 (m-30) REVERT: C 1001 LEU cc_start: 0.9343 (tp) cc_final: 0.8990 (tp) REVERT: C 1002 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8461 (mm110) REVERT: C 1010 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8067 (tm-30) REVERT: C 1011 GLN cc_start: 0.8900 (pt0) cc_final: 0.8465 (pt0) REVERT: C 1013 ILE cc_start: 0.9494 (mm) cc_final: 0.9067 (pt) REVERT: C 1017 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 1050 MET cc_start: 0.2623 (ttt) cc_final: 0.2015 (ttt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.4598 time to fit residues: 363.6157 Evaluate side-chains 477 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 180 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C1048 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.172781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.124692 restraints weight = 64308.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.129177 restraints weight = 46930.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.132516 restraints weight = 36694.691| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 26386 Z= 0.211 Angle : 0.743 16.758 36017 Z= 0.379 Chirality : 0.049 0.370 4182 Planarity : 0.006 0.082 4587 Dihedral : 8.019 102.810 4373 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.27 (0.14), residues: 3187 helix: 0.40 (0.20), residues: 679 sheet: -0.75 (0.20), residues: 627 loop : -1.38 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.016 0.002 HIS B 66 PHE 0.043 0.002 PHE B 135 TYR 0.035 0.002 TYR A 674 ARG 0.011 0.001 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 32) link_NAG-ASN : angle 3.30171 ( 96) link_BETA1-4 : bond 0.00443 ( 10) link_BETA1-4 : angle 1.40009 ( 30) hydrogen bonds : bond 0.04870 ( 872) hydrogen bonds : angle 6.21920 ( 2433) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.85488 ( 84) covalent geometry : bond 0.00421 (26300) covalent geometry : angle 0.71879 (35807) Misc. bond : bond 0.00337 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 7.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8393 (t80) cc_final: 0.8122 (t80) REVERT: A 53 ASP cc_start: 0.8522 (t0) cc_final: 0.8051 (t0) REVERT: A 65 PHE cc_start: 0.8068 (m-80) cc_final: 0.7504 (m-80) REVERT: A 84 LEU cc_start: 0.9238 (mp) cc_final: 0.9008 (mm) REVERT: A 99 ASN cc_start: 0.9520 (t0) cc_final: 0.9270 (t0) REVERT: A 104 TRP cc_start: 0.6675 (m-90) cc_final: 0.6085 (m-10) REVERT: A 118 LEU cc_start: 0.8738 (tp) cc_final: 0.8450 (mm) REVERT: A 128 ILE cc_start: 0.8553 (mt) cc_final: 0.7923 (mm) REVERT: A 129 LYS cc_start: 0.9243 (mmtm) cc_final: 0.8936 (mmmt) REVERT: A 135 PHE cc_start: 0.8470 (m-10) cc_final: 0.8153 (m-10) REVERT: A 189 LEU cc_start: 0.8669 (tp) cc_final: 0.8462 (tp) REVERT: A 192 PHE cc_start: 0.7998 (m-80) cc_final: 0.7634 (m-80) REVERT: A 194 PHE cc_start: 0.8010 (m-80) cc_final: 0.7000 (m-80) REVERT: A 195 LYS cc_start: 0.8390 (tmmt) cc_final: 0.7688 (tmmt) REVERT: A 201 PHE cc_start: 0.8205 (m-80) cc_final: 0.7409 (m-80) REVERT: A 207 HIS cc_start: 0.9254 (p-80) cc_final: 0.8941 (p-80) REVERT: A 275 PHE cc_start: 0.6630 (m-10) cc_final: 0.6022 (m-10) REVERT: A 304 LYS cc_start: 0.9271 (ptpp) cc_final: 0.9022 (mmtt) REVERT: A 310 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8602 (tppt) REVERT: A 357 ARG cc_start: 0.7673 (tmm160) cc_final: 0.7271 (tmm160) REVERT: A 365 TYR cc_start: 0.8267 (m-80) cc_final: 0.7741 (m-80) REVERT: A 380 TYR cc_start: 0.8162 (m-80) cc_final: 0.7667 (m-80) REVERT: A 389 ASP cc_start: 0.8751 (m-30) cc_final: 0.8356 (p0) REVERT: A 557 LYS cc_start: 0.8356 (mttt) cc_final: 0.7530 (tptp) REVERT: A 562 PHE cc_start: 0.8232 (p90) cc_final: 0.7619 (p90) REVERT: A 740 MET cc_start: 0.8755 (tpt) cc_final: 0.8492 (tpp) REVERT: A 752 LEU cc_start: 0.9225 (tt) cc_final: 0.8913 (tt) REVERT: A 759 PHE cc_start: 0.8810 (m-80) cc_final: 0.8004 (m-80) REVERT: A 764 ASN cc_start: 0.8960 (m110) cc_final: 0.8706 (m110) REVERT: A 774 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8284 (mm-40) REVERT: A 776 LYS cc_start: 0.9023 (tptm) cc_final: 0.8457 (tptp) REVERT: A 856 ASN cc_start: 0.8239 (t0) cc_final: 0.7961 (p0) REVERT: A 869 MET cc_start: 0.8376 (ptp) cc_final: 0.7704 (ptp) REVERT: A 873 TYR cc_start: 0.8494 (m-10) cc_final: 0.8212 (m-80) REVERT: A 917 TYR cc_start: 0.8136 (m-80) cc_final: 0.7465 (m-10) REVERT: A 927 PHE cc_start: 0.7905 (t80) cc_final: 0.7406 (t80) REVERT: A 947 LYS cc_start: 0.7050 (ptpt) cc_final: 0.6817 (mmmt) REVERT: A 954 GLN cc_start: 0.8990 (tp40) cc_final: 0.8582 (tm-30) REVERT: A 960 ASN cc_start: 0.8745 (t0) cc_final: 0.8419 (m110) REVERT: A 964 LYS cc_start: 0.9265 (ttmm) cc_final: 0.8752 (ptpp) REVERT: A 965 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 979 ASP cc_start: 0.9217 (m-30) cc_final: 0.8632 (t0) REVERT: A 983 ARG cc_start: 0.8723 (ptt90) cc_final: 0.7712 (ttp80) REVERT: A 990 GLU cc_start: 0.8811 (tt0) cc_final: 0.8413 (mt-10) REVERT: A 994 ASP cc_start: 0.8706 (m-30) cc_final: 0.8229 (m-30) REVERT: A 1000 ARG cc_start: 0.9085 (mmt180) cc_final: 0.8802 (mmt180) REVERT: A 1002 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 1014 ARG cc_start: 0.8836 (mmp-170) cc_final: 0.8421 (mmp80) REVERT: A 1023 ASN cc_start: 0.8950 (m110) cc_final: 0.8726 (m-40) REVERT: A 1050 MET cc_start: 0.5666 (ttt) cc_final: 0.5088 (ttt) REVERT: B 37 TYR cc_start: 0.8653 (p90) cc_final: 0.7946 (p90) REVERT: B 41 LYS cc_start: 0.8722 (tppt) cc_final: 0.8409 (tppt) REVERT: B 53 ASP cc_start: 0.8835 (m-30) cc_final: 0.8589 (m-30) REVERT: B 58 PHE cc_start: 0.8082 (m-80) cc_final: 0.7230 (m-80) REVERT: B 65 PHE cc_start: 0.8605 (m-80) cc_final: 0.7981 (m-80) REVERT: B 86 PHE cc_start: 0.8135 (t80) cc_final: 0.7697 (t80) REVERT: B 129 LYS cc_start: 0.8368 (mppt) cc_final: 0.8070 (mmtm) REVERT: B 194 PHE cc_start: 0.7923 (m-80) cc_final: 0.7365 (m-10) REVERT: B 265 TYR cc_start: 0.6962 (p90) cc_final: 0.6749 (p90) REVERT: B 276 LEU cc_start: 0.8737 (tt) cc_final: 0.8057 (mt) REVERT: B 298 GLU cc_start: 0.8661 (tt0) cc_final: 0.8317 (tt0) REVERT: B 313 TYR cc_start: 0.7706 (m-80) cc_final: 0.7101 (m-10) REVERT: B 319 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8184 (ptp90) REVERT: B 321 GLN cc_start: 0.8324 (mp10) cc_final: 0.7986 (mp10) REVERT: B 562 PHE cc_start: 0.8853 (p90) cc_final: 0.8098 (p90) REVERT: B 586 ASP cc_start: 0.8171 (t0) cc_final: 0.7451 (p0) REVERT: B 587 ILE cc_start: 0.8688 (tp) cc_final: 0.8458 (tp) REVERT: B 603 ASN cc_start: 0.9365 (t0) cc_final: 0.9106 (p0) REVERT: B 697 MET cc_start: 0.7954 (pmm) cc_final: 0.7753 (pmm) REVERT: B 731 MET cc_start: 0.7577 (tmm) cc_final: 0.7142 (tmm) REVERT: B 753 LEU cc_start: 0.8997 (mm) cc_final: 0.8638 (mt) REVERT: B 759 PHE cc_start: 0.8243 (m-80) cc_final: 0.7903 (m-80) REVERT: B 819 GLU cc_start: 0.8805 (pt0) cc_final: 0.8443 (pt0) REVERT: B 822 LEU cc_start: 0.9125 (tp) cc_final: 0.8673 (mt) REVERT: B 824 ASN cc_start: 0.8811 (m110) cc_final: 0.8486 (m110) REVERT: B 869 MET cc_start: 0.8867 (mtt) cc_final: 0.8100 (mmt) REVERT: B 873 TYR cc_start: 0.7662 (m-10) cc_final: 0.7322 (m-80) REVERT: B 927 PHE cc_start: 0.8455 (t80) cc_final: 0.7733 (t80) REVERT: B 937 SER cc_start: 0.8802 (t) cc_final: 0.8470 (p) REVERT: B 954 GLN cc_start: 0.9149 (mt0) cc_final: 0.8694 (tm-30) REVERT: B 960 ASN cc_start: 0.8690 (m-40) cc_final: 0.8482 (t0) REVERT: B 979 ASP cc_start: 0.8708 (t0) cc_final: 0.8462 (t0) REVERT: B 995 ARG cc_start: 0.8524 (ptt180) cc_final: 0.8170 (ptt180) REVERT: B 1002 GLN cc_start: 0.8758 (mp10) cc_final: 0.8522 (mp10) REVERT: B 1011 GLN cc_start: 0.8521 (mm-40) cc_final: 0.7920 (mm-40) REVERT: B 1017 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 1018 ILE cc_start: 0.9119 (pt) cc_final: 0.8604 (pt) REVERT: B 1028 LYS cc_start: 0.7327 (tptm) cc_final: 0.6981 (tptt) REVERT: C 41 LYS cc_start: 0.8487 (tppt) cc_final: 0.7838 (tppt) REVERT: C 56 LEU cc_start: 0.8573 (tp) cc_final: 0.8305 (tp) REVERT: C 65 PHE cc_start: 0.8113 (m-80) cc_final: 0.7701 (m-80) REVERT: C 91 TYR cc_start: 0.7708 (t80) cc_final: 0.6911 (t80) REVERT: C 117 LEU cc_start: 0.8771 (tt) cc_final: 0.8191 (pt) REVERT: C 129 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8473 (mmmt) REVERT: C 133 PHE cc_start: 0.8142 (m-80) cc_final: 0.7649 (m-80) REVERT: C 135 PHE cc_start: 0.8995 (m-80) cc_final: 0.8663 (m-80) REVERT: C 192 PHE cc_start: 0.8683 (m-80) cc_final: 0.8145 (m-80) REVERT: C 194 PHE cc_start: 0.8036 (m-80) cc_final: 0.7666 (m-80) REVERT: C 201 PHE cc_start: 0.8579 (t80) cc_final: 0.8372 (t80) REVERT: C 223 LEU cc_start: 0.8417 (pt) cc_final: 0.8095 (pt) REVERT: C 235 ILE cc_start: 0.7386 (mt) cc_final: 0.7110 (mm) REVERT: C 237 ARG cc_start: 0.8753 (mtp85) cc_final: 0.8395 (mtp180) REVERT: C 281 GLU cc_start: 0.8339 (tp30) cc_final: 0.7965 (tp30) REVERT: C 298 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7344 (mp0) REVERT: C 300 LYS cc_start: 0.8313 (mttt) cc_final: 0.7868 (mmtt) REVERT: C 313 TYR cc_start: 0.7337 (m-80) cc_final: 0.6970 (m-80) REVERT: C 324 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8306 (mp0) REVERT: C 338 PHE cc_start: 0.9245 (m-80) cc_final: 0.8631 (m-10) REVERT: C 342 PHE cc_start: 0.8707 (m-80) cc_final: 0.8361 (m-80) REVERT: C 365 TYR cc_start: 0.8861 (m-80) cc_final: 0.8459 (m-80) REVERT: C 380 TYR cc_start: 0.7383 (m-80) cc_final: 0.7131 (m-80) REVERT: C 386 LYS cc_start: 0.8600 (mttt) cc_final: 0.8200 (mtmm) REVERT: C 409 GLN cc_start: 0.8594 (mp10) cc_final: 0.8194 (mp10) REVERT: C 417 LYS cc_start: 0.8969 (tppp) cc_final: 0.8542 (tppt) REVERT: C 421 TYR cc_start: 0.8765 (m-10) cc_final: 0.8428 (m-10) REVERT: C 424 LYS cc_start: 0.7270 (ttpt) cc_final: 0.6805 (mtpt) REVERT: C 425 LEU cc_start: 0.8447 (mt) cc_final: 0.7919 (tp) REVERT: C 426 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8114 (Cg_endo) REVERT: C 460 ASN cc_start: 0.7921 (t0) cc_final: 0.7597 (t0) REVERT: C 471 GLU cc_start: 0.8200 (mp0) cc_final: 0.7958 (mp0) REVERT: C 505 TYR cc_start: 0.8425 (t80) cc_final: 0.8105 (t80) REVERT: C 543 PHE cc_start: 0.8464 (m-80) cc_final: 0.8230 (m-80) REVERT: C 563 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7044 (mm-40) REVERT: C 737 ASP cc_start: 0.8664 (t0) cc_final: 0.7864 (p0) REVERT: C 755 GLN cc_start: 0.9198 (pt0) cc_final: 0.8911 (pt0) REVERT: C 759 PHE cc_start: 0.8553 (m-80) cc_final: 0.7956 (m-10) REVERT: C 762 GLN cc_start: 0.9011 (mt0) cc_final: 0.8752 (mt0) REVERT: C 763 LEU cc_start: 0.9092 (mt) cc_final: 0.8785 (mt) REVERT: C 764 ASN cc_start: 0.8936 (m110) cc_final: 0.8514 (m110) REVERT: C 765 ARG cc_start: 0.8929 (ptp-110) cc_final: 0.8714 (ptp-110) REVERT: C 776 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8079 (tptp) REVERT: C 858 LEU cc_start: 0.8871 (mp) cc_final: 0.8596 (mm) REVERT: C 869 MET cc_start: 0.9139 (mtm) cc_final: 0.8219 (tmm) REVERT: C 882 ILE cc_start: 0.1824 (pt) cc_final: 0.1565 (tt) REVERT: C 898 PHE cc_start: 0.6524 (t80) cc_final: 0.5892 (t80) REVERT: C 902 MET cc_start: 0.5250 (tmm) cc_final: 0.4906 (ptm) REVERT: C 955 ASN cc_start: 0.8145 (p0) cc_final: 0.7829 (p0) REVERT: C 957 GLN cc_start: 0.9014 (tt0) cc_final: 0.8449 (pp30) REVERT: C 959 LEU cc_start: 0.9189 (mp) cc_final: 0.8879 (pp) REVERT: C 964 LYS cc_start: 0.9437 (tttt) cc_final: 0.8783 (tppt) REVERT: C 966 LEU cc_start: 0.9508 (mt) cc_final: 0.9255 (mm) REVERT: C 970 PHE cc_start: 0.8283 (m-80) cc_final: 0.7745 (m-10) REVERT: C 979 ASP cc_start: 0.9059 (m-30) cc_final: 0.8657 (m-30) REVERT: C 981 LEU cc_start: 0.9224 (mt) cc_final: 0.9020 (mt) REVERT: C 994 ASP cc_start: 0.8829 (m-30) cc_final: 0.8575 (m-30) REVERT: C 1000 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8875 (mmt180) REVERT: C 1001 LEU cc_start: 0.9369 (tp) cc_final: 0.9048 (tp) REVERT: C 1002 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8459 (mm110) REVERT: C 1010 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8086 (tm-30) REVERT: C 1011 GLN cc_start: 0.8931 (pt0) cc_final: 0.8543 (pt0) REVERT: C 1013 ILE cc_start: 0.9480 (mm) cc_final: 0.9033 (pt) REVERT: C 1017 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8439 (mt-10) REVERT: C 1050 MET cc_start: 0.3022 (ttt) cc_final: 0.2011 (ttt) REVERT: C 1052 PHE cc_start: 0.7650 (m-80) cc_final: 0.7189 (m-80) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.6781 time to fit residues: 567.7072 Evaluate side-chains 472 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 267 optimal weight: 9.9990 chunk 198 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 223 optimal weight: 0.8980 chunk 300 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 251 optimal weight: 0.2980 chunk 125 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 165 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 764 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.176656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.128643 restraints weight = 64556.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.133503 restraints weight = 46408.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.137060 restraints weight = 35823.170| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26386 Z= 0.136 Angle : 0.706 10.559 36017 Z= 0.354 Chirality : 0.048 0.358 4182 Planarity : 0.005 0.069 4587 Dihedral : 7.810 99.965 4373 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.16 (0.14), residues: 3187 helix: 0.54 (0.20), residues: 680 sheet: -0.65 (0.20), residues: 600 loop : -1.33 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 436 HIS 0.011 0.001 HIS B 66 PHE 0.022 0.002 PHE A 106 TYR 0.018 0.001 TYR B 904 ARG 0.010 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 32) link_NAG-ASN : angle 3.17869 ( 96) link_BETA1-4 : bond 0.00326 ( 10) link_BETA1-4 : angle 1.42851 ( 30) hydrogen bonds : bond 0.04290 ( 872) hydrogen bonds : angle 6.03496 ( 2433) SS BOND : bond 0.00309 ( 42) SS BOND : angle 1.71629 ( 84) covalent geometry : bond 0.00294 (26300) covalent geometry : angle 0.68255 (35807) Misc. bond : bond 0.00402 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8326 (t80) cc_final: 0.7991 (t80) REVERT: A 53 ASP cc_start: 0.8502 (t0) cc_final: 0.8028 (t0) REVERT: A 54 LEU cc_start: 0.8711 (tp) cc_final: 0.8259 (tp) REVERT: A 56 LEU cc_start: 0.9150 (tp) cc_final: 0.8945 (tp) REVERT: A 65 PHE cc_start: 0.8002 (m-80) cc_final: 0.7491 (m-80) REVERT: A 84 LEU cc_start: 0.9244 (mp) cc_final: 0.9041 (mm) REVERT: A 99 ASN cc_start: 0.9504 (t0) cc_final: 0.9292 (t0) REVERT: A 104 TRP cc_start: 0.6464 (m-90) cc_final: 0.5890 (m-10) REVERT: A 106 PHE cc_start: 0.7915 (m-10) cc_final: 0.7555 (m-10) REVERT: A 118 LEU cc_start: 0.8652 (tp) cc_final: 0.8384 (mm) REVERT: A 128 ILE cc_start: 0.8438 (mt) cc_final: 0.7815 (mm) REVERT: A 129 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8872 (mmmt) REVERT: A 135 PHE cc_start: 0.8481 (m-10) cc_final: 0.8057 (m-10) REVERT: A 192 PHE cc_start: 0.7995 (m-80) cc_final: 0.7558 (m-80) REVERT: A 194 PHE cc_start: 0.7821 (m-80) cc_final: 0.6643 (m-80) REVERT: A 195 LYS cc_start: 0.8245 (tmmt) cc_final: 0.7577 (tmmt) REVERT: A 201 PHE cc_start: 0.8045 (m-80) cc_final: 0.7342 (m-80) REVERT: A 207 HIS cc_start: 0.9324 (p-80) cc_final: 0.8975 (p-80) REVERT: A 223 LEU cc_start: 0.8804 (mm) cc_final: 0.8533 (mp) REVERT: A 275 PHE cc_start: 0.6533 (m-10) cc_final: 0.6003 (m-10) REVERT: A 304 LYS cc_start: 0.9254 (ptpp) cc_final: 0.9008 (mmtt) REVERT: A 309 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 310 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8344 (tttp) REVERT: A 365 TYR cc_start: 0.8210 (m-80) cc_final: 0.7653 (m-80) REVERT: A 380 TYR cc_start: 0.8028 (m-80) cc_final: 0.7557 (m-80) REVERT: A 389 ASP cc_start: 0.8784 (m-30) cc_final: 0.8363 (p0) REVERT: A 408 ARG cc_start: 0.8611 (pmt-80) cc_final: 0.8399 (pmt-80) REVERT: A 557 LYS cc_start: 0.8348 (mttt) cc_final: 0.7514 (tptp) REVERT: A 567 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7869 (mtt180) REVERT: A 740 MET cc_start: 0.8588 (tpt) cc_final: 0.8336 (tpp) REVERT: A 751 ASN cc_start: 0.8588 (p0) cc_final: 0.8191 (p0) REVERT: A 752 LEU cc_start: 0.9128 (tt) cc_final: 0.8777 (tt) REVERT: A 755 GLN cc_start: 0.9174 (mm110) cc_final: 0.8707 (mm110) REVERT: A 759 PHE cc_start: 0.8789 (m-80) cc_final: 0.8075 (m-80) REVERT: A 762 GLN cc_start: 0.8927 (mt0) cc_final: 0.8177 (mp10) REVERT: A 763 LEU cc_start: 0.9383 (mt) cc_final: 0.9065 (mt) REVERT: A 774 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8290 (mm-40) REVERT: A 776 LYS cc_start: 0.8977 (tptm) cc_final: 0.8351 (tptp) REVERT: A 873 TYR cc_start: 0.8388 (m-10) cc_final: 0.8094 (m-80) REVERT: A 917 TYR cc_start: 0.8052 (m-80) cc_final: 0.7626 (m-10) REVERT: A 927 PHE cc_start: 0.8187 (t80) cc_final: 0.7595 (t80) REVERT: A 947 LYS cc_start: 0.7270 (ptpt) cc_final: 0.6863 (pttm) REVERT: A 954 GLN cc_start: 0.8911 (tp40) cc_final: 0.8547 (tm-30) REVERT: A 960 ASN cc_start: 0.8592 (t0) cc_final: 0.8340 (m110) REVERT: A 964 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8686 (ptpt) REVERT: A 969 ASN cc_start: 0.9056 (p0) cc_final: 0.8829 (t0) REVERT: A 979 ASP cc_start: 0.9154 (m-30) cc_final: 0.8704 (t0) REVERT: A 983 ARG cc_start: 0.8679 (ptt90) cc_final: 0.8288 (ttp-170) REVERT: A 990 GLU cc_start: 0.8743 (tt0) cc_final: 0.8333 (mt-10) REVERT: A 994 ASP cc_start: 0.8673 (m-30) cc_final: 0.8158 (m-30) REVERT: A 1000 ARG cc_start: 0.9000 (mmt180) cc_final: 0.8798 (mmt180) REVERT: A 1002 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 1006 THR cc_start: 0.9013 (m) cc_final: 0.8647 (p) REVERT: A 1014 ARG cc_start: 0.8811 (mmp-170) cc_final: 0.8356 (mmp-170) REVERT: A 1023 ASN cc_start: 0.8889 (m110) cc_final: 0.8644 (m-40) REVERT: A 1050 MET cc_start: 0.5588 (ttt) cc_final: 0.4780 (ttt) REVERT: B 37 TYR cc_start: 0.8509 (p90) cc_final: 0.8120 (p90) REVERT: B 44 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.7253 (ptp-170) REVERT: B 58 PHE cc_start: 0.8112 (m-80) cc_final: 0.7213 (m-80) REVERT: B 65 PHE cc_start: 0.8474 (m-80) cc_final: 0.7846 (m-80) REVERT: B 86 PHE cc_start: 0.7901 (t80) cc_final: 0.7642 (t80) REVERT: B 117 LEU cc_start: 0.8904 (tp) cc_final: 0.8202 (tp) REVERT: B 129 LYS cc_start: 0.8342 (mppt) cc_final: 0.8066 (mmtm) REVERT: B 153 MET cc_start: 0.5562 (ptp) cc_final: 0.5143 (pmm) REVERT: B 194 PHE cc_start: 0.7893 (m-80) cc_final: 0.7348 (m-10) REVERT: B 276 LEU cc_start: 0.8690 (tt) cc_final: 0.7898 (mp) REVERT: B 287 ASP cc_start: 0.8417 (m-30) cc_final: 0.8211 (m-30) REVERT: B 298 GLU cc_start: 0.8609 (tt0) cc_final: 0.8246 (tt0) REVERT: B 313 TYR cc_start: 0.7649 (m-80) cc_final: 0.7090 (m-10) REVERT: B 319 ARG cc_start: 0.8481 (ptp90) cc_final: 0.8227 (ptp90) REVERT: B 321 GLN cc_start: 0.8295 (mp10) cc_final: 0.7933 (mp10) REVERT: B 562 PHE cc_start: 0.8867 (p90) cc_final: 0.7992 (p90) REVERT: B 571 ASP cc_start: 0.9088 (m-30) cc_final: 0.8777 (m-30) REVERT: B 586 ASP cc_start: 0.8125 (t0) cc_final: 0.7587 (p0) REVERT: B 587 ILE cc_start: 0.8622 (tp) cc_final: 0.8412 (tp) REVERT: B 603 ASN cc_start: 0.9278 (t0) cc_final: 0.9053 (p0) REVERT: B 658 ASN cc_start: 0.8335 (t0) cc_final: 0.8131 (t0) REVERT: B 731 MET cc_start: 0.7565 (tmm) cc_final: 0.7354 (tmm) REVERT: B 753 LEU cc_start: 0.8921 (mm) cc_final: 0.8530 (mt) REVERT: B 754 LEU cc_start: 0.8926 (mt) cc_final: 0.8717 (mt) REVERT: B 759 PHE cc_start: 0.8167 (m-80) cc_final: 0.7871 (m-80) REVERT: B 763 LEU cc_start: 0.9365 (mt) cc_final: 0.9033 (mt) REVERT: B 767 LEU cc_start: 0.9483 (mm) cc_final: 0.9132 (mt) REVERT: B 819 GLU cc_start: 0.8817 (pt0) cc_final: 0.8403 (pt0) REVERT: B 822 LEU cc_start: 0.9062 (tp) cc_final: 0.8625 (mt) REVERT: B 824 ASN cc_start: 0.8800 (m110) cc_final: 0.8484 (m110) REVERT: B 917 TYR cc_start: 0.8281 (m-80) cc_final: 0.7639 (m-10) REVERT: B 927 PHE cc_start: 0.8426 (t80) cc_final: 0.7672 (t80) REVERT: B 937 SER cc_start: 0.8635 (t) cc_final: 0.8283 (p) REVERT: B 954 GLN cc_start: 0.9051 (mt0) cc_final: 0.8592 (tm-30) REVERT: B 957 GLN cc_start: 0.8872 (pp30) cc_final: 0.8643 (pp30) REVERT: B 960 ASN cc_start: 0.8575 (m-40) cc_final: 0.8221 (m-40) REVERT: B 964 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8739 (pttp) REVERT: B 979 ASP cc_start: 0.8635 (t0) cc_final: 0.8312 (t0) REVERT: B 983 ARG cc_start: 0.7878 (tmm-80) cc_final: 0.7255 (tmm-80) REVERT: B 1002 GLN cc_start: 0.8885 (mp10) cc_final: 0.8624 (mp10) REVERT: B 1011 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8098 (mp10) REVERT: B 1014 ARG cc_start: 0.8983 (mtt90) cc_final: 0.8124 (ptp-110) REVERT: B 1017 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 1018 ILE cc_start: 0.8941 (pt) cc_final: 0.8630 (pt) REVERT: B 1028 LYS cc_start: 0.7260 (tptm) cc_final: 0.6973 (tptt) REVERT: C 34 ARG cc_start: 0.8634 (mmp-170) cc_final: 0.7736 (mmp80) REVERT: C 41 LYS cc_start: 0.8564 (tppt) cc_final: 0.7885 (tppt) REVERT: C 56 LEU cc_start: 0.8462 (tp) cc_final: 0.8130 (tp) REVERT: C 65 PHE cc_start: 0.7973 (m-80) cc_final: 0.7578 (m-80) REVERT: C 91 TYR cc_start: 0.7555 (t80) cc_final: 0.6720 (t80) REVERT: C 117 LEU cc_start: 0.8817 (tt) cc_final: 0.8232 (pt) REVERT: C 129 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8428 (mmmt) REVERT: C 133 PHE cc_start: 0.8026 (m-80) cc_final: 0.7400 (m-80) REVERT: C 135 PHE cc_start: 0.9003 (m-80) cc_final: 0.8717 (m-80) REVERT: C 192 PHE cc_start: 0.8622 (m-80) cc_final: 0.8100 (m-80) REVERT: C 194 PHE cc_start: 0.7984 (m-80) cc_final: 0.7640 (m-80) REVERT: C 223 LEU cc_start: 0.7984 (pt) cc_final: 0.7707 (pt) REVERT: C 235 ILE cc_start: 0.7366 (mt) cc_final: 0.7039 (mm) REVERT: C 237 ARG cc_start: 0.8726 (mtp85) cc_final: 0.8345 (mtp180) REVERT: C 281 GLU cc_start: 0.8259 (tp30) cc_final: 0.7911 (tp30) REVERT: C 298 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7496 (mp0) REVERT: C 300 LYS cc_start: 0.8280 (mttt) cc_final: 0.7792 (mmtp) REVERT: C 313 TYR cc_start: 0.7315 (m-80) cc_final: 0.6898 (m-80) REVERT: C 324 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8293 (mp0) REVERT: C 338 PHE cc_start: 0.9209 (m-80) cc_final: 0.8457 (m-10) REVERT: C 342 PHE cc_start: 0.8644 (m-80) cc_final: 0.8313 (m-80) REVERT: C 353 TRP cc_start: 0.7373 (p-90) cc_final: 0.7083 (p90) REVERT: C 354 ASN cc_start: 0.8827 (t0) cc_final: 0.8511 (t0) REVERT: C 365 TYR cc_start: 0.8821 (m-80) cc_final: 0.8397 (m-80) REVERT: C 380 TYR cc_start: 0.7306 (m-80) cc_final: 0.6999 (m-80) REVERT: C 386 LYS cc_start: 0.8655 (mttt) cc_final: 0.8221 (mtmm) REVERT: C 405 ASP cc_start: 0.8623 (p0) cc_final: 0.8278 (p0) REVERT: C 409 GLN cc_start: 0.8527 (mp10) cc_final: 0.8134 (mp10) REVERT: C 417 LYS cc_start: 0.8978 (tppp) cc_final: 0.8526 (tppt) REVERT: C 418 ILE cc_start: 0.9424 (pt) cc_final: 0.8949 (mt) REVERT: C 421 TYR cc_start: 0.8719 (m-10) cc_final: 0.8396 (m-10) REVERT: C 425 LEU cc_start: 0.8288 (mt) cc_final: 0.8088 (tp) REVERT: C 464 PHE cc_start: 0.7407 (p90) cc_final: 0.7054 (p90) REVERT: C 471 GLU cc_start: 0.8096 (mp0) cc_final: 0.7857 (mp0) REVERT: C 490 PHE cc_start: 0.8684 (t80) cc_final: 0.8446 (t80) REVERT: C 535 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8744 (mmmt) REVERT: C 563 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7043 (mm-40) REVERT: C 737 ASP cc_start: 0.8723 (t0) cc_final: 0.8298 (t0) REVERT: C 752 LEU cc_start: 0.8937 (pp) cc_final: 0.8679 (pp) REVERT: C 755 GLN cc_start: 0.9156 (pt0) cc_final: 0.8859 (pt0) REVERT: C 759 PHE cc_start: 0.8579 (m-80) cc_final: 0.7948 (m-10) REVERT: C 762 GLN cc_start: 0.8901 (mt0) cc_final: 0.8580 (mt0) REVERT: C 763 LEU cc_start: 0.9067 (mt) cc_final: 0.8790 (mt) REVERT: C 764 ASN cc_start: 0.8973 (m110) cc_final: 0.8628 (m110) REVERT: C 765 ARG cc_start: 0.8884 (ptp-110) cc_final: 0.8558 (ptp90) REVERT: C 776 LYS cc_start: 0.8481 (ttpt) cc_final: 0.7966 (tptp) REVERT: C 869 MET cc_start: 0.9144 (mtm) cc_final: 0.8220 (tmm) REVERT: C 955 ASN cc_start: 0.8000 (p0) cc_final: 0.7750 (p0) REVERT: C 957 GLN cc_start: 0.8977 (tt0) cc_final: 0.8481 (pp30) REVERT: C 959 LEU cc_start: 0.9134 (mp) cc_final: 0.8836 (pp) REVERT: C 964 LYS cc_start: 0.9398 (tttt) cc_final: 0.8691 (tppt) REVERT: C 966 LEU cc_start: 0.9533 (mt) cc_final: 0.9173 (mt) REVERT: C 970 PHE cc_start: 0.8174 (m-80) cc_final: 0.7446 (m-10) REVERT: C 979 ASP cc_start: 0.8974 (m-30) cc_final: 0.8600 (m-30) REVERT: C 994 ASP cc_start: 0.8796 (m-30) cc_final: 0.8542 (m-30) REVERT: C 1000 ARG cc_start: 0.9104 (mmm160) cc_final: 0.8759 (mmt180) REVERT: C 1001 LEU cc_start: 0.9340 (tp) cc_final: 0.8943 (tp) REVERT: C 1002 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8376 (mm110) REVERT: C 1010 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8032 (tm-30) REVERT: C 1011 GLN cc_start: 0.8889 (pt0) cc_final: 0.8464 (pt0) REVERT: C 1013 ILE cc_start: 0.9475 (mm) cc_final: 0.9025 (pt) REVERT: C 1017 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 1050 MET cc_start: 0.2532 (ttt) cc_final: 0.1714 (ttt) REVERT: C 1052 PHE cc_start: 0.7456 (m-80) cc_final: 0.7030 (m-80) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.5930 time to fit residues: 474.5731 Evaluate side-chains 461 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 179 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 243 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 265 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1064 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.175014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.126964 restraints weight = 64098.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.131712 restraints weight = 46096.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.135187 restraints weight = 35784.685| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26386 Z= 0.151 Angle : 0.711 14.110 36017 Z= 0.356 Chirality : 0.048 0.349 4182 Planarity : 0.005 0.068 4587 Dihedral : 7.713 95.709 4373 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.16 (0.14), residues: 3187 helix: 0.49 (0.20), residues: 674 sheet: -0.58 (0.21), residues: 589 loop : -1.32 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 104 HIS 0.011 0.001 HIS B 66 PHE 0.029 0.002 PHE B 823 TYR 0.020 0.001 TYR B 904 ARG 0.013 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 32) link_NAG-ASN : angle 3.14609 ( 96) link_BETA1-4 : bond 0.00384 ( 10) link_BETA1-4 : angle 1.36584 ( 30) hydrogen bonds : bond 0.04329 ( 872) hydrogen bonds : angle 6.00629 ( 2433) SS BOND : bond 0.00419 ( 42) SS BOND : angle 1.91739 ( 84) covalent geometry : bond 0.00323 (26300) covalent geometry : angle 0.68653 (35807) Misc. bond : bond 0.00362 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7481 (mmtp) REVERT: A 43 PHE cc_start: 0.8343 (t80) cc_final: 0.8086 (t80) REVERT: A 53 ASP cc_start: 0.8529 (t0) cc_final: 0.8062 (t0) REVERT: A 54 LEU cc_start: 0.8765 (tp) cc_final: 0.8314 (tp) REVERT: A 65 PHE cc_start: 0.8001 (m-80) cc_final: 0.7502 (m-80) REVERT: A 84 LEU cc_start: 0.9273 (mp) cc_final: 0.9053 (mm) REVERT: A 104 TRP cc_start: 0.6665 (m-90) cc_final: 0.6127 (m-10) REVERT: A 106 PHE cc_start: 0.8148 (m-10) cc_final: 0.7935 (m-10) REVERT: A 118 LEU cc_start: 0.8699 (tp) cc_final: 0.8381 (mm) REVERT: A 128 ILE cc_start: 0.8477 (mt) cc_final: 0.7915 (mm) REVERT: A 129 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8893 (mmmt) REVERT: A 135 PHE cc_start: 0.8363 (m-10) cc_final: 0.7987 (m-10) REVERT: A 192 PHE cc_start: 0.8013 (m-80) cc_final: 0.7588 (m-80) REVERT: A 194 PHE cc_start: 0.7864 (m-80) cc_final: 0.6618 (m-80) REVERT: A 195 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7569 (tmmt) REVERT: A 201 PHE cc_start: 0.8106 (m-80) cc_final: 0.7396 (m-80) REVERT: A 207 HIS cc_start: 0.9325 (p-80) cc_final: 0.8972 (p-80) REVERT: A 275 PHE cc_start: 0.6580 (m-10) cc_final: 0.6069 (m-10) REVERT: A 304 LYS cc_start: 0.9265 (ptpp) cc_final: 0.9018 (mmtt) REVERT: A 309 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8267 (tm-30) REVERT: A 310 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8407 (tppt) REVERT: A 365 TYR cc_start: 0.8183 (m-80) cc_final: 0.7638 (m-80) REVERT: A 380 TYR cc_start: 0.8108 (m-80) cc_final: 0.7640 (m-80) REVERT: A 389 ASP cc_start: 0.8890 (m-30) cc_final: 0.8437 (p0) REVERT: A 557 LYS cc_start: 0.8202 (mttt) cc_final: 0.7448 (tptt) REVERT: A 560 LEU cc_start: 0.9322 (tp) cc_final: 0.9048 (tp) REVERT: A 740 MET cc_start: 0.8658 (tpt) cc_final: 0.8422 (tpp) REVERT: A 751 ASN cc_start: 0.8590 (p0) cc_final: 0.8211 (p0) REVERT: A 752 LEU cc_start: 0.9140 (tt) cc_final: 0.8759 (tt) REVERT: A 755 GLN cc_start: 0.9235 (mm110) cc_final: 0.8775 (mm110) REVERT: A 759 PHE cc_start: 0.8660 (m-80) cc_final: 0.7864 (m-10) REVERT: A 763 LEU cc_start: 0.9391 (mt) cc_final: 0.9120 (mt) REVERT: A 774 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8325 (mm-40) REVERT: A 776 LYS cc_start: 0.8971 (tptm) cc_final: 0.8415 (tptp) REVERT: A 873 TYR cc_start: 0.8400 (m-10) cc_final: 0.8105 (m-80) REVERT: A 917 TYR cc_start: 0.8097 (m-80) cc_final: 0.7658 (m-10) REVERT: A 927 PHE cc_start: 0.7851 (t80) cc_final: 0.7316 (t80) REVERT: A 947 LYS cc_start: 0.6968 (ptpt) cc_final: 0.6527 (pttm) REVERT: A 954 GLN cc_start: 0.8934 (tp40) cc_final: 0.8567 (tm-30) REVERT: A 964 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8668 (ptpt) REVERT: A 969 ASN cc_start: 0.9035 (p0) cc_final: 0.8802 (t0) REVERT: A 979 ASP cc_start: 0.9153 (m-30) cc_final: 0.8711 (t0) REVERT: A 983 ARG cc_start: 0.8697 (ptt90) cc_final: 0.8494 (ttp-170) REVERT: A 990 GLU cc_start: 0.8834 (tt0) cc_final: 0.8427 (mt-10) REVERT: A 994 ASP cc_start: 0.8706 (m-30) cc_final: 0.8238 (m-30) REVERT: A 1002 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 1006 THR cc_start: 0.9043 (m) cc_final: 0.8709 (p) REVERT: A 1014 ARG cc_start: 0.8779 (mmp-170) cc_final: 0.8352 (mmp80) REVERT: A 1023 ASN cc_start: 0.8887 (m110) cc_final: 0.8646 (m-40) REVERT: A 1050 MET cc_start: 0.5721 (ttt) cc_final: 0.4916 (ttt) REVERT: B 37 TYR cc_start: 0.8562 (p90) cc_final: 0.8038 (p90) REVERT: B 44 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.7245 (ptp-170) REVERT: B 58 PHE cc_start: 0.8079 (m-80) cc_final: 0.7202 (m-80) REVERT: B 86 PHE cc_start: 0.8169 (t80) cc_final: 0.7675 (t80) REVERT: B 117 LEU cc_start: 0.8873 (tp) cc_final: 0.8598 (tp) REVERT: B 129 LYS cc_start: 0.8403 (mppt) cc_final: 0.8055 (mmtm) REVERT: B 194 PHE cc_start: 0.7855 (m-80) cc_final: 0.7459 (m-10) REVERT: B 265 TYR cc_start: 0.7117 (p90) cc_final: 0.6680 (p90) REVERT: B 276 LEU cc_start: 0.8696 (tt) cc_final: 0.7916 (mp) REVERT: B 298 GLU cc_start: 0.8666 (tt0) cc_final: 0.8342 (tt0) REVERT: B 313 TYR cc_start: 0.7836 (m-80) cc_final: 0.7245 (m-10) REVERT: B 319 ARG cc_start: 0.8547 (ptp90) cc_final: 0.8243 (ptp90) REVERT: B 321 GLN cc_start: 0.8310 (mp10) cc_final: 0.8038 (mp10) REVERT: B 562 PHE cc_start: 0.8900 (p90) cc_final: 0.8200 (p90) REVERT: B 569 ILE cc_start: 0.8904 (tp) cc_final: 0.8688 (tp) REVERT: B 586 ASP cc_start: 0.8146 (t0) cc_final: 0.7639 (p0) REVERT: B 587 ILE cc_start: 0.8646 (tp) cc_final: 0.8443 (tp) REVERT: B 603 ASN cc_start: 0.9301 (t0) cc_final: 0.9073 (p0) REVERT: B 731 MET cc_start: 0.7476 (tmm) cc_final: 0.7180 (tmm) REVERT: B 753 LEU cc_start: 0.8938 (mm) cc_final: 0.8550 (mt) REVERT: B 754 LEU cc_start: 0.8905 (mt) cc_final: 0.8693 (mt) REVERT: B 759 PHE cc_start: 0.8104 (m-80) cc_final: 0.7820 (m-80) REVERT: B 763 LEU cc_start: 0.9369 (mt) cc_final: 0.9071 (mt) REVERT: B 767 LEU cc_start: 0.9486 (mm) cc_final: 0.9130 (mt) REVERT: B 819 GLU cc_start: 0.8681 (pt0) cc_final: 0.8218 (tm-30) REVERT: B 820 ASP cc_start: 0.8701 (t0) cc_final: 0.8482 (t0) REVERT: B 822 LEU cc_start: 0.9070 (tp) cc_final: 0.8593 (mt) REVERT: B 824 ASN cc_start: 0.8803 (m110) cc_final: 0.8545 (m110) REVERT: B 927 PHE cc_start: 0.8458 (t80) cc_final: 0.7805 (t80) REVERT: B 937 SER cc_start: 0.8838 (t) cc_final: 0.8484 (p) REVERT: B 954 GLN cc_start: 0.9043 (mt0) cc_final: 0.8658 (tm-30) REVERT: B 960 ASN cc_start: 0.8595 (m-40) cc_final: 0.8210 (m-40) REVERT: B 964 LYS cc_start: 0.9121 (ptpp) cc_final: 0.8673 (pttt) REVERT: B 979 ASP cc_start: 0.8683 (t0) cc_final: 0.8377 (t0) REVERT: B 983 ARG cc_start: 0.7985 (tmm-80) cc_final: 0.7387 (tmm-80) REVERT: B 995 ARG cc_start: 0.8427 (ptt180) cc_final: 0.8001 (ttp-170) REVERT: B 1002 GLN cc_start: 0.8845 (mp10) cc_final: 0.8616 (mp10) REVERT: B 1011 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8147 (mp10) REVERT: B 1014 ARG cc_start: 0.8952 (mtt90) cc_final: 0.8305 (ptp-110) REVERT: B 1017 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 1018 ILE cc_start: 0.9015 (pt) cc_final: 0.8563 (pt) REVERT: B 1019 ARG cc_start: 0.8897 (ptm-80) cc_final: 0.8490 (ptm160) REVERT: B 1028 LYS cc_start: 0.7208 (tptm) cc_final: 0.6947 (tptt) REVERT: C 34 ARG cc_start: 0.8687 (mmp-170) cc_final: 0.7807 (mmp80) REVERT: C 41 LYS cc_start: 0.8531 (tppt) cc_final: 0.7892 (tppt) REVERT: C 65 PHE cc_start: 0.8073 (m-80) cc_final: 0.7683 (m-80) REVERT: C 91 TYR cc_start: 0.7642 (t80) cc_final: 0.6789 (t80) REVERT: C 117 LEU cc_start: 0.8739 (tt) cc_final: 0.8200 (pt) REVERT: C 118 LEU cc_start: 0.8936 (tp) cc_final: 0.8709 (tp) REVERT: C 129 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8446 (mmmt) REVERT: C 133 PHE cc_start: 0.8073 (m-80) cc_final: 0.7477 (m-80) REVERT: C 135 PHE cc_start: 0.9027 (m-80) cc_final: 0.8694 (m-80) REVERT: C 192 PHE cc_start: 0.8664 (m-80) cc_final: 0.8168 (m-80) REVERT: C 194 PHE cc_start: 0.8027 (m-80) cc_final: 0.7680 (m-80) REVERT: C 223 LEU cc_start: 0.8157 (pt) cc_final: 0.7861 (pt) REVERT: C 235 ILE cc_start: 0.7337 (mt) cc_final: 0.7016 (mm) REVERT: C 237 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8388 (mtp180) REVERT: C 270 LEU cc_start: 0.7026 (mt) cc_final: 0.6807 (mm) REVERT: C 281 GLU cc_start: 0.8279 (tp30) cc_final: 0.7925 (tp30) REVERT: C 298 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7341 (mp0) REVERT: C 300 LYS cc_start: 0.8382 (mttt) cc_final: 0.7892 (mmtt) REVERT: C 313 TYR cc_start: 0.7330 (m-80) cc_final: 0.6931 (m-80) REVERT: C 324 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8262 (mp0) REVERT: C 338 PHE cc_start: 0.9237 (m-80) cc_final: 0.8461 (m-10) REVERT: C 342 PHE cc_start: 0.8629 (m-80) cc_final: 0.8296 (m-80) REVERT: C 353 TRP cc_start: 0.7373 (p-90) cc_final: 0.7100 (p90) REVERT: C 354 ASN cc_start: 0.8818 (t0) cc_final: 0.8511 (t0) REVERT: C 365 TYR cc_start: 0.8851 (m-80) cc_final: 0.8424 (m-80) REVERT: C 377 PHE cc_start: 0.7766 (t80) cc_final: 0.7510 (t80) REVERT: C 380 TYR cc_start: 0.7299 (m-80) cc_final: 0.7067 (m-80) REVERT: C 386 LYS cc_start: 0.8688 (mttt) cc_final: 0.8153 (mtmt) REVERT: C 417 LYS cc_start: 0.8990 (tppp) cc_final: 0.8518 (tppt) REVERT: C 418 ILE cc_start: 0.9487 (pt) cc_final: 0.9020 (mt) REVERT: C 421 TYR cc_start: 0.8728 (m-10) cc_final: 0.8087 (m-10) REVERT: C 425 LEU cc_start: 0.8388 (mt) cc_final: 0.8081 (tp) REVERT: C 464 PHE cc_start: 0.7519 (p90) cc_final: 0.7167 (p90) REVERT: C 471 GLU cc_start: 0.8159 (mp0) cc_final: 0.7942 (mp0) REVERT: C 490 PHE cc_start: 0.8730 (t80) cc_final: 0.8487 (t80) REVERT: C 529 LYS cc_start: 0.8820 (tmmt) cc_final: 0.8585 (mmtm) REVERT: C 562 PHE cc_start: 0.8591 (p90) cc_final: 0.8229 (p90) REVERT: C 563 GLN cc_start: 0.7656 (mm-40) cc_final: 0.6880 (mm-40) REVERT: C 737 ASP cc_start: 0.8674 (t0) cc_final: 0.7849 (p0) REVERT: C 755 GLN cc_start: 0.9188 (pt0) cc_final: 0.8926 (pt0) REVERT: C 759 PHE cc_start: 0.8605 (m-80) cc_final: 0.7986 (m-10) REVERT: C 762 GLN cc_start: 0.8918 (mt0) cc_final: 0.8525 (mt0) REVERT: C 763 LEU cc_start: 0.9080 (mt) cc_final: 0.8796 (mt) REVERT: C 764 ASN cc_start: 0.8944 (m110) cc_final: 0.8590 (m110) REVERT: C 765 ARG cc_start: 0.8895 (ptp-110) cc_final: 0.8562 (ptp90) REVERT: C 770 ILE cc_start: 0.9117 (pt) cc_final: 0.8646 (pt) REVERT: C 773 GLU cc_start: 0.8606 (tt0) cc_final: 0.7742 (pp20) REVERT: C 776 LYS cc_start: 0.8475 (ttpt) cc_final: 0.7951 (tptp) REVERT: C 869 MET cc_start: 0.9173 (mtm) cc_final: 0.8205 (tmm) REVERT: C 902 MET cc_start: 0.5077 (tmm) cc_final: 0.4434 (ptm) REVERT: C 955 ASN cc_start: 0.8041 (p0) cc_final: 0.7836 (p0) REVERT: C 957 GLN cc_start: 0.9018 (tt0) cc_final: 0.8549 (pp30) REVERT: C 959 LEU cc_start: 0.9195 (mp) cc_final: 0.8883 (pp) REVERT: C 964 LYS cc_start: 0.9456 (tttt) cc_final: 0.8971 (mtpp) REVERT: C 966 LEU cc_start: 0.9546 (mt) cc_final: 0.9146 (mt) REVERT: C 970 PHE cc_start: 0.8189 (m-80) cc_final: 0.7395 (m-10) REVERT: C 979 ASP cc_start: 0.8941 (m-30) cc_final: 0.8562 (m-30) REVERT: C 994 ASP cc_start: 0.8794 (m-30) cc_final: 0.8578 (m-30) REVERT: C 1000 ARG cc_start: 0.9071 (mmm160) cc_final: 0.8664 (mmt180) REVERT: C 1010 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8009 (tm-30) REVERT: C 1011 GLN cc_start: 0.8907 (pt0) cc_final: 0.8522 (pt0) REVERT: C 1013 ILE cc_start: 0.9483 (mm) cc_final: 0.8828 (pt) REVERT: C 1017 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8342 (mp0) REVERT: C 1050 MET cc_start: 0.2458 (ttt) cc_final: 0.1642 (ttt) REVERT: C 1052 PHE cc_start: 0.7516 (m-80) cc_final: 0.7203 (m-80) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.4098 time to fit residues: 316.0322 Evaluate side-chains 459 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 227 optimal weight: 9.9990 chunk 158 optimal weight: 0.0270 chunk 80 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 178 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 204 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 764 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.176718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.130193 restraints weight = 67678.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.135014 restraints weight = 48315.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.138590 restraints weight = 37357.368| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.7488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26386 Z= 0.134 Angle : 0.711 13.100 36017 Z= 0.354 Chirality : 0.048 0.339 4182 Planarity : 0.005 0.063 4587 Dihedral : 7.578 93.022 4373 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3187 helix: 0.52 (0.20), residues: 681 sheet: -0.65 (0.20), residues: 609 loop : -1.37 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 436 HIS 0.009 0.001 HIS B 66 PHE 0.024 0.002 PHE B 898 TYR 0.035 0.001 TYR A 674 ARG 0.011 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 32) link_NAG-ASN : angle 3.07575 ( 96) link_BETA1-4 : bond 0.00367 ( 10) link_BETA1-4 : angle 1.39141 ( 30) hydrogen bonds : bond 0.04158 ( 872) hydrogen bonds : angle 5.91543 ( 2433) SS BOND : bond 0.00503 ( 42) SS BOND : angle 2.04090 ( 84) covalent geometry : bond 0.00295 (26300) covalent geometry : angle 0.68715 (35807) Misc. bond : bond 0.00314 ( 2) =============================================================================== Job complete usr+sys time: 12276.65 seconds wall clock time: 221 minutes 41.44 seconds (13301.44 seconds total)