Starting phenix.real_space_refine on Thu Mar 5 20:58:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdh_13919/03_2026/7qdh_13919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdh_13919/03_2026/7qdh_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_13919/03_2026/7qdh_13919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdh_13919/03_2026/7qdh_13919.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdh_13919/03_2026/7qdh_13919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdh_13919/03_2026/7qdh_13919.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 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: 6.03, per 1000 atoms: 0.23 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: 2.52 Conformation dependent library (CDL) restraints added in 1.0 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: 1.08 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: 5.83 Time building geometry restraints manager: 3.26 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 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 \ 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 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: 1.620 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.550 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- 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 : 62.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.030 0.003 ARG C 357 TYR 0.049 0.005 TYR A 266 PHE 0.049 0.005 PHE B 329 TRP 0.066 0.005 TRP A 64 HIS 0.019 0.003 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.01085 (26300) covalent geometry : angle 1.49889 (35807) SS BOND : bond 0.35443 ( 42) SS BOND : angle 13.24096 ( 84) hydrogen bonds : bond 0.28264 ( 872) hydrogen bonds : angle 9.68542 ( 2433) Misc. bond : bond 0.32817 ( 2) link_BETA1-4 : bond 0.00312 ( 10) link_BETA1-4 : angle 2.00118 ( 30) link_NAG-ASN : bond 0.01451 ( 32) link_NAG-ASN : angle 7.39878 ( 96) *********************** 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 : 0.860 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: A 41 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8112 (mmmt) REVERT: A 53 ASP cc_start: 0.7724 (t0) cc_final: 0.7371 (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: 0.7761 (m-80) REVERT: A 202 LYS cc_start: 0.7945 (mttt) cc_final: 0.7682 (mtmm) REVERT: A 223 LEU cc_start: 0.8806 (mt) cc_final: 0.8601 (mm) REVERT: A 229 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7890 (mt) REVERT: A 238 PHE cc_start: 0.7143 (p90) cc_final: 0.6859 (p90) REVERT: A 240 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7481 (t) REVERT: A 241 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7354 (tp) REVERT: A 275 PHE cc_start: 0.5045 (m-10) cc_final: 0.4103 (m-10) REVERT: A 304 LYS cc_start: 0.8393 (tppp) cc_final: 0.7991 (tppp) REVERT: A 323 THR cc_start: 0.7940 (p) cc_final: 0.7633 (p) REVERT: A 380 TYR cc_start: 0.7925 (m-80) cc_final: 0.7348 (m-80) REVERT: A 386 LYS cc_start: 0.8258 (mttp) cc_final: 0.7937 (mmmm) REVERT: A 462 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7287 (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: 0.7147 (tt) REVERT: A 592 PHE cc_start: 0.6830 (t80) cc_final: 0.6548 (t80) REVERT: A 751 ASN cc_start: 0.8597 (m110) cc_final: 0.8351 (m-40) REVERT: A 752 LEU cc_start: 0.8554 (mt) cc_final: 0.8184 (mp) REVERT: A 770 ILE cc_start: 0.8968 (mt) cc_final: 0.8596 (tt) REVERT: A 776 LYS cc_start: 0.8809 (tptm) cc_final: 0.8564 (mmmt) REVERT: A 777 ASN cc_start: 0.8289 (m-40) cc_final: 0.7855 (m110) REVERT: A 796 ASP cc_start: 0.7799 (m-30) cc_final: 0.7503 (p0) REVERT: A 824 ASN cc_start: 0.7554 (m-40) cc_final: 0.7344 (m-40) REVERT: A 860 VAL cc_start: 0.7487 (t) cc_final: 0.7224 (p) REVERT: A 867 ASP cc_start: 0.7599 (m-30) cc_final: 0.7090 (p0) REVERT: A 917 TYR cc_start: 0.8281 (m-80) cc_final: 0.8033 (m-10) REVERT: A 968 SER cc_start: 0.8404 (m) cc_final: 0.7968 (t) REVERT: A 970 PHE cc_start: 0.7281 (m-10) cc_final: 0.7049 (m-80) REVERT: A 990 GLU cc_start: 0.8611 (tt0) cc_final: 0.8368 (mt-10) REVERT: A 991 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.8884 (m) REVERT: A 996 LEU cc_start: 0.8800 (mt) cc_final: 0.8479 (mt) REVERT: A 1141 LEU cc_start: -0.7109 (OUTLIER) cc_final: -0.7954 (mt) REVERT: B 48 LEU cc_start: 0.8646 (mp) cc_final: 0.7962 (mp) REVERT: B 58 PHE cc_start: 0.7683 (m-80) cc_final: 0.7362 (m-80) REVERT: B 63 THR cc_start: 0.7989 (p) cc_final: 0.6728 (t) REVERT: B 64 TRP cc_start: 0.8335 (t60) cc_final: 0.8064 (t60) REVERT: B 65 PHE cc_start: 0.8121 (m-80) cc_final: 0.7449 (m-10) REVERT: B 119 ILE cc_start: 0.4067 (OUTLIER) cc_final: 0.2630 (pt) REVERT: B 122 ASN cc_start: 0.1670 (OUTLIER) cc_final: -0.0332 (m-40) REVERT: B 194 PHE cc_start: 0.6981 (m-80) cc_final: 0.6532 (m-80) REVERT: B 210 ILE cc_start: 0.3997 (tp) cc_final: 0.3504 (mm) REVERT: B 223 LEU cc_start: 0.7835 (mt) cc_final: 0.7616 (mm) REVERT: B 266 TYR cc_start: 0.5955 (m-10) cc_final: 0.5749 (m-10) REVERT: B 278 LYS cc_start: 0.7566 (tttm) cc_final: 0.7248 (ttpp) REVERT: B 289 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6893 (p) REVERT: B 300 LYS cc_start: 0.7848 (mttt) cc_final: 0.7569 (mtmm) REVERT: B 306 PHE cc_start: 0.6531 (m-80) cc_final: 0.5103 (m-80) REVERT: B 312 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7761 (pt) REVERT: B 396 TYR cc_start: 0.8088 (m-80) cc_final: 0.7734 (m-80) REVERT: B 560 LEU cc_start: 0.8536 (mt) cc_final: 0.8235 (mt) 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: 0.6189 (m-30) REVERT: B 603 ASN cc_start: 0.8815 (t0) cc_final: 0.8478 (p0) REVERT: B 613 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6379 (mm110) REVERT: B 620 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.5897 (p) REVERT: B 656 VAL cc_start: 0.8712 (m) cc_final: 0.7651 (p) REVERT: B 765 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7473 (ttm110) REVERT: B 776 LYS cc_start: 0.8558 (tptp) cc_final: 0.8173 (mmmt) REVERT: B 822 LEU cc_start: 0.9116 (tp) cc_final: 0.8880 (mt) REVERT: B 869 MET cc_start: 0.8445 (mtt) cc_final: 0.8070 (mmp) REVERT: B 873 TYR cc_start: 0.7499 (m-80) cc_final: 0.7118 (m-80) REVERT: B 927 PHE cc_start: 0.8191 (t80) cc_final: 0.7896 (t80) REVERT: B 937 SER cc_start: 0.8696 (t) cc_final: 0.8450 (p) REVERT: B 954 GLN cc_start: 0.8562 (mt0) cc_final: 0.8334 (pp30) REVERT: B 955 ASN cc_start: 0.8403 (m110) cc_final: 0.7963 (t0) REVERT: B 964 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8278 (tmtt) REVERT: B 1003 SER cc_start: 0.8982 (m) cc_final: 0.8599 (p) REVERT: B 1018 ILE cc_start: 0.8916 (mm) cc_final: 0.8430 (tt) REVERT: B 1019 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7819 (mtp-110) REVERT: B 1021 SER cc_start: 0.8673 (t) cc_final: 0.8409 (p) REVERT: B 1034 LEU cc_start: 0.5367 (mt) cc_final: 0.4941 (mt) REVERT: B 1116 THR cc_start: -0.2698 (OUTLIER) cc_final: -0.3797 (m) REVERT: C 36 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.5949 (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: 0.7563 (m-40) REVERT: C 128 ILE cc_start: 0.7083 (mt) cc_final: 0.6632 (mt) REVERT: C 170 TYR cc_start: 0.7896 (t80) cc_final: 0.6845 (t80) REVERT: C 177 MET cc_start: 0.5838 (mtp) cc_final: 0.5142 (mmm) REVERT: C 206 LYS cc_start: 0.6998 (tptm) cc_final: 0.6673 (tttt) REVERT: C 220 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7047 (t80) REVERT: C 223 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5091 (mp) REVERT: C 229 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7630 (mt) REVERT: C 269 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.3051 (m-80) REVERT: C 276 LEU cc_start: 0.8372 (tp) cc_final: 0.8008 (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: 0.8081 (mmmt) REVERT: C 310 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8070 (ttmm) REVERT: C 317 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7935 (p0) REVERT: C 324 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7805 (mp0) REVERT: C 338 PHE cc_start: 0.8870 (m-80) cc_final: 0.8302 (m-10) REVERT: C 342 PHE cc_start: 0.8848 (m-80) cc_final: 0.8538 (m-10) REVERT: C 365 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: C 385 THR cc_start: 0.7988 (t) cc_final: 0.7685 (p) REVERT: C 386 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8337 (mttp) REVERT: C 388 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.6502 (m-40) REVERT: C 409 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: C 462 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6598 (ttpp) REVERT: C 508 TYR cc_start: 0.8493 (m-80) cc_final: 0.8143 (m-10) REVERT: C 531 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7853 (m) REVERT: C 535 LYS cc_start: 0.8944 (mttt) cc_final: 0.8546 (ttpp) REVERT: C 562 PHE cc_start: 0.8369 (p90) cc_final: 0.7752 (p90) REVERT: C 563 GLN cc_start: 0.7986 (mt0) cc_final: 0.7630 (pt0) REVERT: C 585 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7209 (mt) REVERT: C 655 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6869 (p90) REVERT: C 699 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.5759 (mt) REVERT: C 776 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8521 (tptp) REVERT: C 795 LYS cc_start: 0.8207 (mttt) cc_final: 0.7979 (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: 0.4183 (p90) REVERT: C 895 GLN cc_start: -0.0323 (OUTLIER) cc_final: -0.2477 (tm-30) REVERT: C 898 PHE cc_start: 0.5891 (t80) cc_final: 0.5591 (t80) REVERT: C 931 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8848 (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: 0.8331 (pp30) REVERT: C 964 LYS cc_start: 0.8886 (tttt) cc_final: 0.8518 (tptp) REVERT: C 973 ILE cc_start: 0.8048 (pt) cc_final: 0.7692 (pt) REVERT: C 981 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7824 (mt) REVERT: C 988 GLU cc_start: 0.6844 (tp30) cc_final: 0.6283 (tp30) REVERT: C 1008 VAL cc_start: 0.8485 (t) cc_final: 0.8130 (m) outliers start: 215 outliers final: 47 residues processed: 845 average time/residue: 0.1835 time to fit residues: 239.8991 Evaluate side-chains 606 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 527 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 165 ASN A 207 HIS A 239 GLN 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 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 764 ASN B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B 978 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 C 388 ASN C 394 ASN 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 ** 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: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.182509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.136484 restraints weight = 66768.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.141599 restraints weight = 46882.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.145267 restraints weight = 35555.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.147978 restraints weight = 28739.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.149631 restraints weight = 24343.897| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 26386 Z= 0.232 Angle : 0.917 21.891 36017 Z= 0.456 Chirality : 0.055 0.675 4182 Planarity : 0.006 0.062 4587 Dihedral : 9.581 102.987 4373 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 0.61 % Allowed : 5.73 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3187 helix: 1.28 (0.19), residues: 674 sheet: 0.09 (0.20), residues: 655 loop : -1.03 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B1107 TYR 0.042 0.002 TYR C 904 PHE 0.032 0.003 PHE B 823 TRP 0.053 0.003 TRP A 64 HIS 0.019 0.003 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00484 (26300) covalent geometry : angle 0.86713 (35807) SS BOND : bond 0.01273 ( 42) SS BOND : angle 2.88723 ( 84) hydrogen bonds : bond 0.06607 ( 872) hydrogen bonds : angle 7.25406 ( 2433) Misc. bond : bond 0.00563 ( 2) link_BETA1-4 : bond 0.00585 ( 10) link_BETA1-4 : angle 1.81406 ( 30) link_NAG-ASN : bond 0.00990 ( 32) link_NAG-ASN : angle 5.13827 ( 96) *********************** 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 584 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 567 time to evaluate : 0.900 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: A 41 LYS cc_start: 0.8524 (mmtt) cc_final: 0.7815 (ttpt) REVERT: A 53 ASP cc_start: 0.8398 (t0) cc_final: 0.8000 (t0) REVERT: A 65 PHE cc_start: 0.7684 (m-80) cc_final: 0.7163 (m-80) REVERT: A 104 TRP cc_start: 0.6078 (m-90) cc_final: 0.5392 (m-90) REVERT: A 128 ILE cc_start: 0.8543 (mt) cc_final: 0.7452 (mt) REVERT: A 170 TYR cc_start: 0.7404 (t80) cc_final: 0.6942 (t80) REVERT: A 189 LEU cc_start: 0.8331 (tp) cc_final: 0.7774 (tp) REVERT: A 194 PHE cc_start: 0.9034 (m-80) cc_final: 0.8124 (m-80) REVERT: A 195 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8488 (ttpp) REVERT: A 202 LYS cc_start: 0.7872 (mttt) cc_final: 0.7291 (mttp) REVERT: A 275 PHE cc_start: 0.6792 (m-10) cc_final: 0.5880 (m-10) REVERT: A 304 LYS cc_start: 0.8828 (tppp) cc_final: 0.8470 (tptt) REVERT: A 312 ILE cc_start: 0.8402 (tt) cc_final: 0.8150 (tt) REVERT: A 313 TYR cc_start: 0.8302 (m-10) cc_final: 0.7947 (m-10) REVERT: A 355 ARG cc_start: 0.8747 (mtm-85) cc_final: 0.8208 (ttm-80) REVERT: A 380 TYR cc_start: 0.7848 (m-80) cc_final: 0.7420 (m-80) REVERT: A 386 LYS cc_start: 0.8649 (mttp) cc_final: 0.8383 (mmmm) REVERT: A 421 TYR cc_start: 0.8480 (m-10) cc_final: 0.7965 (m-10) REVERT: A 462 LYS cc_start: 0.7939 (mmtm) cc_final: 0.6899 (ttpp) REVERT: A 535 LYS cc_start: 0.7949 (mttm) cc_final: 0.7659 (ttmm) REVERT: A 562 PHE cc_start: 0.7957 (p90) cc_final: 0.7667 (p90) REVERT: A 585 LEU cc_start: 0.8487 (mt) cc_final: 0.7973 (tt) REVERT: A 586 ASP cc_start: 0.7293 (p0) cc_final: 0.6976 (p0) REVERT: A 751 ASN cc_start: 0.8833 (m110) cc_final: 0.8392 (m-40) REVERT: A 752 LEU cc_start: 0.8856 (mt) cc_final: 0.8524 (tt) REVERT: A 759 PHE cc_start: 0.8669 (m-80) cc_final: 0.8428 (m-80) REVERT: A 762 GLN cc_start: 0.8944 (pt0) cc_final: 0.8660 (pt0) REVERT: A 763 LEU cc_start: 0.9060 (pp) cc_final: 0.8853 (pp) REVERT: A 764 ASN cc_start: 0.8807 (m110) cc_final: 0.8487 (m110) REVERT: A 776 LYS cc_start: 0.8934 (tptm) cc_final: 0.8714 (mmmt) REVERT: A 796 ASP cc_start: 0.7766 (m-30) cc_final: 0.7274 (p0) REVERT: A 867 ASP cc_start: 0.7602 (m-30) cc_final: 0.7203 (p0) REVERT: A 900 MET cc_start: 0.7556 (tmm) cc_final: 0.7191 (tmm) REVERT: A 917 TYR cc_start: 0.8690 (m-80) cc_final: 0.8190 (m-10) REVERT: A 927 PHE cc_start: 0.7577 (t80) cc_final: 0.7216 (t80) REVERT: A 947 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7470 (pttt) REVERT: A 954 GLN cc_start: 0.9106 (tp40) cc_final: 0.8588 (tm-30) REVERT: A 968 SER cc_start: 0.8439 (m) cc_final: 0.8140 (t) REVERT: A 970 PHE cc_start: 0.8203 (m-10) cc_final: 0.7726 (m-10) REVERT: A 983 ARG cc_start: 0.8846 (ptt90) cc_final: 0.8505 (ttp80) REVERT: A 990 GLU cc_start: 0.8793 (tt0) cc_final: 0.8472 (mt-10) REVERT: A 993 ILE cc_start: 0.8898 (mt) cc_final: 0.8073 (tp) REVERT: A 994 ASP cc_start: 0.8704 (m-30) cc_final: 0.8023 (m-30) REVERT: A 1001 LEU cc_start: 0.9351 (mt) cc_final: 0.8828 (pp) REVERT: A 1002 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 1018 ILE cc_start: 0.8798 (mm) cc_final: 0.8448 (tt) REVERT: A 1019 ARG cc_start: 0.8940 (ttt180) cc_final: 0.8175 (ttm110) REVERT: A 1109 PHE cc_start: 0.7328 (t80) cc_final: 0.6986 (t80) REVERT: B 44 ARG cc_start: 0.7634 (mtt90) cc_final: 0.6631 (ptp90) REVERT: B 48 LEU cc_start: 0.8484 (mp) cc_final: 0.7686 (mt) REVERT: B 58 PHE cc_start: 0.8010 (m-80) cc_final: 0.7307 (m-80) REVERT: B 59 PHE cc_start: 0.7221 (t80) cc_final: 0.6976 (t80) REVERT: B 63 THR cc_start: 0.7944 (p) cc_final: 0.6678 (t) REVERT: B 64 TRP cc_start: 0.8760 (t60) cc_final: 0.8536 (t-100) REVERT: B 65 PHE cc_start: 0.8254 (m-80) cc_final: 0.7577 (m-80) REVERT: B 119 ILE cc_start: 0.4282 (OUTLIER) cc_final: 0.3647 (pt) REVERT: B 129 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7814 (mmmt) REVERT: B 194 PHE cc_start: 0.7736 (m-80) cc_final: 0.6996 (m-10) REVERT: B 212 LEU cc_start: 0.8563 (tp) cc_final: 0.8315 (tp) REVERT: B 223 LEU cc_start: 0.8518 (mt) cc_final: 0.8218 (mm) REVERT: B 276 LEU cc_start: 0.8700 (tt) cc_final: 0.8329 (tt) REVERT: B 300 LYS cc_start: 0.8235 (mttt) cc_final: 0.7835 (mtmm) REVERT: B 304 LYS cc_start: 0.8583 (ptpp) cc_final: 0.7999 (tppt) REVERT: B 306 PHE cc_start: 0.6851 (m-80) cc_final: 0.5492 (m-80) REVERT: B 313 TYR cc_start: 0.7357 (m-10) cc_final: 0.6828 (m-10) REVERT: B 396 TYR cc_start: 0.8197 (m-80) cc_final: 0.7856 (m-80) REVERT: B 528 LYS cc_start: 0.7431 (mmtm) cc_final: 0.7230 (mmmm) REVERT: B 560 LEU cc_start: 0.8840 (mt) cc_final: 0.8479 (mt) REVERT: B 603 ASN cc_start: 0.9220 (t0) cc_final: 0.8793 (p0) REVERT: B 612 TYR cc_start: 0.7289 (m-10) cc_final: 0.6851 (m-10) REVERT: B 656 VAL cc_start: 0.8106 (m) cc_final: 0.7895 (m) REVERT: B 748 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8763 (pp20) REVERT: B 753 LEU cc_start: 0.9139 (tp) cc_final: 0.8840 (tp) REVERT: B 775 ASP cc_start: 0.8313 (m-30) cc_final: 0.7659 (m-30) REVERT: B 776 LYS cc_start: 0.8498 (tptp) cc_final: 0.8283 (ptpt) REVERT: B 819 GLU cc_start: 0.8909 (pt0) cc_final: 0.8430 (pt0) REVERT: B 822 LEU cc_start: 0.9147 (tp) cc_final: 0.8724 (mt) REVERT: B 869 MET cc_start: 0.8509 (mtt) cc_final: 0.8231 (mmp) REVERT: B 927 PHE cc_start: 0.8576 (t80) cc_final: 0.7949 (t80) REVERT: B 954 GLN cc_start: 0.9035 (mt0) cc_final: 0.8204 (tm-30) REVERT: B 955 ASN cc_start: 0.8778 (m110) cc_final: 0.8535 (t0) REVERT: B 957 GLN cc_start: 0.9222 (pt0) cc_final: 0.8602 (pp30) REVERT: B 959 LEU cc_start: 0.8657 (pp) cc_final: 0.8390 (pp) REVERT: B 960 ASN cc_start: 0.8896 (m-40) cc_final: 0.8545 (m-40) REVERT: B 964 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8580 (tmtt) REVERT: B 965 GLN cc_start: 0.9310 (mm110) cc_final: 0.8327 (mm110) REVERT: B 978 ASN cc_start: 0.8740 (t160) cc_final: 0.8530 (t0) REVERT: B 998 THR cc_start: 0.9026 (p) cc_final: 0.8685 (p) REVERT: B 1010 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8713 (mm-40) REVERT: B 1012 LEU cc_start: 0.9381 (mt) cc_final: 0.9152 (mt) REVERT: B 1019 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8268 (ptm160) REVERT: B 1021 SER cc_start: 0.8734 (t) cc_final: 0.8439 (p) REVERT: B 1028 LYS cc_start: 0.7254 (tptt) cc_final: 0.7019 (tptt) REVERT: B 1050 MET cc_start: 0.7247 (tpt) cc_final: 0.6562 (mtp) REVERT: C 33 THR cc_start: 0.6368 (p) cc_final: 0.5962 (t) REVERT: C 59 PHE cc_start: 0.7512 (m-80) cc_final: 0.7223 (m-10) REVERT: C 91 TYR cc_start: 0.7636 (t80) cc_final: 0.6638 (t80) REVERT: C 117 LEU cc_start: 0.8669 (tt) cc_final: 0.8147 (pt) REVERT: C 192 PHE cc_start: 0.8527 (m-80) cc_final: 0.8094 (m-80) REVERT: C 194 PHE cc_start: 0.7983 (m-80) cc_final: 0.7704 (m-80) REVERT: C 235 ILE cc_start: 0.7039 (mt) cc_final: 0.6711 (mm) REVERT: C 276 LEU cc_start: 0.7993 (tp) cc_final: 0.7787 (tp) REVERT: C 281 GLU cc_start: 0.8201 (tp30) cc_final: 0.7904 (tp30) REVERT: C 324 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8091 (mp0) REVERT: C 338 PHE cc_start: 0.8855 (m-80) cc_final: 0.8484 (m-10) REVERT: C 342 PHE cc_start: 0.8802 (m-80) cc_final: 0.8474 (m-10) REVERT: C 365 TYR cc_start: 0.8765 (m-10) cc_final: 0.8517 (m-80) REVERT: C 386 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8113 (mttt) REVERT: C 417 LYS cc_start: 0.9093 (tppp) cc_final: 0.8862 (tppt) REVERT: C 425 LEU cc_start: 0.8164 (mt) cc_final: 0.7915 (tp) REVERT: C 517 LEU cc_start: 0.6804 (pp) cc_final: 0.6214 (pp) REVERT: C 562 PHE cc_start: 0.8772 (p90) cc_final: 0.8246 (p90) REVERT: C 563 GLN cc_start: 0.8271 (mt0) cc_final: 0.7925 (mt0) REVERT: C 583 GLU cc_start: 0.8476 (tp30) cc_final: 0.7933 (tm-30) REVERT: C 588 THR cc_start: 0.8422 (m) cc_final: 0.8164 (p) REVERT: C 738 CYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6563 (p) REVERT: C 748 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8511 (mt-10) REVERT: C 756 TYR cc_start: 0.8148 (m-10) cc_final: 0.7790 (m-10) REVERT: C 759 PHE cc_start: 0.8612 (m-80) cc_final: 0.7958 (m-10) REVERT: C 765 ARG cc_start: 0.9026 (ptp-170) cc_final: 0.8751 (ptp-170) REVERT: C 770 ILE cc_start: 0.9290 (mm) cc_final: 0.9048 (mm) REVERT: C 773 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7811 (tm-30) REVERT: C 776 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8275 (tmtt) REVERT: C 869 MET cc_start: 0.9038 (mtm) cc_final: 0.8093 (tmm) REVERT: C 917 TYR cc_start: 0.8117 (m-80) cc_final: 0.7857 (m-10) REVERT: C 954 GLN cc_start: 0.9093 (mt0) cc_final: 0.8373 (pp30) REVERT: C 955 ASN cc_start: 0.7911 (p0) cc_final: 0.7448 (p0) REVERT: C 957 GLN cc_start: 0.8914 (tt0) cc_final: 0.8596 (pp30) REVERT: C 959 LEU cc_start: 0.9346 (mp) cc_final: 0.9050 (pp) REVERT: C 964 LYS cc_start: 0.9199 (tttt) cc_final: 0.8914 (tmtt) REVERT: C 965 GLN cc_start: 0.9269 (mm110) cc_final: 0.8491 (mm110) REVERT: C 979 ASP cc_start: 0.9029 (m-30) cc_final: 0.8723 (m-30) REVERT: C 983 ARG cc_start: 0.8992 (tmt-80) cc_final: 0.8741 (tpt90) REVERT: C 1000 ARG cc_start: 0.9066 (mmm160) cc_final: 0.8860 (mmm160) REVERT: C 1001 LEU cc_start: 0.9580 (tt) cc_final: 0.9242 (tt) REVERT: C 1002 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8622 (mm110) REVERT: C 1010 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8294 (tm-30) REVERT: C 1014 ARG cc_start: 0.8601 (mmp80) cc_final: 0.8209 (mmt-90) REVERT: C 1017 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8069 (mp0) REVERT: C 1028 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7304 (ttmt) outliers start: 17 outliers final: 1 residues processed: 581 average time/residue: 0.1855 time to fit residues: 165.4474 Evaluate side-chains 480 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 477 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 314 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 29 optimal weight: 0.0060 chunk 181 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 227 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 563 GLN A 564 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 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 49 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 655 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.177574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.134354 restraints weight = 68310.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.139628 restraints weight = 46943.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.143427 restraints weight = 35098.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.146253 restraints weight = 27968.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.148301 restraints weight = 23356.050| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26386 Z= 0.182 Angle : 0.779 16.145 36017 Z= 0.387 Chirality : 0.051 0.577 4182 Planarity : 0.005 0.070 4587 Dihedral : 8.807 103.358 4373 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3187 helix: 0.93 (0.19), residues: 694 sheet: -0.03 (0.19), residues: 644 loop : -1.17 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 454 TYR 0.020 0.002 TYR A 674 PHE 0.027 0.002 PHE C 797 TRP 0.021 0.002 TRP A 64 HIS 0.008 0.002 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00381 (26300) covalent geometry : angle 0.73782 (35807) SS BOND : bond 0.00450 ( 42) SS BOND : angle 2.08818 ( 84) hydrogen bonds : bond 0.05345 ( 872) hydrogen bonds : angle 6.61258 ( 2433) Misc. bond : bond 0.00051 ( 2) link_BETA1-4 : bond 0.00461 ( 10) link_BETA1-4 : angle 1.25531 ( 30) link_NAG-ASN : bond 0.00729 ( 32) link_NAG-ASN : angle 4.51211 ( 96) *********************** 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 547 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 546 time to evaluate : 0.890 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: A 53 ASP cc_start: 0.8435 (t0) cc_final: 0.8097 (t0) REVERT: A 65 PHE cc_start: 0.7825 (m-80) cc_final: 0.7264 (m-80) REVERT: A 87 ASN cc_start: 0.8361 (m-40) cc_final: 0.8161 (p0) REVERT: A 128 ILE cc_start: 0.8608 (mt) cc_final: 0.7559 (mt) REVERT: A 133 PHE cc_start: 0.5597 (m-80) cc_final: 0.5113 (m-80) REVERT: A 170 TYR cc_start: 0.7449 (t80) cc_final: 0.6930 (t80) REVERT: A 194 PHE cc_start: 0.8676 (m-80) cc_final: 0.8173 (m-80) REVERT: A 275 PHE cc_start: 0.6834 (m-10) cc_final: 0.6266 (m-10) REVERT: A 303 LEU cc_start: 0.8818 (mt) cc_final: 0.8534 (mt) REVERT: A 310 LYS cc_start: 0.8455 (mttt) cc_final: 0.7848 (tptp) REVERT: A 313 TYR cc_start: 0.8276 (m-10) cc_final: 0.7948 (m-10) REVERT: A 380 TYR cc_start: 0.7976 (m-80) cc_final: 0.7496 (m-80) REVERT: A 386 LYS cc_start: 0.8697 (mttp) cc_final: 0.8172 (mmmm) REVERT: A 400 PHE cc_start: 0.6088 (p90) cc_final: 0.5352 (p90) REVERT: A 414 GLN cc_start: 0.6484 (pt0) cc_final: 0.5954 (pm20) REVERT: A 461 LEU cc_start: 0.8050 (mt) cc_final: 0.7105 (mt) REVERT: A 462 LYS cc_start: 0.7816 (mmtm) cc_final: 0.7052 (ttpp) REVERT: A 529 LYS cc_start: 0.8799 (tttm) cc_final: 0.8449 (tmtt) REVERT: A 535 LYS cc_start: 0.8096 (mttm) cc_final: 0.7663 (mmmt) REVERT: A 731 MET cc_start: 0.8723 (ppp) cc_final: 0.8353 (ppp) REVERT: A 752 LEU cc_start: 0.8796 (mt) cc_final: 0.8478 (tt) REVERT: A 755 GLN cc_start: 0.8423 (mp10) cc_final: 0.8073 (tt0) REVERT: A 759 PHE cc_start: 0.8779 (m-80) cc_final: 0.8494 (m-80) REVERT: A 762 GLN cc_start: 0.8875 (pt0) cc_final: 0.8569 (pt0) REVERT: A 764 ASN cc_start: 0.8944 (m110) cc_final: 0.8610 (m110) REVERT: A 776 LYS cc_start: 0.8999 (tptm) cc_final: 0.8368 (tptp) REVERT: A 796 ASP cc_start: 0.7744 (m-30) cc_final: 0.7274 (p0) REVERT: A 867 ASP cc_start: 0.7466 (m-30) cc_final: 0.7103 (p0) REVERT: A 917 TYR cc_start: 0.7979 (m-80) cc_final: 0.7603 (m-80) REVERT: A 927 PHE cc_start: 0.7659 (t80) cc_final: 0.7248 (t80) REVERT: A 947 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7534 (pttt) REVERT: A 949 GLN cc_start: 0.8177 (pp30) cc_final: 0.7976 (pp30) REVERT: A 954 GLN cc_start: 0.8981 (tp40) cc_final: 0.8442 (tm-30) REVERT: A 964 LYS cc_start: 0.9294 (ttmm) cc_final: 0.8936 (mmtt) REVERT: A 979 ASP cc_start: 0.9100 (m-30) cc_final: 0.8507 (t0) REVERT: A 990 GLU cc_start: 0.8774 (tt0) cc_final: 0.8473 (mt-10) REVERT: A 993 ILE cc_start: 0.8875 (mt) cc_final: 0.8131 (tp) REVERT: A 994 ASP cc_start: 0.8705 (m-30) cc_final: 0.8090 (m-30) REVERT: A 995 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8334 (ptp-110) REVERT: A 997 ILE cc_start: 0.9378 (mt) cc_final: 0.9085 (pt) REVERT: A 1001 LEU cc_start: 0.9198 (mt) cc_final: 0.8803 (mm) REVERT: A 1002 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 1005 GLN cc_start: 0.8908 (mt0) cc_final: 0.8684 (mm-40) REVERT: A 1014 ARG cc_start: 0.8763 (mmp-170) cc_final: 0.8382 (mmm160) REVERT: B 37 TYR cc_start: 0.8449 (p90) cc_final: 0.8209 (p90) REVERT: B 41 LYS cc_start: 0.8824 (tppt) cc_final: 0.8279 (tppt) REVERT: B 44 ARG cc_start: 0.7882 (mtt90) cc_final: 0.6919 (ptp-170) REVERT: B 58 PHE cc_start: 0.7863 (m-80) cc_final: 0.6501 (m-80) REVERT: B 63 THR cc_start: 0.7971 (p) cc_final: 0.6795 (t) REVERT: B 65 PHE cc_start: 0.8205 (m-80) cc_final: 0.7603 (m-80) REVERT: B 127 VAL cc_start: 0.8839 (p) cc_final: 0.8316 (m) REVERT: B 128 ILE cc_start: 0.8621 (mt) cc_final: 0.7919 (mt) REVERT: B 194 PHE cc_start: 0.7731 (m-80) cc_final: 0.7126 (m-10) REVERT: B 212 LEU cc_start: 0.8562 (tp) cc_final: 0.8175 (tt) REVERT: B 266 TYR cc_start: 0.7182 (m-10) cc_final: 0.6836 (m-10) REVERT: B 275 PHE cc_start: 0.6414 (m-10) cc_final: 0.5188 (m-10) REVERT: B 276 LEU cc_start: 0.8991 (tt) cc_final: 0.7976 (mp) REVERT: B 287 ASP cc_start: 0.8038 (m-30) cc_final: 0.7576 (t70) REVERT: B 313 TYR cc_start: 0.7690 (m-10) cc_final: 0.7192 (m-10) REVERT: B 396 TYR cc_start: 0.8132 (m-80) cc_final: 0.7832 (m-80) REVERT: B 537 LYS cc_start: 0.8813 (mppt) cc_final: 0.8505 (tppt) REVERT: B 562 PHE cc_start: 0.8407 (p90) cc_final: 0.7643 (p90) REVERT: B 603 ASN cc_start: 0.9239 (t0) cc_final: 0.8825 (p0) REVERT: B 753 LEU cc_start: 0.8991 (tp) cc_final: 0.8654 (pp) REVERT: B 754 LEU cc_start: 0.9032 (mt) cc_final: 0.8823 (mt) REVERT: B 819 GLU cc_start: 0.8861 (pt0) cc_final: 0.8299 (pt0) REVERT: B 822 LEU cc_start: 0.9127 (tp) cc_final: 0.8704 (mt) REVERT: B 824 ASN cc_start: 0.8616 (m110) cc_final: 0.8387 (m110) REVERT: B 867 ASP cc_start: 0.8361 (p0) cc_final: 0.8084 (p0) REVERT: B 869 MET cc_start: 0.8523 (mtt) cc_final: 0.8185 (mmp) REVERT: B 927 PHE cc_start: 0.8532 (t80) cc_final: 0.7878 (t80) REVERT: B 954 GLN cc_start: 0.8984 (mt0) cc_final: 0.8521 (pp30) REVERT: B 955 ASN cc_start: 0.8701 (m110) cc_final: 0.8490 (t0) REVERT: B 957 GLN cc_start: 0.9157 (pt0) cc_final: 0.8595 (pp30) REVERT: B 959 LEU cc_start: 0.8684 (pp) cc_final: 0.8440 (pp) REVERT: B 960 ASN cc_start: 0.8642 (m-40) cc_final: 0.8285 (m-40) REVERT: B 965 GLN cc_start: 0.9201 (mm110) cc_final: 0.8860 (mm110) REVERT: B 979 ASP cc_start: 0.8586 (t0) cc_final: 0.8242 (t0) REVERT: B 1000 ARG cc_start: 0.8457 (ptp-110) cc_final: 0.8129 (ptp-110) REVERT: B 1002 GLN cc_start: 0.8744 (mp10) cc_final: 0.8543 (mp10) REVERT: B 1009 THR cc_start: 0.9156 (p) cc_final: 0.8884 (p) REVERT: B 1010 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8523 (mm-40) REVERT: B 1011 GLN cc_start: 0.8526 (mm110) cc_final: 0.8129 (mp10) REVERT: B 1012 LEU cc_start: 0.9380 (mt) cc_final: 0.9173 (mt) REVERT: B 1017 GLU cc_start: 0.8608 (pp20) cc_final: 0.8127 (pp20) REVERT: B 1019 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8115 (ptm160) REVERT: B 1021 SER cc_start: 0.8640 (t) cc_final: 0.8364 (p) REVERT: B 1028 LYS cc_start: 0.7448 (tptm) cc_final: 0.7110 (tptt) REVERT: C 56 LEU cc_start: 0.8565 (tp) cc_final: 0.8363 (tp) REVERT: C 59 PHE cc_start: 0.7546 (m-80) cc_final: 0.7150 (m-10) REVERT: C 65 PHE cc_start: 0.7559 (m-80) cc_final: 0.7094 (m-80) REVERT: C 91 TYR cc_start: 0.7564 (t80) cc_final: 0.7027 (t80) REVERT: C 160 TYR cc_start: 0.8316 (p90) cc_final: 0.7078 (p90) REVERT: C 194 PHE cc_start: 0.7896 (m-80) cc_final: 0.7569 (m-80) REVERT: C 235 ILE cc_start: 0.6761 (mt) cc_final: 0.6543 (mm) REVERT: C 237 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8445 (mmm-85) REVERT: C 276 LEU cc_start: 0.7982 (tp) cc_final: 0.7723 (tp) REVERT: C 281 GLU cc_start: 0.8290 (tp30) cc_final: 0.7732 (tp30) REVERT: C 313 TYR cc_start: 0.7557 (m-10) cc_final: 0.7300 (m-10) REVERT: C 324 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8080 (pm20) REVERT: C 338 PHE cc_start: 0.9004 (m-80) cc_final: 0.8630 (m-10) REVERT: C 342 PHE cc_start: 0.8858 (m-80) cc_final: 0.8499 (m-10) REVERT: C 356 LYS cc_start: 0.8444 (tptp) cc_final: 0.7775 (tmmt) REVERT: C 365 TYR cc_start: 0.8769 (m-10) cc_final: 0.8373 (m-80) REVERT: C 380 TYR cc_start: 0.7769 (m-10) cc_final: 0.7520 (m-80) REVERT: C 386 LYS cc_start: 0.8316 (mmmt) cc_final: 0.8079 (mttm) REVERT: C 409 GLN cc_start: 0.8143 (mp10) cc_final: 0.7847 (mp10) REVERT: C 417 LYS cc_start: 0.9082 (tppp) cc_final: 0.8834 (tppt) REVERT: C 425 LEU cc_start: 0.8289 (mt) cc_final: 0.7969 (tp) REVERT: C 516 GLU cc_start: 0.6407 (mp0) cc_final: 0.6170 (mp0) REVERT: C 543 PHE cc_start: 0.8360 (m-80) cc_final: 0.8124 (m-80) REVERT: C 562 PHE cc_start: 0.8775 (p90) cc_final: 0.8548 (p90) REVERT: C 563 GLN cc_start: 0.8298 (mt0) cc_final: 0.8095 (mt0) REVERT: C 571 ASP cc_start: 0.9112 (t0) cc_final: 0.8786 (t0) REVERT: C 583 GLU cc_start: 0.8394 (tp30) cc_final: 0.8102 (tm-30) REVERT: C 747 THR cc_start: 0.9139 (p) cc_final: 0.8852 (p) REVERT: C 748 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8675 (mp0) REVERT: C 756 TYR cc_start: 0.8247 (m-10) cc_final: 0.7978 (m-10) REVERT: C 759 PHE cc_start: 0.8570 (m-80) cc_final: 0.8010 (m-10) REVERT: C 762 GLN cc_start: 0.9073 (mt0) cc_final: 0.8782 (mt0) REVERT: C 763 LEU cc_start: 0.9114 (mt) cc_final: 0.8856 (mt) REVERT: C 764 ASN cc_start: 0.9020 (m110) cc_final: 0.8629 (m110) REVERT: C 765 ARG cc_start: 0.9094 (ptp-170) cc_final: 0.8573 (ptt-90) REVERT: C 770 ILE cc_start: 0.9100 (mm) cc_final: 0.8895 (mt) REVERT: C 773 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7837 (mm-30) REVERT: C 776 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8377 (tmtt) REVERT: C 858 LEU cc_start: 0.8829 (mp) cc_final: 0.8535 (mm) REVERT: C 869 MET cc_start: 0.9012 (mtm) cc_final: 0.8176 (tmm) REVERT: C 900 MET cc_start: 0.8010 (ppp) cc_final: 0.7693 (ppp) REVERT: C 917 TYR cc_start: 0.7916 (m-80) cc_final: 0.7691 (m-10) REVERT: C 954 GLN cc_start: 0.9028 (mt0) cc_final: 0.8612 (pp30) REVERT: C 957 GLN cc_start: 0.9007 (tt0) cc_final: 0.8696 (pp30) REVERT: C 959 LEU cc_start: 0.9238 (mp) cc_final: 0.9011 (pp) REVERT: C 964 LYS cc_start: 0.9272 (tttt) cc_final: 0.8910 (ptmm) REVERT: C 965 GLN cc_start: 0.9198 (mm110) cc_final: 0.8661 (mm110) REVERT: C 969 ASN cc_start: 0.8046 (p0) cc_final: 0.7221 (p0) REVERT: C 970 PHE cc_start: 0.7999 (m-80) cc_final: 0.7609 (m-10) REVERT: C 978 ASN cc_start: 0.9470 (m110) cc_final: 0.9164 (m110) REVERT: C 979 ASP cc_start: 0.8998 (m-30) cc_final: 0.8794 (m-30) REVERT: C 981 LEU cc_start: 0.8871 (mp) cc_final: 0.8519 (pp) REVERT: C 983 ARG cc_start: 0.8980 (tmt-80) cc_final: 0.8686 (tpt90) REVERT: C 1000 ARG cc_start: 0.9138 (mtt-85) cc_final: 0.8578 (mmm160) REVERT: C 1001 LEU cc_start: 0.9438 (tt) cc_final: 0.9234 (tp) REVERT: C 1002 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8450 (mm110) REVERT: C 1010 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8098 (tm-30) REVERT: C 1012 LEU cc_start: 0.9230 (mt) cc_final: 0.8941 (mt) REVERT: C 1017 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8137 (mp0) REVERT: C 1019 ARG cc_start: 0.8812 (ptp-170) cc_final: 0.8525 (ptt-90) outliers start: 1 outliers final: 0 residues processed: 547 average time/residue: 0.1893 time to fit residues: 157.8263 Evaluate side-chains 468 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** 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** A1023 ASN A1036 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 360 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.158613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.114549 restraints weight = 66484.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.118749 restraints weight = 47722.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.121787 restraints weight = 37121.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.124097 restraints weight = 30626.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.125838 restraints weight = 26581.055| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.217 26386 Z= 0.496 Angle : 1.075 19.367 36017 Z= 0.577 Chirality : 0.059 0.497 4182 Planarity : 0.008 0.114 4587 Dihedral : 9.274 105.576 4373 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 36.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 0.25 % Allowed : 5.77 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.13), residues: 3187 helix: -0.85 (0.17), residues: 701 sheet: -0.92 (0.19), residues: 680 loop : -1.69 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 355 TYR 0.037 0.004 TYR B 695 PHE 0.049 0.004 PHE A 800 TRP 0.035 0.004 TRP B 64 HIS 0.019 0.004 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00929 (26300) covalent geometry : angle 1.04631 (35807) SS BOND : bond 0.01226 ( 42) SS BOND : angle 2.27988 ( 84) hydrogen bonds : bond 0.07842 ( 872) hydrogen bonds : angle 7.77368 ( 2433) Misc. bond : bond 0.00253 ( 2) link_BETA1-4 : bond 0.00612 ( 10) link_BETA1-4 : angle 1.85581 ( 30) link_NAG-ASN : bond 0.01061 ( 32) link_NAG-ASN : angle 4.39796 ( 96) *********************** 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 562 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 555 time to evaluate : 0.830 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: A 53 ASP cc_start: 0.8604 (t0) cc_final: 0.8238 (t0) REVERT: A 65 PHE cc_start: 0.8120 (m-80) cc_final: 0.7270 (m-80) REVERT: A 91 TYR cc_start: 0.7632 (t80) cc_final: 0.7214 (t80) REVERT: A 104 TRP cc_start: 0.7195 (m-90) cc_final: 0.6473 (m-90) REVERT: A 118 LEU cc_start: 0.8861 (tp) cc_final: 0.8511 (mm) REVERT: A 119 ILE cc_start: 0.7357 (mp) cc_final: 0.6968 (mm) REVERT: A 128 ILE cc_start: 0.8829 (mt) cc_final: 0.7777 (mt) REVERT: A 170 TYR cc_start: 0.7969 (t80) cc_final: 0.7140 (t80) REVERT: A 195 LYS cc_start: 0.8345 (tptt) cc_final: 0.7936 (tppt) REVERT: A 201 PHE cc_start: 0.7799 (m-80) cc_final: 0.6647 (m-80) REVERT: A 277 LEU cc_start: 0.8900 (pp) cc_final: 0.8635 (mm) REVERT: A 303 LEU cc_start: 0.8845 (mt) cc_final: 0.8576 (mt) REVERT: A 365 TYR cc_start: 0.8299 (m-80) cc_final: 0.8061 (m-80) REVERT: A 380 TYR cc_start: 0.8203 (m-80) cc_final: 0.7766 (m-80) REVERT: A 389 ASP cc_start: 0.9082 (m-30) cc_final: 0.8582 (p0) REVERT: A 505 TYR cc_start: 0.8792 (t80) cc_final: 0.8406 (t80) REVERT: A 529 LYS cc_start: 0.9171 (tttm) cc_final: 0.8863 (mmtm) REVERT: A 560 LEU cc_start: 0.9385 (tp) cc_final: 0.9165 (tp) REVERT: A 740 MET cc_start: 0.8929 (tpt) cc_final: 0.8638 (tpp) REVERT: A 741 TYR cc_start: 0.8604 (t80) cc_final: 0.8338 (t80) REVERT: A 756 TYR cc_start: 0.8758 (m-80) cc_final: 0.8378 (m-10) REVERT: A 759 PHE cc_start: 0.8838 (m-80) cc_final: 0.8439 (m-80) REVERT: A 762 GLN cc_start: 0.8893 (pt0) cc_final: 0.8635 (pt0) REVERT: A 776 LYS cc_start: 0.9101 (tptm) cc_final: 0.8574 (tptp) REVERT: A 873 TYR cc_start: 0.8781 (m-10) cc_final: 0.8447 (m-80) REVERT: A 927 PHE cc_start: 0.8019 (t80) cc_final: 0.7656 (t80) REVERT: A 934 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8619 (mt) REVERT: A 947 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7614 (mmtm) REVERT: A 954 GLN cc_start: 0.9070 (tp40) cc_final: 0.8614 (tm-30) REVERT: A 964 LYS cc_start: 0.9415 (ttmm) cc_final: 0.8900 (tptp) REVERT: A 965 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 979 ASP cc_start: 0.9283 (m-30) cc_final: 0.8722 (t0) REVERT: A 983 ARG cc_start: 0.8984 (ptt90) cc_final: 0.8065 (ttp80) REVERT: A 990 GLU cc_start: 0.8889 (tt0) cc_final: 0.8554 (mt-10) REVERT: A 993 ILE cc_start: 0.9230 (mt) cc_final: 0.8818 (tt) REVERT: A 994 ASP cc_start: 0.8932 (m-30) cc_final: 0.8418 (m-30) REVERT: A 995 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8315 (ptm160) REVERT: A 1000 ARG cc_start: 0.9338 (mmt180) cc_final: 0.8810 (mmt180) REVERT: A 1001 LEU cc_start: 0.9437 (mt) cc_final: 0.8908 (mm) REVERT: A 1002 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8488 (tm-30) REVERT: A 1005 GLN cc_start: 0.8978 (mt0) cc_final: 0.8687 (mm-40) REVERT: A 1014 ARG cc_start: 0.9012 (mmp-170) cc_final: 0.8794 (mmm160) REVERT: A 1019 ARG cc_start: 0.9104 (ttt180) cc_final: 0.8386 (ttm110) REVERT: A 1023 ASN cc_start: 0.8914 (m110) cc_final: 0.8656 (m-40) REVERT: A 1050 MET cc_start: 0.6015 (ttt) cc_final: 0.5617 (ttt) REVERT: A 1062 PHE cc_start: 0.6517 (m-80) cc_final: 0.6232 (m-80) REVERT: B 37 TYR cc_start: 0.8936 (p90) cc_final: 0.7991 (p90) REVERT: B 41 LYS cc_start: 0.8796 (tppt) cc_final: 0.8222 (tppp) REVERT: B 44 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7261 (mtt90) REVERT: B 56 LEU cc_start: 0.8942 (tp) cc_final: 0.8630 (pp) REVERT: B 58 PHE cc_start: 0.8005 (m-80) cc_final: 0.7276 (m-80) REVERT: B 86 PHE cc_start: 0.8134 (t80) cc_final: 0.7662 (t80) REVERT: B 129 LYS cc_start: 0.8599 (mppt) cc_final: 0.8350 (mmtm) REVERT: B 170 TYR cc_start: 0.8584 (t80) cc_final: 0.8246 (t80) REVERT: B 194 PHE cc_start: 0.7850 (m-80) cc_final: 0.7404 (m-10) REVERT: B 265 TYR cc_start: 0.6773 (p90) cc_final: 0.6558 (p90) REVERT: B 276 LEU cc_start: 0.9094 (tt) cc_final: 0.8456 (mp) REVERT: B 298 GLU cc_start: 0.8528 (tt0) cc_final: 0.8107 (tt0) REVERT: B 300 LYS cc_start: 0.8191 (mttt) cc_final: 0.7630 (mtmm) REVERT: B 313 TYR cc_start: 0.7733 (m-10) cc_final: 0.6948 (m-10) REVERT: B 365 TYR cc_start: 0.8822 (t80) cc_final: 0.8445 (t80) REVERT: B 396 TYR cc_start: 0.8193 (m-80) cc_final: 0.7942 (m-80) REVERT: B 562 PHE cc_start: 0.8988 (p90) cc_final: 0.8525 (p90) REVERT: B 586 ASP cc_start: 0.8456 (t0) cc_final: 0.7756 (p0) REVERT: B 603 ASN cc_start: 0.9422 (t0) cc_final: 0.9100 (p0) REVERT: B 674 TYR cc_start: 0.8028 (t80) cc_final: 0.7790 (t80) REVERT: B 753 LEU cc_start: 0.9051 (tp) cc_final: 0.8848 (tp) REVERT: B 764 ASN cc_start: 0.8923 (m-40) cc_final: 0.8631 (m110) REVERT: B 776 LYS cc_start: 0.8810 (tptp) cc_final: 0.7994 (tptp) REVERT: B 802 PHE cc_start: 0.8169 (m-80) cc_final: 0.7603 (m-80) REVERT: B 819 GLU cc_start: 0.8997 (pt0) cc_final: 0.8725 (pt0) REVERT: B 822 LEU cc_start: 0.9159 (tp) cc_final: 0.8762 (mt) REVERT: B 824 ASN cc_start: 0.8963 (m110) cc_final: 0.8705 (m-40) REVERT: B 917 TYR cc_start: 0.8708 (m-10) cc_final: 0.8328 (m-80) REVERT: B 927 PHE cc_start: 0.8538 (t80) cc_final: 0.7973 (t80) REVERT: B 937 SER cc_start: 0.8878 (t) cc_final: 0.8586 (p) REVERT: B 954 GLN cc_start: 0.9130 (mt0) cc_final: 0.8540 (tm-30) REVERT: B 955 ASN cc_start: 0.8991 (m110) cc_final: 0.8765 (t0) REVERT: B 957 GLN cc_start: 0.9220 (pt0) cc_final: 0.8986 (pp30) REVERT: B 978 ASN cc_start: 0.8958 (p0) cc_final: 0.8506 (p0) REVERT: B 979 ASP cc_start: 0.8951 (t0) cc_final: 0.8405 (m-30) REVERT: B 983 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7960 (ttp-110) REVERT: B 995 ARG cc_start: 0.8713 (ptt180) cc_final: 0.8405 (ptt180) REVERT: B 998 THR cc_start: 0.9147 (p) cc_final: 0.8872 (p) REVERT: B 1002 GLN cc_start: 0.8874 (mp10) cc_final: 0.8530 (mp10) REVERT: B 1010 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8445 (mm-40) REVERT: B 1011 GLN cc_start: 0.8648 (mm110) cc_final: 0.8145 (mm-40) REVERT: B 1017 GLU cc_start: 0.8886 (pp20) cc_final: 0.8620 (pp20) REVERT: B 1023 ASN cc_start: 0.8510 (m-40) cc_final: 0.8302 (m110) REVERT: B 1028 LYS cc_start: 0.7744 (tptm) cc_final: 0.7391 (tptt) REVERT: B 1116 THR cc_start: 0.3190 (OUTLIER) cc_final: 0.2650 (m) REVERT: C 41 LYS cc_start: 0.8188 (tppt) cc_final: 0.7817 (tppt) REVERT: C 65 PHE cc_start: 0.8196 (m-80) cc_final: 0.7615 (m-80) REVERT: C 92 PHE cc_start: 0.8592 (t80) cc_final: 0.8064 (t80) REVERT: C 117 LEU cc_start: 0.8877 (tt) cc_final: 0.8505 (pp) REVERT: C 128 ILE cc_start: 0.8416 (mp) cc_final: 0.7978 (mp) REVERT: C 129 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8526 (tptp) REVERT: C 192 PHE cc_start: 0.8889 (m-10) cc_final: 0.8459 (m-10) REVERT: C 194 PHE cc_start: 0.7873 (m-80) cc_final: 0.7670 (m-80) REVERT: C 223 LEU cc_start: 0.8634 (pt) cc_final: 0.8200 (pt) REVERT: C 235 ILE cc_start: 0.7224 (mt) cc_final: 0.7023 (mm) REVERT: C 276 LEU cc_start: 0.8245 (tp) cc_final: 0.7951 (tp) REVERT: C 281 GLU cc_start: 0.8210 (tp30) cc_final: 0.7847 (tp30) REVERT: C 300 LYS cc_start: 0.8588 (mttt) cc_final: 0.8147 (mmtt) REVERT: C 313 TYR cc_start: 0.7654 (m-10) cc_final: 0.7235 (m-10) REVERT: C 324 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8578 (mp0) REVERT: C 338 PHE cc_start: 0.9104 (m-80) cc_final: 0.8723 (m-10) REVERT: C 342 PHE cc_start: 0.8809 (m-80) cc_final: 0.8405 (m-10) REVERT: C 365 TYR cc_start: 0.9122 (m-10) cc_final: 0.8632 (m-10) REVERT: C 377 PHE cc_start: 0.8470 (t80) cc_final: 0.8198 (t80) REVERT: C 386 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8157 (mtmm) REVERT: C 424 LYS cc_start: 0.7453 (ttpp) cc_final: 0.6935 (mtpt) REVERT: C 425 LEU cc_start: 0.8540 (mt) cc_final: 0.7922 (tp) REVERT: C 426 PRO cc_start: 0.8680 (Cg_exo) cc_final: 0.8287 (Cg_endo) REVERT: C 460 ASN cc_start: 0.7744 (t0) cc_final: 0.7536 (t0) REVERT: C 516 GLU cc_start: 0.7719 (mp0) cc_final: 0.7239 (mp0) REVERT: C 543 PHE cc_start: 0.8527 (m-80) cc_final: 0.8318 (m-80) REVERT: C 562 PHE cc_start: 0.8992 (p90) cc_final: 0.8482 (p90) REVERT: C 659 SER cc_start: 0.8122 (p) cc_final: 0.7677 (t) REVERT: C 735 SER cc_start: 0.8214 (t) cc_final: 0.7990 (p) REVERT: C 737 ASP cc_start: 0.8603 (t0) cc_final: 0.8356 (t0) REVERT: C 748 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8937 (mp0) REVERT: C 759 PHE cc_start: 0.8657 (m-80) cc_final: 0.8168 (m-10) REVERT: C 762 GLN cc_start: 0.9175 (mt0) cc_final: 0.8855 (mt0) REVERT: C 764 ASN cc_start: 0.8869 (m110) cc_final: 0.8571 (m-40) REVERT: C 765 ARG cc_start: 0.9143 (ptp-170) cc_final: 0.8925 (ptp90) REVERT: C 776 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8415 (tmtt) REVERT: C 858 LEU cc_start: 0.9037 (mp) cc_final: 0.8716 (mm) REVERT: C 869 MET cc_start: 0.9184 (mtm) cc_final: 0.8341 (tmm) REVERT: C 898 PHE cc_start: 0.6461 (t80) cc_final: 0.5885 (t80) REVERT: C 900 MET cc_start: 0.7988 (ppp) cc_final: 0.7746 (ppp) REVERT: C 902 MET cc_start: 0.5723 (ttp) cc_final: 0.5308 (ptm) REVERT: C 904 TYR cc_start: 0.1758 (m-80) cc_final: -0.0260 (m-80) REVERT: C 954 GLN cc_start: 0.9120 (mt0) cc_final: 0.8646 (tm-30) REVERT: C 957 GLN cc_start: 0.9203 (tt0) cc_final: 0.8822 (pp30) REVERT: C 959 LEU cc_start: 0.9365 (mp) cc_final: 0.9125 (pp) REVERT: C 960 ASN cc_start: 0.9016 (m110) cc_final: 0.8537 (m110) REVERT: C 964 LYS cc_start: 0.9551 (tttt) cc_final: 0.9135 (mmmt) REVERT: C 969 ASN cc_start: 0.8794 (p0) cc_final: 0.8531 (p0) REVERT: C 970 PHE cc_start: 0.8339 (m-80) cc_final: 0.7970 (m-10) REVERT: C 978 ASN cc_start: 0.9531 (m110) cc_final: 0.9301 (m110) REVERT: C 979 ASP cc_start: 0.9119 (m-30) cc_final: 0.8808 (m-30) REVERT: C 981 LEU cc_start: 0.9170 (mp) cc_final: 0.8790 (pp) REVERT: C 983 ARG cc_start: 0.9123 (tmt-80) cc_final: 0.8864 (tpt90) REVERT: C 994 ASP cc_start: 0.8770 (m-30) cc_final: 0.8436 (m-30) REVERT: C 1000 ARG cc_start: 0.9312 (mtt-85) cc_final: 0.8678 (mmt90) REVERT: C 1001 LEU cc_start: 0.9537 (tt) cc_final: 0.9337 (tp) REVERT: C 1010 GLN cc_start: 0.8820 (tp-100) cc_final: 0.7707 (tm-30) REVERT: C 1011 GLN cc_start: 0.8944 (pt0) cc_final: 0.8410 (pt0) REVERT: C 1014 ARG cc_start: 0.8554 (mmp80) cc_final: 0.7535 (mmp80) REVERT: C 1017 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8648 (tm-30) REVERT: C 1018 ILE cc_start: 0.8991 (pt) cc_final: 0.8396 (pt) REVERT: C 1019 ARG cc_start: 0.8909 (ptp-170) cc_final: 0.8564 (ptt-90) REVERT: C 1028 LYS cc_start: 0.6803 (ttmt) cc_final: 0.6337 (ttmt) REVERT: C 1052 PHE cc_start: 0.8324 (m-80) cc_final: 0.7813 (m-80) outliers start: 7 outliers final: 2 residues processed: 561 average time/residue: 0.1826 time to fit residues: 157.7461 Evaluate side-chains 484 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 480 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 206 optimal weight: 0.0370 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 258 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 146 HIS ** A 164 ASN ** 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 A1054 GLN ** B 66 HIS ** 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 66 HIS ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 774 GLN C 779 GLN C 901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.176194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.127735 restraints weight = 63361.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.132394 restraints weight = 45659.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.135797 restraints weight = 35248.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.138263 restraints weight = 29171.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.140053 restraints weight = 25230.184| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26386 Z= 0.165 Angle : 0.777 13.754 36017 Z= 0.387 Chirality : 0.051 0.462 4182 Planarity : 0.005 0.079 4587 Dihedral : 8.476 103.410 4373 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3187 helix: 0.07 (0.18), residues: 689 sheet: -0.67 (0.21), residues: 558 loop : -1.45 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 815 TYR 0.029 0.002 TYR C 91 PHE 0.025 0.002 PHE B 201 TRP 0.032 0.002 TRP B 436 HIS 0.017 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00357 (26300) covalent geometry : angle 0.74599 (35807) SS BOND : bond 0.00301 ( 42) SS BOND : angle 2.04281 ( 84) hydrogen bonds : bond 0.05092 ( 872) hydrogen bonds : angle 6.61712 ( 2433) Misc. bond : bond 0.02142 ( 2) link_BETA1-4 : bond 0.00447 ( 10) link_BETA1-4 : angle 1.46500 ( 30) link_NAG-ASN : bond 0.00639 ( 32) link_NAG-ASN : angle 3.78443 ( 96) *********************** 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 542 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 541 time to evaluate : 0.882 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: A 43 PHE cc_start: 0.8324 (t80) cc_final: 0.8084 (t80) REVERT: A 53 ASP cc_start: 0.8610 (t0) cc_final: 0.8202 (t0) REVERT: A 65 PHE cc_start: 0.8109 (m-80) cc_final: 0.7463 (m-80) REVERT: A 104 TRP cc_start: 0.6889 (m-90) cc_final: 0.6649 (m-90) REVERT: A 128 ILE cc_start: 0.8551 (mt) cc_final: 0.7449 (mm) REVERT: A 170 TYR cc_start: 0.7451 (t80) cc_final: 0.6962 (t80) REVERT: A 194 PHE cc_start: 0.8590 (m-80) cc_final: 0.8054 (m-80) REVERT: A 195 LYS cc_start: 0.8202 (tptt) cc_final: 0.7866 (tptt) REVERT: A 207 HIS cc_start: 0.8998 (p90) cc_final: 0.8756 (p-80) REVERT: A 275 PHE cc_start: 0.6681 (m-10) cc_final: 0.6128 (m-10) REVERT: A 310 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8494 (tptp) REVERT: A 317 ASN cc_start: 0.8308 (p0) cc_final: 0.7834 (p0) REVERT: A 321 GLN cc_start: 0.9406 (pm20) cc_final: 0.9159 (pm20) REVERT: A 365 TYR cc_start: 0.8222 (m-80) cc_final: 0.7897 (m-80) REVERT: A 380 TYR cc_start: 0.8123 (m-80) cc_final: 0.7675 (m-80) REVERT: A 389 ASP cc_start: 0.8819 (m-30) cc_final: 0.8485 (p0) REVERT: A 408 ARG cc_start: 0.8931 (pmt-80) cc_final: 0.8625 (pmt-80) REVERT: A 731 MET cc_start: 0.8834 (ppp) cc_final: 0.8311 (ppp) REVERT: A 753 LEU cc_start: 0.8954 (tt) cc_final: 0.8664 (tp) REVERT: A 759 PHE cc_start: 0.8815 (m-80) cc_final: 0.8186 (m-80) REVERT: A 764 ASN cc_start: 0.8894 (m110) cc_final: 0.8251 (m110) REVERT: A 776 LYS cc_start: 0.9037 (tptm) cc_final: 0.8500 (tptp) REVERT: A 856 ASN cc_start: 0.8259 (t0) cc_final: 0.7969 (p0) REVERT: A 869 MET cc_start: 0.8038 (pmm) cc_final: 0.7467 (pmm) REVERT: A 873 TYR cc_start: 0.8382 (m-10) cc_final: 0.7990 (m-80) REVERT: A 917 TYR cc_start: 0.7939 (m-80) cc_final: 0.7401 (m-80) REVERT: A 927 PHE cc_start: 0.7818 (t80) cc_final: 0.7394 (t80) REVERT: A 934 ILE cc_start: 0.8569 (tp) cc_final: 0.8351 (mt) REVERT: A 936 ASP cc_start: 0.8644 (m-30) cc_final: 0.8436 (m-30) REVERT: A 947 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7534 (mmmt) REVERT: A 954 GLN cc_start: 0.9006 (tp40) cc_final: 0.8487 (tm-30) REVERT: A 964 LYS cc_start: 0.9317 (ttmm) cc_final: 0.8573 (tptp) REVERT: A 974 SER cc_start: 0.8894 (t) cc_final: 0.8694 (t) REVERT: A 979 ASP cc_start: 0.8957 (m-30) cc_final: 0.8383 (t0) REVERT: A 983 ARG cc_start: 0.8789 (ptt90) cc_final: 0.7884 (ttp80) REVERT: A 990 GLU cc_start: 0.8739 (tt0) cc_final: 0.8458 (mt-10) REVERT: A 993 ILE cc_start: 0.9151 (mt) cc_final: 0.8463 (tp) REVERT: A 994 ASP cc_start: 0.8674 (m-30) cc_final: 0.8173 (m-30) REVERT: A 995 ARG cc_start: 0.8772 (ttm110) cc_final: 0.7940 (ptm160) REVERT: A 1000 ARG cc_start: 0.8989 (mmt180) cc_final: 0.8721 (mmt180) REVERT: A 1001 LEU cc_start: 0.8973 (mt) cc_final: 0.8657 (mm) REVERT: A 1002 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 1005 GLN cc_start: 0.8825 (mt0) cc_final: 0.8613 (mm-40) REVERT: A 1014 ARG cc_start: 0.8794 (mmp-170) cc_final: 0.8526 (mmm160) REVERT: A 1019 ARG cc_start: 0.8825 (ttt180) cc_final: 0.8090 (ttm110) REVERT: A 1050 MET cc_start: 0.5811 (ttt) cc_final: 0.5336 (ttt) REVERT: B 37 TYR cc_start: 0.8596 (p90) cc_final: 0.7972 (p90) REVERT: B 41 LYS cc_start: 0.8794 (tppt) cc_final: 0.8045 (tppp) REVERT: B 44 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7104 (mtt180) REVERT: B 58 PHE cc_start: 0.7895 (m-80) cc_final: 0.7385 (m-10) REVERT: B 86 PHE cc_start: 0.7903 (t80) cc_final: 0.7424 (t80) REVERT: B 194 PHE cc_start: 0.7596 (m-80) cc_final: 0.6966 (m-10) REVERT: B 266 TYR cc_start: 0.6936 (m-80) cc_final: 0.6645 (m-80) REVERT: B 275 PHE cc_start: 0.7270 (m-10) cc_final: 0.5674 (m-10) REVERT: B 276 LEU cc_start: 0.8711 (tt) cc_final: 0.8283 (tt) REVERT: B 287 ASP cc_start: 0.8242 (m-30) cc_final: 0.7537 (p0) REVERT: B 298 GLU cc_start: 0.8551 (tt0) cc_final: 0.8107 (tt0) REVERT: B 300 LYS cc_start: 0.8003 (mttt) cc_final: 0.7408 (mtmm) REVERT: B 313 TYR cc_start: 0.7629 (m-80) cc_final: 0.6979 (m-10) REVERT: B 553 THR cc_start: 0.7879 (m) cc_final: 0.6747 (m) REVERT: B 562 PHE cc_start: 0.8889 (p90) cc_final: 0.8357 (p90) REVERT: B 586 ASP cc_start: 0.8403 (t0) cc_final: 0.7580 (p0) REVERT: B 587 ILE cc_start: 0.8936 (mp) cc_final: 0.8727 (mp) REVERT: B 603 ASN cc_start: 0.9359 (t0) cc_final: 0.9061 (p0) REVERT: B 674 TYR cc_start: 0.7761 (t80) cc_final: 0.7553 (t80) REVERT: B 753 LEU cc_start: 0.8906 (tp) cc_final: 0.8655 (tp) REVERT: B 790 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7967 (tptt) REVERT: B 819 GLU cc_start: 0.8912 (pt0) cc_final: 0.8527 (pt0) REVERT: B 822 LEU cc_start: 0.9141 (tp) cc_final: 0.8641 (mt) REVERT: B 824 ASN cc_start: 0.8836 (m110) cc_final: 0.8609 (m110) REVERT: B 917 TYR cc_start: 0.8459 (m-10) cc_final: 0.8051 (m-10) REVERT: B 927 PHE cc_start: 0.8444 (t80) cc_final: 0.7733 (t80) REVERT: B 937 SER cc_start: 0.8724 (t) cc_final: 0.8388 (p) REVERT: B 954 GLN cc_start: 0.9084 (mt0) cc_final: 0.8476 (tm-30) REVERT: B 955 ASN cc_start: 0.8842 (m110) cc_final: 0.8621 (t0) REVERT: B 957 GLN cc_start: 0.9088 (pt0) cc_final: 0.8872 (pp30) REVERT: B 964 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8602 (tmtt) REVERT: B 978 ASN cc_start: 0.8848 (p0) cc_final: 0.8646 (p0) REVERT: B 979 ASP cc_start: 0.8709 (t0) cc_final: 0.8457 (t0) REVERT: B 983 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7299 (tmm-80) REVERT: B 984 LEU cc_start: 0.8623 (mt) cc_final: 0.7973 (tp) REVERT: B 995 ARG cc_start: 0.8677 (ptt180) cc_final: 0.8351 (ptt180) REVERT: B 1010 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8649 (mm-40) REVERT: B 1011 GLN cc_start: 0.8695 (mm110) cc_final: 0.8335 (mp10) REVERT: B 1012 LEU cc_start: 0.9373 (mt) cc_final: 0.9171 (mt) REVERT: B 1017 GLU cc_start: 0.8725 (pp20) cc_final: 0.8327 (pp20) REVERT: B 1028 LYS cc_start: 0.7675 (tptm) cc_final: 0.7305 (tptt) REVERT: C 65 PHE cc_start: 0.8039 (m-80) cc_final: 0.7739 (m-80) REVERT: C 91 TYR cc_start: 0.7653 (t80) cc_final: 0.7010 (t80) REVERT: C 92 PHE cc_start: 0.8176 (t80) cc_final: 0.7539 (t80) REVERT: C 117 LEU cc_start: 0.8808 (tt) cc_final: 0.8350 (pp) REVERT: C 128 ILE cc_start: 0.8481 (mp) cc_final: 0.8084 (mp) REVERT: C 129 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8539 (tptp) REVERT: C 160 TYR cc_start: 0.8659 (p90) cc_final: 0.8265 (p90) REVERT: C 192 PHE cc_start: 0.8784 (m-10) cc_final: 0.8334 (m-10) REVERT: C 194 PHE cc_start: 0.7594 (m-80) cc_final: 0.7180 (m-80) REVERT: C 223 LEU cc_start: 0.8115 (pt) cc_final: 0.7786 (pt) REVERT: C 237 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8516 (mmm-85) REVERT: C 276 LEU cc_start: 0.8173 (tp) cc_final: 0.7795 (tp) REVERT: C 281 GLU cc_start: 0.8169 (tp30) cc_final: 0.7962 (tm-30) REVERT: C 298 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7796 (mt-10) REVERT: C 300 LYS cc_start: 0.8346 (mttt) cc_final: 0.7852 (mmtp) REVERT: C 313 TYR cc_start: 0.7490 (m-10) cc_final: 0.7098 (m-10) REVERT: C 324 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8435 (mp0) REVERT: C 338 PHE cc_start: 0.8993 (m-80) cc_final: 0.8614 (m-10) REVERT: C 342 PHE cc_start: 0.8719 (m-80) cc_final: 0.8370 (m-80) REVERT: C 356 LYS cc_start: 0.8426 (tptp) cc_final: 0.7892 (tmmt) REVERT: C 365 TYR cc_start: 0.8961 (m-10) cc_final: 0.8443 (m-10) REVERT: C 377 PHE cc_start: 0.7598 (t80) cc_final: 0.7366 (t80) REVERT: C 380 TYR cc_start: 0.7440 (m-80) cc_final: 0.7009 (m-80) REVERT: C 386 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8123 (mtmm) REVERT: C 409 GLN cc_start: 0.8371 (mp10) cc_final: 0.7923 (mp10) REVERT: C 417 LYS cc_start: 0.9148 (tptt) cc_final: 0.8665 (tppt) REVERT: C 418 ILE cc_start: 0.9508 (pt) cc_final: 0.9092 (mm) REVERT: C 421 TYR cc_start: 0.8579 (m-10) cc_final: 0.8205 (m-10) REVERT: C 425 LEU cc_start: 0.8187 (mt) cc_final: 0.7847 (tp) REVERT: C 426 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: C 451 TYR cc_start: 0.6287 (m-80) cc_final: 0.5965 (m-80) REVERT: C 490 PHE cc_start: 0.8693 (t80) cc_final: 0.8431 (t80) REVERT: C 558 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8455 (tptp) REVERT: C 563 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7186 (mm-40) REVERT: C 571 ASP cc_start: 0.9151 (t0) cc_final: 0.8931 (t0) REVERT: C 722 VAL cc_start: 0.4674 (p) cc_final: 0.4334 (p) REVERT: C 737 ASP cc_start: 0.8500 (t0) cc_final: 0.8188 (t0) REVERT: C 747 THR cc_start: 0.8920 (p) cc_final: 0.8636 (p) REVERT: C 748 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8744 (mp0) REVERT: C 756 TYR cc_start: 0.8467 (m-10) cc_final: 0.8167 (m-10) REVERT: C 759 PHE cc_start: 0.8597 (m-80) cc_final: 0.8000 (m-10) REVERT: C 762 GLN cc_start: 0.9051 (mt0) cc_final: 0.8455 (mt0) REVERT: C 763 LEU cc_start: 0.9066 (mt) cc_final: 0.8736 (mt) REVERT: C 764 ASN cc_start: 0.8635 (m110) cc_final: 0.8357 (m-40) REVERT: C 765 ARG cc_start: 0.9089 (ptp-170) cc_final: 0.8553 (ptp90) REVERT: C 770 ILE cc_start: 0.9185 (mm) cc_final: 0.8756 (mm) REVERT: C 773 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7729 (pp20) REVERT: C 776 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8328 (tmtt) REVERT: C 858 LEU cc_start: 0.8872 (mp) cc_final: 0.8499 (mm) REVERT: C 869 MET cc_start: 0.9077 (mtm) cc_final: 0.8280 (mmt) REVERT: C 873 TYR cc_start: 0.8109 (m-10) cc_final: 0.7773 (m-80) REVERT: C 898 PHE cc_start: 0.6216 (t80) cc_final: 0.5907 (t80) REVERT: C 954 GLN cc_start: 0.9047 (mt0) cc_final: 0.8674 (tm-30) REVERT: C 957 GLN cc_start: 0.8969 (tt0) cc_final: 0.8702 (pp30) REVERT: C 959 LEU cc_start: 0.9116 (mp) cc_final: 0.8889 (pp) REVERT: C 960 ASN cc_start: 0.8824 (m110) cc_final: 0.8473 (m110) REVERT: C 964 LYS cc_start: 0.9436 (tttt) cc_final: 0.9061 (ptmm) REVERT: C 969 ASN cc_start: 0.8715 (p0) cc_final: 0.8379 (p0) REVERT: C 970 PHE cc_start: 0.8078 (m-80) cc_final: 0.7366 (m-10) REVERT: C 979 ASP cc_start: 0.9035 (m-30) cc_final: 0.8776 (m-30) REVERT: C 981 LEU cc_start: 0.9060 (mp) cc_final: 0.8838 (pp) REVERT: C 983 ARG cc_start: 0.9043 (tmt-80) cc_final: 0.8817 (tpt90) REVERT: C 1000 ARG cc_start: 0.9105 (mtt-85) cc_final: 0.8314 (mmt90) REVERT: C 1001 LEU cc_start: 0.9503 (tt) cc_final: 0.9274 (tp) REVERT: C 1010 GLN cc_start: 0.8718 (tp-100) cc_final: 0.7721 (tm-30) REVERT: C 1011 GLN cc_start: 0.9028 (pt0) cc_final: 0.8589 (pt0) REVERT: C 1013 ILE cc_start: 0.9396 (mm) cc_final: 0.9116 (pt) REVERT: C 1017 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8496 (tm-30) REVERT: C 1018 ILE cc_start: 0.8727 (pt) cc_final: 0.8249 (pt) REVERT: C 1019 ARG cc_start: 0.8958 (ptp90) cc_final: 0.8603 (ptt180) REVERT: C 1052 PHE cc_start: 0.7592 (m-80) cc_final: 0.7270 (m-80) outliers start: 1 outliers final: 0 residues processed: 542 average time/residue: 0.1875 time to fit residues: 155.5527 Evaluate side-chains 480 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 119 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 259 optimal weight: 0.0570 chunk 100 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 856 ASN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.176137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.128443 restraints weight = 63142.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.132891 restraints weight = 46305.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.136031 restraints weight = 36477.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.138433 restraints weight = 30515.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.140112 restraints weight = 26519.165| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 26386 Z= 0.224 Angle : 0.766 13.026 36017 Z= 0.392 Chirality : 0.050 0.423 4182 Planarity : 0.005 0.083 4587 Dihedral : 8.375 101.858 4373 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3187 helix: 0.04 (0.19), residues: 694 sheet: -0.73 (0.21), residues: 582 loop : -1.50 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 567 TYR 0.021 0.002 TYR A 904 PHE 0.024 0.002 PHE A1109 TRP 0.029 0.002 TRP C 64 HIS 0.024 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00453 (26300) covalent geometry : angle 0.73614 (35807) SS BOND : bond 0.00544 ( 42) SS BOND : angle 2.26574 ( 84) hydrogen bonds : bond 0.05302 ( 872) hydrogen bonds : angle 6.63899 ( 2433) Misc. bond : bond 0.00234 ( 2) link_BETA1-4 : bond 0.00412 ( 10) link_BETA1-4 : angle 1.46593 ( 30) link_NAG-ASN : bond 0.00612 ( 32) link_NAG-ASN : angle 3.61197 ( 96) *********************** 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 518 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.942 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 53 ASP cc_start: 0.8630 (t0) cc_final: 0.8188 (t0) REVERT: A 65 PHE cc_start: 0.8125 (m-80) cc_final: 0.7510 (m-80) REVERT: A 99 ASN cc_start: 0.9486 (t0) cc_final: 0.9271 (t0) REVERT: A 104 TRP cc_start: 0.7002 (m-90) cc_final: 0.6544 (m-90) REVERT: A 118 LEU cc_start: 0.8712 (tp) cc_final: 0.8386 (mm) REVERT: A 128 ILE cc_start: 0.8683 (mt) cc_final: 0.7640 (mm) REVERT: A 135 PHE cc_start: 0.8316 (m-10) cc_final: 0.8069 (m-10) REVERT: A 170 TYR cc_start: 0.7471 (t80) cc_final: 0.6960 (t80) REVERT: A 189 LEU cc_start: 0.8568 (tp) cc_final: 0.8359 (tp) REVERT: A 194 PHE cc_start: 0.8650 (m-80) cc_final: 0.8223 (m-80) REVERT: A 275 PHE cc_start: 0.6848 (m-10) cc_final: 0.6418 (m-10) REVERT: A 304 LYS cc_start: 0.8854 (mppt) cc_final: 0.8574 (mmtt) REVERT: A 317 ASN cc_start: 0.8399 (p0) cc_final: 0.7903 (p0) REVERT: A 319 ARG cc_start: 0.8391 (ppt170) cc_final: 0.7957 (tmt170) REVERT: A 365 TYR cc_start: 0.8202 (m-80) cc_final: 0.7923 (m-80) REVERT: A 380 TYR cc_start: 0.8162 (m-80) cc_final: 0.7789 (m-80) REVERT: A 389 ASP cc_start: 0.8758 (m-30) cc_final: 0.8389 (p0) REVERT: A 408 ARG cc_start: 0.8923 (pmt-80) cc_final: 0.8723 (pmt-80) REVERT: A 731 MET cc_start: 0.8513 (ppp) cc_final: 0.8311 (ppp) REVERT: A 759 PHE cc_start: 0.8881 (m-80) cc_final: 0.8091 (m-80) REVERT: A 762 GLN cc_start: 0.9083 (pt0) cc_final: 0.8399 (pp30) REVERT: A 776 LYS cc_start: 0.9048 (tptm) cc_final: 0.8518 (tptp) REVERT: A 856 ASN cc_start: 0.8405 (t0) cc_final: 0.8004 (p0) REVERT: A 869 MET cc_start: 0.8102 (pmm) cc_final: 0.7595 (pmm) REVERT: A 873 TYR cc_start: 0.8550 (m-10) cc_final: 0.8155 (m-80) REVERT: A 917 TYR cc_start: 0.8060 (m-80) cc_final: 0.7674 (m-10) REVERT: A 927 PHE cc_start: 0.7844 (t80) cc_final: 0.7411 (t80) REVERT: A 934 ILE cc_start: 0.8643 (tp) cc_final: 0.8244 (mt) REVERT: A 936 ASP cc_start: 0.8721 (m-30) cc_final: 0.8487 (m-30) REVERT: A 947 LYS cc_start: 0.7688 (mtpt) cc_final: 0.7373 (mmmt) REVERT: A 954 GLN cc_start: 0.9059 (tp40) cc_final: 0.8603 (tm-30) REVERT: A 960 ASN cc_start: 0.8686 (t0) cc_final: 0.8196 (m110) REVERT: A 964 LYS cc_start: 0.9240 (ttmm) cc_final: 0.8831 (ptpp) REVERT: A 979 ASP cc_start: 0.9167 (m-30) cc_final: 0.8597 (t0) REVERT: A 983 ARG cc_start: 0.8762 (ptt90) cc_final: 0.7853 (ttp80) REVERT: A 990 GLU cc_start: 0.8712 (tt0) cc_final: 0.8415 (mt-10) REVERT: A 994 ASP cc_start: 0.8851 (m-30) cc_final: 0.8254 (m-30) REVERT: A 995 ARG cc_start: 0.8894 (ttm110) cc_final: 0.8262 (ttm-80) REVERT: A 997 ILE cc_start: 0.9279 (pt) cc_final: 0.9057 (pt) REVERT: A 1000 ARG cc_start: 0.9038 (mmt180) cc_final: 0.8655 (mmt180) REVERT: A 1001 LEU cc_start: 0.9049 (mt) cc_final: 0.8622 (mm) REVERT: A 1002 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 1005 GLN cc_start: 0.8887 (mt0) cc_final: 0.8666 (mm-40) REVERT: A 1014 ARG cc_start: 0.8854 (mmp-170) cc_final: 0.8592 (mmm160) REVERT: A 1023 ASN cc_start: 0.8880 (m110) cc_final: 0.8635 (m-40) REVERT: A 1050 MET cc_start: 0.5835 (ttt) cc_final: 0.5284 (ttt) REVERT: A 1053 PRO cc_start: 0.8882 (Cg_endo) cc_final: 0.8413 (Cg_exo) REVERT: A 1054 GLN cc_start: 0.6323 (mp10) cc_final: 0.5946 (mp10) REVERT: B 37 TYR cc_start: 0.8627 (p90) cc_final: 0.8083 (p90) REVERT: B 41 LYS cc_start: 0.8827 (tppt) cc_final: 0.8099 (tppp) REVERT: B 86 PHE cc_start: 0.7932 (t80) cc_final: 0.7452 (t80) REVERT: B 128 ILE cc_start: 0.9094 (tt) cc_final: 0.8879 (tt) REVERT: B 159 VAL cc_start: 0.9401 (t) cc_final: 0.9033 (t) REVERT: B 194 PHE cc_start: 0.7882 (m-80) cc_final: 0.7128 (m-10) REVERT: B 275 PHE cc_start: 0.6951 (m-10) cc_final: 0.5508 (m-10) REVERT: B 276 LEU cc_start: 0.8755 (tt) cc_final: 0.8203 (mp) REVERT: B 298 GLU cc_start: 0.8609 (tt0) cc_final: 0.7842 (mm-30) REVERT: B 300 LYS cc_start: 0.8112 (mttt) cc_final: 0.7521 (mtmm) REVERT: B 313 TYR cc_start: 0.7660 (m-80) cc_final: 0.7042 (m-10) REVERT: B 543 PHE cc_start: 0.8523 (p90) cc_final: 0.8224 (p90) REVERT: B 562 PHE cc_start: 0.8953 (p90) cc_final: 0.8451 (p90) REVERT: B 577 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7634 (ttm170) REVERT: B 586 ASP cc_start: 0.8426 (t0) cc_final: 0.7666 (p0) REVERT: B 603 ASN cc_start: 0.9401 (t0) cc_final: 0.9134 (p0) REVERT: B 674 TYR cc_start: 0.7870 (t80) cc_final: 0.7658 (t80) REVERT: B 749 CYS cc_start: 0.6035 (p) cc_final: 0.5795 (p) REVERT: B 753 LEU cc_start: 0.8881 (tp) cc_final: 0.8608 (tp) REVERT: B 754 LEU cc_start: 0.8925 (mt) cc_final: 0.8715 (mt) REVERT: B 802 PHE cc_start: 0.7406 (m-80) cc_final: 0.6782 (m-80) REVERT: B 819 GLU cc_start: 0.8923 (pt0) cc_final: 0.8701 (pt0) REVERT: B 824 ASN cc_start: 0.8880 (m110) cc_final: 0.8639 (m110) REVERT: B 917 TYR cc_start: 0.8624 (m-10) cc_final: 0.8222 (m-10) REVERT: B 927 PHE cc_start: 0.8458 (t80) cc_final: 0.7868 (t80) REVERT: B 937 SER cc_start: 0.8781 (t) cc_final: 0.8479 (p) REVERT: B 954 GLN cc_start: 0.9093 (mt0) cc_final: 0.8547 (tm-30) REVERT: B 964 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8313 (tptp) REVERT: B 978 ASN cc_start: 0.8876 (p0) cc_final: 0.8337 (p0) REVERT: B 979 ASP cc_start: 0.8746 (t0) cc_final: 0.8313 (m-30) REVERT: B 983 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7583 (ttp-110) REVERT: B 995 ARG cc_start: 0.8672 (ptt180) cc_final: 0.8328 (ptt180) REVERT: B 1000 ARG cc_start: 0.8843 (ptp-110) cc_final: 0.8485 (mtp-110) REVERT: B 1002 GLN cc_start: 0.8738 (mp10) cc_final: 0.8506 (mp10) REVERT: B 1011 GLN cc_start: 0.8819 (mm110) cc_final: 0.8520 (mp10) REVERT: B 1014 ARG cc_start: 0.8829 (mmt-90) cc_final: 0.8382 (mmt-90) REVERT: B 1017 GLU cc_start: 0.8770 (pp20) cc_final: 0.8235 (pp20) REVERT: B 1019 ARG cc_start: 0.8923 (ptm-80) cc_final: 0.8426 (ptm-80) REVERT: C 34 ARG cc_start: 0.8551 (mmm160) cc_final: 0.8242 (mmm160) REVERT: C 41 LYS cc_start: 0.8228 (tppt) cc_final: 0.7811 (tppt) REVERT: C 65 PHE cc_start: 0.8298 (m-80) cc_final: 0.7638 (m-80) REVERT: C 91 TYR cc_start: 0.7826 (t80) cc_final: 0.7081 (t80) REVERT: C 92 PHE cc_start: 0.8213 (t80) cc_final: 0.7581 (t80) REVERT: C 117 LEU cc_start: 0.8834 (tt) cc_final: 0.8337 (pp) REVERT: C 128 ILE cc_start: 0.8482 (mp) cc_final: 0.8045 (mm) REVERT: C 129 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8664 (tptp) REVERT: C 160 TYR cc_start: 0.8679 (p90) cc_final: 0.8260 (p90) REVERT: C 192 PHE cc_start: 0.8847 (m-10) cc_final: 0.8424 (m-10) REVERT: C 194 PHE cc_start: 0.7781 (m-80) cc_final: 0.7309 (m-80) REVERT: C 223 LEU cc_start: 0.8449 (pt) cc_final: 0.8084 (pt) REVERT: C 237 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8506 (mmm-85) REVERT: C 276 LEU cc_start: 0.8260 (tp) cc_final: 0.8002 (tp) REVERT: C 281 GLU cc_start: 0.8223 (tp30) cc_final: 0.7905 (tp30) REVERT: C 298 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7586 (mp0) REVERT: C 300 LYS cc_start: 0.8396 (mttt) cc_final: 0.7920 (mmtp) REVERT: C 313 TYR cc_start: 0.7521 (m-10) cc_final: 0.7100 (m-10) REVERT: C 324 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8476 (mp0) REVERT: C 338 PHE cc_start: 0.9017 (m-80) cc_final: 0.8628 (m-10) REVERT: C 342 PHE cc_start: 0.8712 (m-80) cc_final: 0.8377 (m-80) REVERT: C 356 LYS cc_start: 0.8461 (tptp) cc_final: 0.7960 (tmmt) REVERT: C 365 TYR cc_start: 0.9023 (m-10) cc_final: 0.8455 (m-10) REVERT: C 380 TYR cc_start: 0.7361 (m-80) cc_final: 0.7081 (m-80) REVERT: C 386 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8212 (mtmm) REVERT: C 417 LYS cc_start: 0.9179 (tptt) cc_final: 0.8804 (tppt) REVERT: C 421 TYR cc_start: 0.8594 (m-10) cc_final: 0.8304 (m-80) REVERT: C 424 LYS cc_start: 0.7307 (ttpt) cc_final: 0.7054 (ttmm) REVERT: C 425 LEU cc_start: 0.8249 (mt) cc_final: 0.7858 (tp) REVERT: C 426 PRO cc_start: 0.8682 (Cg_exo) cc_final: 0.8130 (Cg_endo) REVERT: C 451 TYR cc_start: 0.6418 (m-80) cc_final: 0.6158 (m-80) REVERT: C 460 ASN cc_start: 0.7737 (t0) cc_final: 0.7361 (t0) REVERT: C 490 PHE cc_start: 0.8782 (t80) cc_final: 0.8441 (t80) REVERT: C 505 TYR cc_start: 0.8449 (t80) cc_final: 0.8150 (t80) REVERT: C 558 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8483 (tptp) REVERT: C 563 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7029 (mm-40) REVERT: C 659 SER cc_start: 0.8038 (p) cc_final: 0.7579 (t) REVERT: C 737 ASP cc_start: 0.8668 (t0) cc_final: 0.8287 (t0) REVERT: C 748 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8934 (mp0) REVERT: C 755 GLN cc_start: 0.9227 (pt0) cc_final: 0.8653 (pp30) REVERT: C 756 TYR cc_start: 0.8409 (m-10) cc_final: 0.7580 (m-10) REVERT: C 759 PHE cc_start: 0.8661 (m-80) cc_final: 0.8026 (m-10) REVERT: C 762 GLN cc_start: 0.9041 (mt0) cc_final: 0.8822 (mt0) REVERT: C 763 LEU cc_start: 0.9101 (mt) cc_final: 0.8826 (mt) REVERT: C 764 ASN cc_start: 0.8922 (m110) cc_final: 0.8652 (m110) REVERT: C 765 ARG cc_start: 0.9156 (ptp-170) cc_final: 0.8856 (ptp90) REVERT: C 770 ILE cc_start: 0.9186 (mm) cc_final: 0.8859 (mm) REVERT: C 773 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7680 (pp20) REVERT: C 774 GLN cc_start: 0.9101 (pt0) cc_final: 0.8766 (pt0) REVERT: C 776 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8320 (tmtt) REVERT: C 858 LEU cc_start: 0.8853 (mp) cc_final: 0.8514 (mm) REVERT: C 869 MET cc_start: 0.9124 (mtm) cc_final: 0.8339 (mmt) REVERT: C 873 TYR cc_start: 0.8319 (m-10) cc_final: 0.7734 (m-80) REVERT: C 954 GLN cc_start: 0.9040 (mt0) cc_final: 0.8721 (tm-30) REVERT: C 959 LEU cc_start: 0.9223 (mp) cc_final: 0.8983 (pp) REVERT: C 960 ASN cc_start: 0.8927 (m110) cc_final: 0.8307 (m110) REVERT: C 964 LYS cc_start: 0.9452 (tttt) cc_final: 0.8989 (mmtm) REVERT: C 969 ASN cc_start: 0.8755 (p0) cc_final: 0.8376 (p0) REVERT: C 970 PHE cc_start: 0.8152 (m-80) cc_final: 0.7417 (m-10) REVERT: C 978 ASN cc_start: 0.9546 (m110) cc_final: 0.9336 (m110) REVERT: C 979 ASP cc_start: 0.9069 (m-30) cc_final: 0.8667 (m-30) REVERT: C 981 LEU cc_start: 0.9168 (mp) cc_final: 0.8824 (pp) REVERT: C 983 ARG cc_start: 0.9035 (tmt-80) cc_final: 0.8733 (tpt90) REVERT: C 994 ASP cc_start: 0.8841 (m-30) cc_final: 0.8573 (m-30) REVERT: C 995 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8175 (mtm180) REVERT: C 1000 ARG cc_start: 0.9149 (mtt-85) cc_final: 0.8516 (mmm-85) REVERT: C 1010 GLN cc_start: 0.8794 (tp-100) cc_final: 0.7785 (tm-30) REVERT: C 1011 GLN cc_start: 0.8998 (pt0) cc_final: 0.8491 (pt0) REVERT: C 1013 ILE cc_start: 0.9399 (mm) cc_final: 0.9111 (pt) REVERT: C 1017 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8649 (tm-30) REVERT: C 1018 ILE cc_start: 0.8805 (pt) cc_final: 0.8275 (pt) REVERT: C 1019 ARG cc_start: 0.9026 (ptp90) cc_final: 0.8674 (ptt-90) REVERT: C 1050 MET cc_start: 0.2676 (ttt) cc_final: 0.1814 (ttt) REVERT: C 1052 PHE cc_start: 0.7637 (m-80) cc_final: 0.7383 (m-80) REVERT: C 1054 GLN cc_start: 0.6441 (mp10) cc_final: 0.6114 (mp-120) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.1940 time to fit residues: 153.0636 Evaluate side-chains 487 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 223 optimal weight: 0.8980 chunk 271 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 308 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 218 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 164 ASN A 409 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.174724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.126650 restraints weight = 63687.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.131229 restraints weight = 46127.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.134510 restraints weight = 36283.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.136932 restraints weight = 30178.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.138645 restraints weight = 26208.758| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.7308 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= 0.160 Angle : 0.745 12.499 36017 Z= 0.372 Chirality : 0.049 0.393 4182 Planarity : 0.005 0.078 4587 Dihedral : 8.224 102.223 4373 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3187 helix: 0.28 (0.19), residues: 689 sheet: -0.73 (0.21), residues: 548 loop : -1.48 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 408 TYR 0.026 0.001 TYR A 904 PHE 0.020 0.002 PHE A 515 TRP 0.020 0.002 TRP B 436 HIS 0.011 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00343 (26300) covalent geometry : angle 0.71446 (35807) SS BOND : bond 0.00379 ( 42) SS BOND : angle 2.26765 ( 84) hydrogen bonds : bond 0.04740 ( 872) hydrogen bonds : angle 6.41862 ( 2433) Misc. bond : bond 0.00244 ( 2) link_BETA1-4 : bond 0.00384 ( 10) link_BETA1-4 : angle 1.46931 ( 30) link_NAG-ASN : bond 0.00573 ( 32) link_NAG-ASN : angle 3.58236 ( 96) *********************** 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 526 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.911 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 43 PHE cc_start: 0.8309 (t80) cc_final: 0.8045 (t80) REVERT: A 53 ASP cc_start: 0.8616 (t0) cc_final: 0.8133 (t0) REVERT: A 65 PHE cc_start: 0.8153 (m-80) cc_final: 0.7535 (m-80) REVERT: A 104 TRP cc_start: 0.6839 (m-90) cc_final: 0.6236 (m-90) REVERT: A 129 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8991 (mmmt) REVERT: A 194 PHE cc_start: 0.8410 (m-80) cc_final: 0.7914 (m-80) REVERT: A 207 HIS cc_start: 0.8998 (p90) cc_final: 0.8793 (p-80) REVERT: A 240 THR cc_start: 0.8290 (m) cc_final: 0.7706 (m) REVERT: A 275 PHE cc_start: 0.6524 (m-10) cc_final: 0.5993 (m-10) REVERT: A 304 LYS cc_start: 0.8883 (mppt) cc_final: 0.8602 (mmtt) REVERT: A 310 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8078 (mmtt) REVERT: A 317 ASN cc_start: 0.8319 (p0) cc_final: 0.7835 (p0) REVERT: A 319 ARG cc_start: 0.8357 (ppt170) cc_final: 0.7963 (tmt170) REVERT: A 355 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8180 (tpp80) REVERT: A 365 TYR cc_start: 0.8149 (m-80) cc_final: 0.7621 (m-80) REVERT: A 380 TYR cc_start: 0.8137 (m-80) cc_final: 0.7803 (m-80) REVERT: A 389 ASP cc_start: 0.8772 (m-30) cc_final: 0.8419 (p0) REVERT: A 560 LEU cc_start: 0.9172 (tp) cc_final: 0.8965 (tp) REVERT: A 562 PHE cc_start: 0.8262 (p90) cc_final: 0.7674 (p90) REVERT: A 759 PHE cc_start: 0.8845 (m-80) cc_final: 0.7977 (m-80) REVERT: A 762 GLN cc_start: 0.9058 (pt0) cc_final: 0.8319 (pp30) REVERT: A 776 LYS cc_start: 0.9020 (tptm) cc_final: 0.8451 (tptp) REVERT: A 820 ASP cc_start: 0.9023 (m-30) cc_final: 0.8814 (m-30) REVERT: A 869 MET cc_start: 0.8154 (pmm) cc_final: 0.7615 (pmm) REVERT: A 873 TYR cc_start: 0.8412 (m-10) cc_final: 0.8010 (m-80) REVERT: A 917 TYR cc_start: 0.8025 (m-80) cc_final: 0.7432 (m-10) REVERT: A 927 PHE cc_start: 0.7859 (t80) cc_final: 0.7507 (t80) REVERT: A 934 ILE cc_start: 0.8622 (tp) cc_final: 0.8120 (mt) REVERT: A 935 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8379 (mm110) REVERT: A 936 ASP cc_start: 0.8707 (m-30) cc_final: 0.8461 (m-30) REVERT: A 947 LYS cc_start: 0.7475 (mtpt) cc_final: 0.7192 (mmmt) REVERT: A 954 GLN cc_start: 0.9017 (tp40) cc_final: 0.8578 (tm-30) REVERT: A 959 LEU cc_start: 0.9249 (mp) cc_final: 0.8955 (mm) REVERT: A 960 ASN cc_start: 0.8594 (t0) cc_final: 0.7984 (m110) REVERT: A 964 LYS cc_start: 0.9192 (ttmm) cc_final: 0.8762 (ptpp) REVERT: A 979 ASP cc_start: 0.9071 (m-30) cc_final: 0.8484 (t0) REVERT: A 983 ARG cc_start: 0.8733 (ptt90) cc_final: 0.7772 (ttp80) REVERT: A 990 GLU cc_start: 0.8608 (tt0) cc_final: 0.8213 (mt-10) REVERT: A 994 ASP cc_start: 0.8636 (m-30) cc_final: 0.8116 (m-30) REVERT: A 995 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8263 (ttm-80) REVERT: A 997 ILE cc_start: 0.9303 (pt) cc_final: 0.9097 (pt) REVERT: A 998 THR cc_start: 0.9227 (m) cc_final: 0.9006 (p) REVERT: A 1000 ARG cc_start: 0.8954 (mmt180) cc_final: 0.8408 (mmt180) REVERT: A 1001 LEU cc_start: 0.9024 (mt) cc_final: 0.8508 (mm) REVERT: A 1002 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 1005 GLN cc_start: 0.8800 (mt0) cc_final: 0.8508 (mm-40) REVERT: A 1011 GLN cc_start: 0.8940 (tp40) cc_final: 0.7939 (mm-40) REVERT: A 1014 ARG cc_start: 0.8789 (mmp-170) cc_final: 0.8506 (mmm160) REVERT: A 1023 ASN cc_start: 0.8825 (m110) cc_final: 0.8575 (m-40) REVERT: A 1050 MET cc_start: 0.5769 (ttt) cc_final: 0.5210 (ttt) REVERT: A 1053 PRO cc_start: 0.8885 (Cg_endo) cc_final: 0.8589 (Cg_exo) REVERT: A 1054 GLN cc_start: 0.6529 (mp10) cc_final: 0.6165 (mp10) REVERT: B 37 TYR cc_start: 0.8385 (p90) cc_final: 0.7967 (p90) REVERT: B 41 LYS cc_start: 0.8863 (tppt) cc_final: 0.8422 (tppt) REVERT: B 58 PHE cc_start: 0.7257 (m-10) cc_final: 0.6252 (m-80) REVERT: B 86 PHE cc_start: 0.7758 (t80) cc_final: 0.7274 (t80) REVERT: B 105 ILE cc_start: 0.8868 (mp) cc_final: 0.8608 (tp) REVERT: B 266 TYR cc_start: 0.7481 (m-80) cc_final: 0.7175 (m-10) REVERT: B 275 PHE cc_start: 0.6868 (m-10) cc_final: 0.6228 (m-10) REVERT: B 276 LEU cc_start: 0.8926 (tt) cc_final: 0.8257 (mp) REVERT: B 298 GLU cc_start: 0.8540 (tt0) cc_final: 0.8155 (tt0) REVERT: B 313 TYR cc_start: 0.7623 (m-80) cc_final: 0.7010 (m-10) REVERT: B 321 GLN cc_start: 0.8198 (pp30) cc_final: 0.7908 (pp30) REVERT: B 543 PHE cc_start: 0.8448 (p90) cc_final: 0.8046 (p90) REVERT: B 562 PHE cc_start: 0.8958 (p90) cc_final: 0.8485 (p90) REVERT: B 586 ASP cc_start: 0.8419 (t0) cc_final: 0.7676 (p0) REVERT: B 749 CYS cc_start: 0.5823 (p) cc_final: 0.5612 (p) REVERT: B 753 LEU cc_start: 0.8787 (tp) cc_final: 0.8511 (tp) REVERT: B 777 ASN cc_start: 0.8355 (m110) cc_final: 0.8151 (m110) REVERT: B 802 PHE cc_start: 0.7454 (m-80) cc_final: 0.6628 (m-80) REVERT: B 819 GLU cc_start: 0.8887 (pt0) cc_final: 0.8622 (pt0) REVERT: B 824 ASN cc_start: 0.8853 (m110) cc_final: 0.8595 (m110) REVERT: B 917 TYR cc_start: 0.8611 (m-10) cc_final: 0.8185 (m-10) REVERT: B 927 PHE cc_start: 0.8440 (t80) cc_final: 0.7800 (t80) REVERT: B 937 SER cc_start: 0.8731 (t) cc_final: 0.8409 (p) REVERT: B 954 GLN cc_start: 0.9026 (mt0) cc_final: 0.8638 (tm-30) REVERT: B 960 ASN cc_start: 0.8799 (t0) cc_final: 0.7874 (t0) REVERT: B 962 LEU cc_start: 0.9358 (tp) cc_final: 0.9150 (tp) REVERT: B 978 ASN cc_start: 0.8795 (p0) cc_final: 0.8568 (p0) REVERT: B 979 ASP cc_start: 0.8747 (t0) cc_final: 0.8487 (t0) REVERT: B 983 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7459 (ttp-170) REVERT: B 995 ARG cc_start: 0.8682 (ptt180) cc_final: 0.8470 (ptt-90) REVERT: B 1000 ARG cc_start: 0.8790 (ptp-110) cc_final: 0.8453 (mtp-110) REVERT: B 1010 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8273 (mm-40) REVERT: B 1011 GLN cc_start: 0.8753 (mm110) cc_final: 0.8138 (mm-40) REVERT: B 1014 ARG cc_start: 0.8841 (mmt-90) cc_final: 0.8477 (mmt-90) REVERT: B 1017 GLU cc_start: 0.8722 (pp20) cc_final: 0.8217 (pp20) REVERT: B 1019 ARG cc_start: 0.8923 (ptm-80) cc_final: 0.8374 (ptm-80) REVERT: C 34 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8231 (mmm160) REVERT: C 41 LYS cc_start: 0.8273 (tppt) cc_final: 0.7775 (tppt) REVERT: C 65 PHE cc_start: 0.8004 (m-80) cc_final: 0.7506 (m-80) REVERT: C 91 TYR cc_start: 0.7739 (t80) cc_final: 0.7038 (t80) REVERT: C 92 PHE cc_start: 0.8204 (t80) cc_final: 0.7682 (t80) REVERT: C 117 LEU cc_start: 0.8704 (tt) cc_final: 0.8196 (pp) REVERT: C 129 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8539 (tptp) REVERT: C 133 PHE cc_start: 0.8279 (m-80) cc_final: 0.7675 (m-80) REVERT: C 194 PHE cc_start: 0.7684 (m-80) cc_final: 0.7195 (m-80) REVERT: C 223 LEU cc_start: 0.8281 (pt) cc_final: 0.7944 (pt) REVERT: C 237 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8450 (mmm-85) REVERT: C 276 LEU cc_start: 0.8280 (tp) cc_final: 0.8016 (tp) REVERT: C 281 GLU cc_start: 0.8183 (tp30) cc_final: 0.7867 (tp30) REVERT: C 298 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7353 (mp0) REVERT: C 300 LYS cc_start: 0.8318 (mttt) cc_final: 0.7903 (mmtt) REVERT: C 313 TYR cc_start: 0.7488 (m-10) cc_final: 0.7047 (m-10) REVERT: C 324 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8414 (mp0) REVERT: C 338 PHE cc_start: 0.9021 (m-80) cc_final: 0.8514 (m-10) REVERT: C 342 PHE cc_start: 0.8659 (m-80) cc_final: 0.8322 (m-80) REVERT: C 365 TYR cc_start: 0.9022 (m-10) cc_final: 0.8420 (m-10) REVERT: C 380 TYR cc_start: 0.7271 (m-80) cc_final: 0.6915 (m-80) REVERT: C 386 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8174 (mtmm) REVERT: C 417 LYS cc_start: 0.9116 (tptt) cc_final: 0.8650 (tppt) REVERT: C 421 TYR cc_start: 0.8523 (m-10) cc_final: 0.8069 (m-10) REVERT: C 424 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6978 (ttmm) REVERT: C 425 LEU cc_start: 0.8217 (mt) cc_final: 0.7843 (tp) REVERT: C 426 PRO cc_start: 0.8712 (Cg_exo) cc_final: 0.8122 (Cg_endo) REVERT: C 451 TYR cc_start: 0.5987 (m-80) cc_final: 0.5667 (m-80) REVERT: C 490 PHE cc_start: 0.8779 (t80) cc_final: 0.8402 (t80) REVERT: C 505 TYR cc_start: 0.8356 (t80) cc_final: 0.7986 (t80) REVERT: C 543 PHE cc_start: 0.8524 (m-80) cc_final: 0.8311 (m-80) REVERT: C 563 GLN cc_start: 0.7685 (mm-40) cc_final: 0.6991 (mm-40) REVERT: C 737 ASP cc_start: 0.8759 (t0) cc_final: 0.8330 (t0) REVERT: C 755 GLN cc_start: 0.9225 (pt0) cc_final: 0.8936 (pt0) REVERT: C 762 GLN cc_start: 0.8879 (mt0) cc_final: 0.8306 (mp10) REVERT: C 763 LEU cc_start: 0.9073 (mt) cc_final: 0.8822 (mt) REVERT: C 764 ASN cc_start: 0.8907 (m110) cc_final: 0.8623 (m110) REVERT: C 765 ARG cc_start: 0.8949 (ptp-170) cc_final: 0.8595 (ptp90) REVERT: C 776 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8251 (tmtt) REVERT: C 869 MET cc_start: 0.9097 (mtm) cc_final: 0.8313 (mmt) REVERT: C 873 TYR cc_start: 0.8161 (m-10) cc_final: 0.7771 (m-80) REVERT: C 954 GLN cc_start: 0.8976 (mt0) cc_final: 0.8661 (tm-30) REVERT: C 957 GLN cc_start: 0.8973 (tt0) cc_final: 0.8669 (pp30) REVERT: C 959 LEU cc_start: 0.9157 (mp) cc_final: 0.8879 (pp) REVERT: C 960 ASN cc_start: 0.8836 (m110) cc_final: 0.8454 (m110) REVERT: C 969 ASN cc_start: 0.8723 (p0) cc_final: 0.8362 (p0) REVERT: C 970 PHE cc_start: 0.8108 (m-80) cc_final: 0.7367 (m-10) REVERT: C 978 ASN cc_start: 0.9510 (m110) cc_final: 0.9307 (m110) REVERT: C 979 ASP cc_start: 0.8991 (m-30) cc_final: 0.8584 (m-30) REVERT: C 981 LEU cc_start: 0.9136 (mp) cc_final: 0.8817 (pp) REVERT: C 983 ARG cc_start: 0.8982 (tmt-80) cc_final: 0.8621 (tpt90) REVERT: C 994 ASP cc_start: 0.8804 (m-30) cc_final: 0.8565 (m-30) REVERT: C 995 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8155 (mtm180) REVERT: C 1000 ARG cc_start: 0.9040 (mtt-85) cc_final: 0.8679 (mmm160) REVERT: C 1001 LEU cc_start: 0.9454 (tp) cc_final: 0.9239 (tp) REVERT: C 1005 GLN cc_start: 0.8884 (pp30) cc_final: 0.8527 (pp30) REVERT: C 1010 GLN cc_start: 0.8748 (tp-100) cc_final: 0.7506 (tm-30) REVERT: C 1011 GLN cc_start: 0.8981 (pt0) cc_final: 0.8397 (pt0) REVERT: C 1014 ARG cc_start: 0.8604 (mmp80) cc_final: 0.7409 (mmp80) REVERT: C 1017 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8542 (tm-30) REVERT: C 1018 ILE cc_start: 0.8637 (pt) cc_final: 0.8140 (pt) REVERT: C 1019 ARG cc_start: 0.8959 (ptp90) cc_final: 0.8615 (ptt-90) REVERT: C 1052 PHE cc_start: 0.7696 (m-80) cc_final: 0.7338 (m-80) REVERT: C 1054 GLN cc_start: 0.6476 (mp10) cc_final: 0.6167 (mp-120) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.1836 time to fit residues: 147.0092 Evaluate side-chains 478 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 228 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 227 optimal weight: 0.0670 chunk 174 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 47 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 164 ASN A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** 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 764 ASN C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.175203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.126873 restraints weight = 63522.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.131554 restraints weight = 46139.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.134976 restraints weight = 35906.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.137519 restraints weight = 29664.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.139258 restraints weight = 25596.327| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.7447 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= 0.145 Angle : 0.731 13.672 36017 Z= 0.365 Chirality : 0.049 0.367 4182 Planarity : 0.005 0.075 4587 Dihedral : 8.072 102.730 4373 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3187 helix: 0.33 (0.19), residues: 676 sheet: -0.74 (0.21), residues: 556 loop : -1.44 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 102 TYR 0.021 0.001 TYR A 904 PHE 0.041 0.002 PHE B 194 TRP 0.034 0.002 TRP B 104 HIS 0.011 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00315 (26300) covalent geometry : angle 0.70358 (35807) SS BOND : bond 0.00288 ( 42) SS BOND : angle 2.23981 ( 84) hydrogen bonds : bond 0.04517 ( 872) hydrogen bonds : angle 6.22224 ( 2433) Misc. bond : bond 0.00319 ( 2) link_BETA1-4 : bond 0.00353 ( 10) link_BETA1-4 : angle 1.45334 ( 30) link_NAG-ASN : bond 0.00583 ( 32) link_NAG-ASN : angle 3.31083 ( 96) *********************** 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 523 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 1.370 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: A 53 ASP cc_start: 0.8414 (t0) cc_final: 0.8049 (t0) REVERT: A 65 PHE cc_start: 0.8134 (m-80) cc_final: 0.7538 (m-80) REVERT: A 135 PHE cc_start: 0.8418 (m-10) cc_final: 0.8016 (m-10) REVERT: A 189 LEU cc_start: 0.8534 (tp) cc_final: 0.8325 (tp) REVERT: A 194 PHE cc_start: 0.8341 (m-80) cc_final: 0.8016 (m-80) REVERT: A 240 THR cc_start: 0.8352 (m) cc_final: 0.7786 (m) REVERT: A 275 PHE cc_start: 0.6520 (m-10) cc_final: 0.6011 (m-10) REVERT: A 310 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8263 (mptt) REVERT: A 317 ASN cc_start: 0.8291 (p0) cc_final: 0.7843 (p0) REVERT: A 319 ARG cc_start: 0.8361 (ppt170) cc_final: 0.7923 (tmt170) REVERT: A 365 TYR cc_start: 0.8085 (m-80) cc_final: 0.7762 (m-80) REVERT: A 380 TYR cc_start: 0.8053 (m-80) cc_final: 0.7678 (m-80) REVERT: A 389 ASP cc_start: 0.8840 (m-30) cc_final: 0.8349 (p0) REVERT: A 408 ARG cc_start: 0.8759 (pmt-80) cc_final: 0.8508 (pmt-80) REVERT: A 461 LEU cc_start: 0.8119 (mt) cc_final: 0.7621 (mt) REVERT: A 557 LYS cc_start: 0.8280 (mttt) cc_final: 0.7407 (tptp) REVERT: A 562 PHE cc_start: 0.8270 (p90) cc_final: 0.7565 (p90) REVERT: A 585 LEU cc_start: 0.8664 (mp) cc_final: 0.8462 (mp) REVERT: A 645 THR cc_start: 0.8096 (p) cc_final: 0.7784 (p) REVERT: A 752 LEU cc_start: 0.9110 (tt) cc_final: 0.8803 (pp) REVERT: A 759 PHE cc_start: 0.8846 (m-80) cc_final: 0.8077 (m-80) REVERT: A 762 GLN cc_start: 0.9087 (pt0) cc_final: 0.8826 (mm-40) REVERT: A 776 LYS cc_start: 0.8974 (tptm) cc_final: 0.8397 (tptp) REVERT: A 820 ASP cc_start: 0.9005 (m-30) cc_final: 0.8803 (m-30) REVERT: A 869 MET cc_start: 0.8165 (pmm) cc_final: 0.7579 (pmm) REVERT: A 873 TYR cc_start: 0.8419 (m-10) cc_final: 0.7998 (m-80) REVERT: A 917 TYR cc_start: 0.7988 (m-80) cc_final: 0.7370 (m-10) REVERT: A 927 PHE cc_start: 0.7861 (t80) cc_final: 0.7387 (t80) REVERT: A 934 ILE cc_start: 0.8552 (tp) cc_final: 0.8129 (mt) REVERT: A 936 ASP cc_start: 0.8711 (m-30) cc_final: 0.8465 (m-30) REVERT: A 947 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7357 (mmmt) REVERT: A 954 GLN cc_start: 0.9031 (tp40) cc_final: 0.8522 (tm-30) REVERT: A 959 LEU cc_start: 0.9287 (mp) cc_final: 0.8999 (mm) REVERT: A 960 ASN cc_start: 0.8637 (t0) cc_final: 0.7908 (m110) REVERT: A 964 LYS cc_start: 0.9157 (ttmm) cc_final: 0.8669 (ptpp) REVERT: A 965 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 979 ASP cc_start: 0.9002 (m-30) cc_final: 0.8450 (t0) REVERT: A 983 ARG cc_start: 0.8738 (ptt90) cc_final: 0.7738 (ttp80) REVERT: A 990 GLU cc_start: 0.8606 (tt0) cc_final: 0.8239 (mt-10) REVERT: A 994 ASP cc_start: 0.8619 (m-30) cc_final: 0.8145 (m-30) REVERT: A 998 THR cc_start: 0.9252 (m) cc_final: 0.9003 (p) REVERT: A 1000 ARG cc_start: 0.8927 (mmt180) cc_final: 0.8292 (mmt180) REVERT: A 1001 LEU cc_start: 0.9069 (mt) cc_final: 0.8598 (mm) REVERT: A 1002 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 1005 GLN cc_start: 0.8802 (mt0) cc_final: 0.8488 (mm-40) REVERT: A 1014 ARG cc_start: 0.8801 (mmp-170) cc_final: 0.8522 (mmp80) REVERT: A 1023 ASN cc_start: 0.8790 (m110) cc_final: 0.8530 (m-40) REVERT: A 1050 MET cc_start: 0.5755 (ttt) cc_final: 0.5231 (ttt) REVERT: A 1053 PRO cc_start: 0.8742 (Cg_endo) cc_final: 0.8298 (Cg_exo) REVERT: A 1054 GLN cc_start: 0.6239 (mp10) cc_final: 0.5881 (mp10) REVERT: A 1062 PHE cc_start: 0.5777 (m-80) cc_final: 0.5026 (m-80) REVERT: B 37 TYR cc_start: 0.8342 (p90) cc_final: 0.8014 (p90) REVERT: B 41 LYS cc_start: 0.8763 (tppt) cc_final: 0.8144 (tppt) REVERT: B 58 PHE cc_start: 0.7620 (m-10) cc_final: 0.6949 (m-80) REVERT: B 86 PHE cc_start: 0.7809 (t80) cc_final: 0.7305 (t80) REVERT: B 104 TRP cc_start: 0.5203 (m-10) cc_final: 0.4259 (m-10) REVERT: B 105 ILE cc_start: 0.8855 (mp) cc_final: 0.8556 (tp) REVERT: B 226 LEU cc_start: 0.9076 (tp) cc_final: 0.8645 (mm) REVERT: B 266 TYR cc_start: 0.7660 (m-80) cc_final: 0.7346 (m-10) REVERT: B 275 PHE cc_start: 0.6923 (m-10) cc_final: 0.6291 (m-10) REVERT: B 276 LEU cc_start: 0.8810 (tt) cc_final: 0.8176 (mp) REVERT: B 298 GLU cc_start: 0.8537 (tt0) cc_final: 0.8173 (tt0) REVERT: B 313 TYR cc_start: 0.7578 (m-80) cc_final: 0.7045 (m-10) REVERT: B 321 GLN cc_start: 0.8226 (pp30) cc_final: 0.7858 (pp30) REVERT: B 543 PHE cc_start: 0.8419 (p90) cc_final: 0.7991 (p90) REVERT: B 562 PHE cc_start: 0.8997 (p90) cc_final: 0.8534 (p90) REVERT: B 577 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7701 (tpt170) REVERT: B 586 ASP cc_start: 0.8396 (t0) cc_final: 0.7672 (p0) REVERT: B 587 ILE cc_start: 0.8869 (mp) cc_final: 0.8628 (mp) REVERT: B 753 LEU cc_start: 0.8742 (tp) cc_final: 0.8436 (tp) REVERT: B 754 LEU cc_start: 0.8901 (mt) cc_final: 0.8695 (tp) REVERT: B 819 GLU cc_start: 0.8888 (pt0) cc_final: 0.8313 (tm-30) REVERT: B 820 ASP cc_start: 0.8693 (t0) cc_final: 0.8445 (t0) REVERT: B 824 ASN cc_start: 0.8789 (m110) cc_final: 0.8499 (m110) REVERT: B 869 MET cc_start: 0.8606 (mpp) cc_final: 0.7732 (mpp) REVERT: B 873 TYR cc_start: 0.7787 (m-10) cc_final: 0.7268 (m-80) REVERT: B 917 TYR cc_start: 0.8556 (m-10) cc_final: 0.8156 (m-10) REVERT: B 927 PHE cc_start: 0.8504 (t80) cc_final: 0.7757 (t80) REVERT: B 937 SER cc_start: 0.8717 (t) cc_final: 0.8343 (p) REVERT: B 954 GLN cc_start: 0.9020 (mt0) cc_final: 0.8666 (tm-30) REVERT: B 978 ASN cc_start: 0.8811 (p0) cc_final: 0.8533 (p0) REVERT: B 979 ASP cc_start: 0.8778 (t0) cc_final: 0.8511 (t0) REVERT: B 983 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7580 (ttp-110) REVERT: B 995 ARG cc_start: 0.8684 (ptt180) cc_final: 0.8413 (ptt-90) REVERT: B 998 THR cc_start: 0.8812 (p) cc_final: 0.8578 (p) REVERT: B 1000 ARG cc_start: 0.8802 (ptp-110) cc_final: 0.8404 (mtp-110) REVERT: B 1002 GLN cc_start: 0.8809 (mp10) cc_final: 0.8508 (mp10) REVERT: B 1009 THR cc_start: 0.9135 (p) cc_final: 0.8632 (p) REVERT: B 1010 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8236 (mm-40) REVERT: B 1011 GLN cc_start: 0.8821 (mm110) cc_final: 0.8165 (mm-40) REVERT: B 1014 ARG cc_start: 0.8871 (mmt-90) cc_final: 0.8500 (mmt-90) REVERT: B 1017 GLU cc_start: 0.8739 (pp20) cc_final: 0.8224 (pp20) REVERT: B 1019 ARG cc_start: 0.8906 (ptm-80) cc_final: 0.8331 (ptm-80) REVERT: B 1048 HIS cc_start: 0.6698 (p-80) cc_final: 0.6380 (p-80) REVERT: B 1049 LEU cc_start: 0.8310 (mt) cc_final: 0.7921 (mt) REVERT: C 34 ARG cc_start: 0.8508 (mmm160) cc_final: 0.8270 (mmm160) REVERT: C 41 LYS cc_start: 0.8232 (tppt) cc_final: 0.7711 (tppt) REVERT: C 65 PHE cc_start: 0.7990 (m-80) cc_final: 0.7587 (m-80) REVERT: C 91 TYR cc_start: 0.7728 (t80) cc_final: 0.7022 (t80) REVERT: C 92 PHE cc_start: 0.8185 (t80) cc_final: 0.7673 (t80) REVERT: C 117 LEU cc_start: 0.8720 (tt) cc_final: 0.8258 (pp) REVERT: C 129 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8519 (mmmt) REVERT: C 133 PHE cc_start: 0.8190 (m-80) cc_final: 0.7520 (m-80) REVERT: C 194 PHE cc_start: 0.7669 (m-80) cc_final: 0.7168 (m-80) REVERT: C 223 LEU cc_start: 0.7830 (pt) cc_final: 0.7416 (pt) REVERT: C 237 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8439 (mmm-85) REVERT: C 276 LEU cc_start: 0.8352 (tp) cc_final: 0.8128 (tp) REVERT: C 281 GLU cc_start: 0.8173 (tp30) cc_final: 0.7863 (tp30) REVERT: C 298 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7362 (mp0) REVERT: C 300 LYS cc_start: 0.8254 (mttt) cc_final: 0.7789 (mmtt) REVERT: C 313 TYR cc_start: 0.7505 (m-10) cc_final: 0.7063 (m-10) REVERT: C 324 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8379 (mp0) REVERT: C 338 PHE cc_start: 0.9064 (m-80) cc_final: 0.8466 (m-10) REVERT: C 342 PHE cc_start: 0.8733 (m-80) cc_final: 0.8337 (m-80) REVERT: C 354 ASN cc_start: 0.8854 (t0) cc_final: 0.8596 (t0) REVERT: C 365 TYR cc_start: 0.9043 (m-10) cc_final: 0.8480 (m-10) REVERT: C 380 TYR cc_start: 0.7280 (m-80) cc_final: 0.6896 (m-80) REVERT: C 386 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8157 (mtmm) REVERT: C 405 ASP cc_start: 0.8470 (p0) cc_final: 0.7944 (p0) REVERT: C 409 GLN cc_start: 0.8476 (mp10) cc_final: 0.7947 (mp10) REVERT: C 417 LYS cc_start: 0.9123 (tptt) cc_final: 0.8843 (tppt) REVERT: C 421 TYR cc_start: 0.8580 (m-10) cc_final: 0.8357 (m-10) REVERT: C 425 LEU cc_start: 0.8362 (mt) cc_final: 0.8097 (tp) REVERT: C 451 TYR cc_start: 0.6033 (m-80) cc_final: 0.5719 (m-80) REVERT: C 490 PHE cc_start: 0.8705 (t80) cc_final: 0.7965 (t80) REVERT: C 493 GLN cc_start: 0.7608 (mp10) cc_final: 0.6631 (mp10) REVERT: C 505 TYR cc_start: 0.8341 (t80) cc_final: 0.7844 (t80) REVERT: C 563 GLN cc_start: 0.7605 (mm-40) cc_final: 0.6868 (mm-40) REVERT: C 737 ASP cc_start: 0.8746 (t0) cc_final: 0.8237 (t0) REVERT: C 747 THR cc_start: 0.8926 (p) cc_final: 0.8691 (p) REVERT: C 755 GLN cc_start: 0.9223 (pt0) cc_final: 0.8929 (pt0) REVERT: C 761 THR cc_start: 0.9257 (p) cc_final: 0.9026 (p) REVERT: C 762 GLN cc_start: 0.8808 (mt0) cc_final: 0.8376 (mt0) REVERT: C 763 LEU cc_start: 0.9025 (mt) cc_final: 0.8775 (mt) REVERT: C 764 ASN cc_start: 0.9028 (m110) cc_final: 0.8790 (m110) REVERT: C 765 ARG cc_start: 0.8987 (ptp-170) cc_final: 0.8489 (ptp90) REVERT: C 770 ILE cc_start: 0.9188 (mm) cc_final: 0.8729 (mt) REVERT: C 773 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7633 (pp20) REVERT: C 776 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8185 (tmtt) REVERT: C 869 MET cc_start: 0.9105 (mtm) cc_final: 0.8363 (mmt) REVERT: C 873 TYR cc_start: 0.8170 (m-10) cc_final: 0.7788 (m-80) REVERT: C 954 GLN cc_start: 0.8956 (mt0) cc_final: 0.8565 (tm-30) REVERT: C 957 GLN cc_start: 0.8980 (tt0) cc_final: 0.8687 (pp30) REVERT: C 959 LEU cc_start: 0.9134 (mp) cc_final: 0.8891 (pp) REVERT: C 960 ASN cc_start: 0.8860 (m110) cc_final: 0.7810 (m110) REVERT: C 964 LYS cc_start: 0.9410 (tttt) cc_final: 0.9102 (mmtt) REVERT: C 969 ASN cc_start: 0.8639 (p0) cc_final: 0.8354 (p0) REVERT: C 970 PHE cc_start: 0.8066 (m-80) cc_final: 0.7364 (m-10) REVERT: C 978 ASN cc_start: 0.9525 (m110) cc_final: 0.9301 (m110) REVERT: C 979 ASP cc_start: 0.9058 (m-30) cc_final: 0.8673 (m-30) REVERT: C 981 LEU cc_start: 0.9170 (mp) cc_final: 0.8875 (pp) REVERT: C 983 ARG cc_start: 0.8982 (tmt-80) cc_final: 0.8612 (tpt90) REVERT: C 995 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8106 (mtm180) REVERT: C 1000 ARG cc_start: 0.9124 (mtt-85) cc_final: 0.8642 (mmm160) REVERT: C 1001 LEU cc_start: 0.9504 (tp) cc_final: 0.9211 (tp) REVERT: C 1005 GLN cc_start: 0.8877 (pp30) cc_final: 0.8510 (pp30) REVERT: C 1010 GLN cc_start: 0.8781 (tp-100) cc_final: 0.7551 (tm-30) REVERT: C 1011 GLN cc_start: 0.8960 (pt0) cc_final: 0.8396 (pt0) REVERT: C 1014 ARG cc_start: 0.8657 (mmp80) cc_final: 0.7380 (mmp80) REVERT: C 1017 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8542 (tm-30) REVERT: C 1018 ILE cc_start: 0.8614 (pt) cc_final: 0.8227 (pt) REVERT: C 1019 ARG cc_start: 0.8941 (ptp90) cc_final: 0.8443 (ptt-90) REVERT: C 1107 ARG cc_start: 0.5816 (ptp90) cc_final: 0.5421 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.1829 time to fit residues: 145.9591 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 : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 153 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 214 optimal weight: 40.0000 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 250 optimal weight: 0.6980 chunk 207 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 164 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 218 GLN B 360 ASN ** 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 ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.171468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.123716 restraints weight = 63863.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.128135 restraints weight = 46592.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.131382 restraints weight = 36701.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.133632 restraints weight = 30621.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.135455 restraints weight = 26783.690| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26386 Z= 0.195 Angle : 0.757 13.982 36017 Z= 0.386 Chirality : 0.049 0.347 4182 Planarity : 0.005 0.078 4587 Dihedral : 8.057 99.412 4373 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3187 helix: 0.24 (0.19), residues: 684 sheet: -0.83 (0.21), residues: 550 loop : -1.50 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 454 TYR 0.021 0.002 TYR B 904 PHE 0.035 0.002 PHE B 194 TRP 0.024 0.002 TRP B 104 HIS 0.014 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00396 (26300) covalent geometry : angle 0.73081 (35807) SS BOND : bond 0.00359 ( 42) SS BOND : angle 2.33609 ( 84) hydrogen bonds : bond 0.04763 ( 872) hydrogen bonds : angle 6.30223 ( 2433) Misc. bond : bond 0.00347 ( 2) link_BETA1-4 : bond 0.00416 ( 10) link_BETA1-4 : angle 1.42685 ( 30) link_NAG-ASN : bond 0.00572 ( 32) link_NAG-ASN : angle 3.22312 ( 96) *********************** 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 519 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 0.865 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: A 53 ASP cc_start: 0.8439 (t0) cc_final: 0.8091 (t0) REVERT: A 65 PHE cc_start: 0.8129 (m-80) cc_final: 0.7538 (m-80) REVERT: A 118 LEU cc_start: 0.8623 (mm) cc_final: 0.8340 (mt) REVERT: A 128 ILE cc_start: 0.8715 (mp) cc_final: 0.8199 (mp) REVERT: A 170 TYR cc_start: 0.7897 (t80) cc_final: 0.7211 (t80) REVERT: A 189 LEU cc_start: 0.8476 (tp) cc_final: 0.8265 (tp) REVERT: A 207 HIS cc_start: 0.9024 (p90) cc_final: 0.8803 (p90) REVERT: A 240 THR cc_start: 0.8385 (m) cc_final: 0.7938 (m) REVERT: A 275 PHE cc_start: 0.6575 (m-10) cc_final: 0.6066 (m-10) REVERT: A 317 ASN cc_start: 0.8337 (p0) cc_final: 0.7879 (p0) REVERT: A 365 TYR cc_start: 0.8129 (m-80) cc_final: 0.7825 (m-80) REVERT: A 380 TYR cc_start: 0.7998 (m-80) cc_final: 0.7763 (m-80) REVERT: A 389 ASP cc_start: 0.8912 (m-30) cc_final: 0.8413 (p0) REVERT: A 408 ARG cc_start: 0.8809 (pmt-80) cc_final: 0.8599 (pmt-80) REVERT: A 461 LEU cc_start: 0.7878 (mt) cc_final: 0.7615 (mt) REVERT: A 562 PHE cc_start: 0.8335 (p90) cc_final: 0.7565 (p90) REVERT: A 585 LEU cc_start: 0.8685 (mp) cc_final: 0.8459 (mp) REVERT: A 752 LEU cc_start: 0.9166 (tt) cc_final: 0.8841 (pp) REVERT: A 759 PHE cc_start: 0.8838 (m-80) cc_final: 0.8013 (m-80) REVERT: A 776 LYS cc_start: 0.8966 (tptm) cc_final: 0.8406 (tptp) REVERT: A 820 ASP cc_start: 0.9070 (m-30) cc_final: 0.8849 (m-30) REVERT: A 869 MET cc_start: 0.8191 (pmm) cc_final: 0.7603 (pmm) REVERT: A 873 TYR cc_start: 0.8502 (m-10) cc_final: 0.8102 (m-80) REVERT: A 917 TYR cc_start: 0.8035 (m-80) cc_final: 0.7387 (m-10) REVERT: A 927 PHE cc_start: 0.7840 (t80) cc_final: 0.7443 (t80) REVERT: A 934 ILE cc_start: 0.8613 (tp) cc_final: 0.7839 (mm) REVERT: A 935 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8489 (mm110) REVERT: A 936 ASP cc_start: 0.8733 (m-30) cc_final: 0.8493 (m-30) REVERT: A 954 GLN cc_start: 0.9044 (tp40) cc_final: 0.8635 (tm-30) REVERT: A 959 LEU cc_start: 0.9361 (mp) cc_final: 0.9116 (mm) REVERT: A 960 ASN cc_start: 0.8731 (t0) cc_final: 0.8055 (m110) REVERT: A 964 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8774 (ptpp) REVERT: A 965 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 979 ASP cc_start: 0.9016 (m-30) cc_final: 0.8470 (t0) REVERT: A 983 ARG cc_start: 0.8762 (ptt90) cc_final: 0.7819 (ttp80) REVERT: A 990 GLU cc_start: 0.8639 (tt0) cc_final: 0.8270 (mt-10) REVERT: A 994 ASP cc_start: 0.8665 (m-30) cc_final: 0.8211 (m-30) REVERT: A 995 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8191 (ttm-80) REVERT: A 996 LEU cc_start: 0.9379 (mt) cc_final: 0.9162 (mt) REVERT: A 998 THR cc_start: 0.9313 (m) cc_final: 0.9042 (p) REVERT: A 1000 ARG cc_start: 0.9076 (mmt180) cc_final: 0.8266 (mmt180) REVERT: A 1001 LEU cc_start: 0.9072 (mt) cc_final: 0.8614 (mm) REVERT: A 1002 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 1005 GLN cc_start: 0.8872 (mt0) cc_final: 0.8584 (mm-40) REVERT: A 1011 GLN cc_start: 0.8983 (tp40) cc_final: 0.8056 (mm-40) REVERT: A 1014 ARG cc_start: 0.8817 (mmp-170) cc_final: 0.8541 (mmp80) REVERT: A 1023 ASN cc_start: 0.8847 (m110) cc_final: 0.8582 (m-40) REVERT: A 1050 MET cc_start: 0.5862 (ttt) cc_final: 0.5297 (ttt) REVERT: A 1053 PRO cc_start: 0.8759 (Cg_endo) cc_final: 0.8354 (Cg_exo) REVERT: A 1054 GLN cc_start: 0.6504 (mp10) cc_final: 0.6093 (mp10) REVERT: B 37 TYR cc_start: 0.8418 (p90) cc_final: 0.8025 (p90) REVERT: B 41 LYS cc_start: 0.8737 (tppt) cc_final: 0.8264 (tppt) REVERT: B 56 LEU cc_start: 0.8967 (tp) cc_final: 0.8477 (pp) REVERT: B 86 PHE cc_start: 0.7876 (t80) cc_final: 0.7589 (t80) REVERT: B 99 ASN cc_start: 0.8530 (t0) cc_final: 0.7970 (t0) REVERT: B 104 TRP cc_start: 0.5557 (m-10) cc_final: 0.4811 (m-10) REVERT: B 105 ILE cc_start: 0.8886 (mp) cc_final: 0.8544 (tp) REVERT: B 129 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8080 (mmmt) REVERT: B 276 LEU cc_start: 0.8799 (tt) cc_final: 0.8277 (mp) REVERT: B 298 GLU cc_start: 0.8567 (tt0) cc_final: 0.8186 (tt0) REVERT: B 313 TYR cc_start: 0.7602 (m-80) cc_final: 0.7045 (m-10) REVERT: B 543 PHE cc_start: 0.8486 (p90) cc_final: 0.8181 (p90) REVERT: B 562 PHE cc_start: 0.8998 (p90) cc_final: 0.8494 (p90) REVERT: B 577 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7770 (tpt170) REVERT: B 586 ASP cc_start: 0.8425 (t0) cc_final: 0.7640 (p0) REVERT: B 587 ILE cc_start: 0.8892 (mp) cc_final: 0.8677 (mp) REVERT: B 753 LEU cc_start: 0.8699 (tp) cc_final: 0.8407 (tp) REVERT: B 754 LEU cc_start: 0.8909 (mt) cc_final: 0.8660 (tp) REVERT: B 819 GLU cc_start: 0.8836 (pt0) cc_final: 0.8391 (tm-30) REVERT: B 820 ASP cc_start: 0.8722 (t0) cc_final: 0.8477 (t0) REVERT: B 824 ASN cc_start: 0.8955 (m110) cc_final: 0.8651 (m110) REVERT: B 869 MET cc_start: 0.8568 (mpp) cc_final: 0.7810 (mpp) REVERT: B 873 TYR cc_start: 0.7848 (m-10) cc_final: 0.7331 (m-80) REVERT: B 917 TYR cc_start: 0.8691 (m-10) cc_final: 0.8349 (m-10) REVERT: B 927 PHE cc_start: 0.8438 (t80) cc_final: 0.7682 (t80) REVERT: B 937 SER cc_start: 0.8781 (t) cc_final: 0.8426 (p) REVERT: B 954 GLN cc_start: 0.9056 (mt0) cc_final: 0.8698 (tm-30) REVERT: B 960 ASN cc_start: 0.8942 (t0) cc_final: 0.8603 (t0) REVERT: B 964 LYS cc_start: 0.9306 (pttt) cc_final: 0.8944 (pttm) REVERT: B 983 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7513 (ttp-170) REVERT: B 1000 ARG cc_start: 0.8928 (ptp-110) cc_final: 0.8501 (mtp-110) REVERT: B 1002 GLN cc_start: 0.8835 (mp10) cc_final: 0.8170 (pm20) REVERT: B 1009 THR cc_start: 0.9185 (p) cc_final: 0.8973 (p) REVERT: B 1010 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8448 (mm-40) REVERT: B 1011 GLN cc_start: 0.8761 (mm110) cc_final: 0.8008 (mm-40) REVERT: B 1014 ARG cc_start: 0.8895 (mmt-90) cc_final: 0.8694 (mpt180) REVERT: B 1017 GLU cc_start: 0.8780 (pp20) cc_final: 0.8256 (pp20) REVERT: B 1019 ARG cc_start: 0.8973 (ptm-80) cc_final: 0.8405 (ptm-80) REVERT: B 1028 LYS cc_start: 0.7281 (tptt) cc_final: 0.6965 (tmtt) REVERT: B 1048 HIS cc_start: 0.6875 (p-80) cc_final: 0.6586 (p-80) REVERT: C 34 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8207 (mmm160) REVERT: C 41 LYS cc_start: 0.8175 (tppt) cc_final: 0.7668 (tppt) REVERT: C 65 PHE cc_start: 0.8276 (m-80) cc_final: 0.7739 (m-80) REVERT: C 91 TYR cc_start: 0.7814 (t80) cc_final: 0.7070 (t80) REVERT: C 92 PHE cc_start: 0.8300 (t80) cc_final: 0.7731 (t80) REVERT: C 117 LEU cc_start: 0.8749 (tt) cc_final: 0.8311 (pp) REVERT: C 129 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8683 (tptp) REVERT: C 133 PHE cc_start: 0.8346 (m-80) cc_final: 0.7694 (m-80) REVERT: C 194 PHE cc_start: 0.7775 (m-80) cc_final: 0.7232 (m-80) REVERT: C 201 PHE cc_start: 0.8501 (t80) cc_final: 0.8297 (t80) REVERT: C 223 LEU cc_start: 0.8067 (pt) cc_final: 0.7673 (pt) REVERT: C 237 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8450 (mmm-85) REVERT: C 276 LEU cc_start: 0.8425 (tp) cc_final: 0.8193 (tp) REVERT: C 281 GLU cc_start: 0.8197 (tp30) cc_final: 0.7897 (tp30) REVERT: C 296 LEU cc_start: 0.8494 (pp) cc_final: 0.8229 (pp) REVERT: C 300 LYS cc_start: 0.8337 (mttt) cc_final: 0.7805 (mmtt) REVERT: C 313 TYR cc_start: 0.7622 (m-10) cc_final: 0.7162 (m-10) REVERT: C 324 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8432 (mp0) REVERT: C 338 PHE cc_start: 0.9057 (m-80) cc_final: 0.8563 (m-10) REVERT: C 342 PHE cc_start: 0.8733 (m-80) cc_final: 0.8317 (m-80) REVERT: C 353 TRP cc_start: 0.7361 (p-90) cc_final: 0.7112 (p90) REVERT: C 354 ASN cc_start: 0.8853 (t0) cc_final: 0.8601 (t0) REVERT: C 365 TYR cc_start: 0.9074 (m-10) cc_final: 0.8551 (m-10) REVERT: C 377 PHE cc_start: 0.7708 (t80) cc_final: 0.7448 (t80) REVERT: C 380 TYR cc_start: 0.7536 (m-80) cc_final: 0.7162 (m-80) REVERT: C 386 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8258 (mtmt) REVERT: C 417 LYS cc_start: 0.9072 (tptt) cc_final: 0.8793 (tppt) REVERT: C 421 TYR cc_start: 0.8712 (m-10) cc_final: 0.8344 (m-80) REVERT: C 425 LEU cc_start: 0.8410 (mt) cc_final: 0.8083 (tp) REVERT: C 451 TYR cc_start: 0.6165 (m-80) cc_final: 0.5868 (m-80) REVERT: C 505 TYR cc_start: 0.8418 (t80) cc_final: 0.7960 (t80) REVERT: C 563 GLN cc_start: 0.7668 (mm-40) cc_final: 0.6905 (mm-40) REVERT: C 737 ASP cc_start: 0.8764 (t0) cc_final: 0.8258 (t0) REVERT: C 747 THR cc_start: 0.8989 (p) cc_final: 0.8771 (p) REVERT: C 755 GLN cc_start: 0.9249 (pt0) cc_final: 0.8986 (pt0) REVERT: C 762 GLN cc_start: 0.8851 (mt0) cc_final: 0.8378 (mt0) REVERT: C 763 LEU cc_start: 0.9102 (mt) cc_final: 0.8862 (mt) REVERT: C 765 ARG cc_start: 0.9097 (ptp-170) cc_final: 0.8514 (ptp90) REVERT: C 776 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8243 (tmtt) REVERT: C 869 MET cc_start: 0.9123 (mtm) cc_final: 0.8370 (mmt) REVERT: C 873 TYR cc_start: 0.8225 (m-10) cc_final: 0.7810 (m-80) REVERT: C 954 GLN cc_start: 0.8957 (mt0) cc_final: 0.8719 (tm-30) REVERT: C 959 LEU cc_start: 0.9176 (mp) cc_final: 0.8917 (pp) REVERT: C 960 ASN cc_start: 0.8836 (m110) cc_final: 0.8452 (m110) REVERT: C 969 ASN cc_start: 0.8689 (p0) cc_final: 0.8389 (p0) REVERT: C 970 PHE cc_start: 0.8084 (m-80) cc_final: 0.7472 (m-10) REVERT: C 979 ASP cc_start: 0.9062 (m-30) cc_final: 0.8676 (m-30) REVERT: C 981 LEU cc_start: 0.9187 (mp) cc_final: 0.8863 (pp) REVERT: C 983 ARG cc_start: 0.8996 (tmt-80) cc_final: 0.8769 (tpt90) REVERT: C 984 LEU cc_start: 0.8814 (tp) cc_final: 0.8610 (tp) REVERT: C 994 ASP cc_start: 0.8855 (m-30) cc_final: 0.8601 (m-30) REVERT: C 995 ARG cc_start: 0.8791 (mtt180) cc_final: 0.8166 (mtm180) REVERT: C 1000 ARG cc_start: 0.9150 (mtt-85) cc_final: 0.8559 (mmm160) REVERT: C 1010 GLN cc_start: 0.8790 (tp-100) cc_final: 0.7776 (tm-30) REVERT: C 1011 GLN cc_start: 0.8984 (pt0) cc_final: 0.8371 (pt0) REVERT: C 1013 ILE cc_start: 0.9461 (mm) cc_final: 0.8554 (pt) REVERT: C 1017 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8438 (mp0) REVERT: C 1019 ARG cc_start: 0.9001 (ptp90) cc_final: 0.8653 (ptt-90) REVERT: C 1028 LYS cc_start: 0.6981 (tttt) cc_final: 0.6619 (tttt) REVERT: C 1050 MET cc_start: 0.3503 (ttt) cc_final: 0.2281 (ttt) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.1886 time to fit residues: 150.0574 Evaluate side-chains 469 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 214 optimal weight: 50.0000 chunk 267 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 164 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 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 606 ASN B 764 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.162981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.119645 restraints weight = 67347.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124583 restraints weight = 46907.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.128146 restraints weight = 35523.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.130777 restraints weight = 28613.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.132633 restraints weight = 24126.451| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 26386 Z= 0.242 Angle : 0.784 11.203 36017 Z= 0.407 Chirality : 0.050 0.342 4182 Planarity : 0.005 0.085 4587 Dihedral : 8.150 94.284 4373 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3187 helix: 0.09 (0.19), residues: 673 sheet: -0.98 (0.20), residues: 616 loop : -1.58 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 454 TYR 0.027 0.002 TYR B 904 PHE 0.041 0.002 PHE B 194 TRP 0.025 0.002 TRP B 104 HIS 0.012 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00478 (26300) covalent geometry : angle 0.76025 (35807) SS BOND : bond 0.00503 ( 42) SS BOND : angle 2.25427 ( 84) hydrogen bonds : bond 0.05177 ( 872) hydrogen bonds : angle 6.50940 ( 2433) Misc. bond : bond 0.00533 ( 2) link_BETA1-4 : bond 0.00656 ( 10) link_BETA1-4 : angle 1.46750 ( 30) link_NAG-ASN : bond 0.00602 ( 32) link_NAG-ASN : angle 3.19312 ( 96) ********************** 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 533 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 0.895 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 43 PHE cc_start: 0.8203 (t80) cc_final: 0.7913 (t80) REVERT: A 53 ASP cc_start: 0.8506 (t0) cc_final: 0.8194 (t0) REVERT: A 56 LEU cc_start: 0.9208 (tp) cc_final: 0.8967 (tp) REVERT: A 65 PHE cc_start: 0.8146 (m-80) cc_final: 0.7591 (m-80) REVERT: A 91 TYR cc_start: 0.7063 (t80) cc_final: 0.6863 (t80) REVERT: A 118 LEU cc_start: 0.8640 (mm) cc_final: 0.8434 (mt) REVERT: A 128 ILE cc_start: 0.8755 (mp) cc_final: 0.8328 (mm) REVERT: A 135 PHE cc_start: 0.8051 (m-80) cc_final: 0.7599 (m-80) REVERT: A 170 TYR cc_start: 0.8044 (t80) cc_final: 0.7565 (t80) REVERT: A 192 PHE cc_start: 0.8411 (m-10) cc_final: 0.8157 (m-10) REVERT: A 194 PHE cc_start: 0.8376 (m-80) cc_final: 0.8154 (m-80) REVERT: A 195 LYS cc_start: 0.8343 (tptp) cc_final: 0.8059 (tptt) REVERT: A 240 THR cc_start: 0.8550 (m) cc_final: 0.8072 (m) REVERT: A 275 PHE cc_start: 0.6690 (m-10) cc_final: 0.6180 (m-10) REVERT: A 317 ASN cc_start: 0.8378 (p0) cc_final: 0.7782 (p0) REVERT: A 365 TYR cc_start: 0.8237 (m-80) cc_final: 0.7932 (m-80) REVERT: A 380 TYR cc_start: 0.8164 (m-80) cc_final: 0.7788 (m-80) REVERT: A 389 ASP cc_start: 0.8936 (m-30) cc_final: 0.8484 (p0) REVERT: A 408 ARG cc_start: 0.8892 (pmt-80) cc_final: 0.8673 (pmt-80) REVERT: A 461 LEU cc_start: 0.8095 (mt) cc_final: 0.7686 (mt) REVERT: A 585 LEU cc_start: 0.8681 (mp) cc_final: 0.8456 (mp) REVERT: A 731 MET cc_start: 0.8721 (ppp) cc_final: 0.8323 (ppp) REVERT: A 752 LEU cc_start: 0.9236 (tt) cc_final: 0.8888 (pp) REVERT: A 759 PHE cc_start: 0.8917 (m-80) cc_final: 0.8079 (m-80) REVERT: A 776 LYS cc_start: 0.8971 (tptm) cc_final: 0.8379 (tptp) REVERT: A 869 MET cc_start: 0.8243 (pmm) cc_final: 0.7731 (pmm) REVERT: A 873 TYR cc_start: 0.8505 (m-10) cc_final: 0.8122 (m-80) REVERT: A 917 TYR cc_start: 0.8081 (m-80) cc_final: 0.7416 (m-10) REVERT: A 927 PHE cc_start: 0.7959 (t80) cc_final: 0.7401 (t80) REVERT: A 936 ASP cc_start: 0.8838 (m-30) cc_final: 0.8421 (t0) REVERT: A 947 LYS cc_start: 0.6989 (pttt) cc_final: 0.6709 (pttm) REVERT: A 954 GLN cc_start: 0.9057 (tp40) cc_final: 0.8692 (tm-30) REVERT: A 959 LEU cc_start: 0.9364 (mp) cc_final: 0.9125 (mm) REVERT: A 960 ASN cc_start: 0.8801 (t0) cc_final: 0.8161 (m110) REVERT: A 964 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8856 (ptpp) REVERT: A 965 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 979 ASP cc_start: 0.9011 (m-30) cc_final: 0.8460 (t0) REVERT: A 983 ARG cc_start: 0.8800 (ptt90) cc_final: 0.7826 (ttp80) REVERT: A 990 GLU cc_start: 0.8756 (tt0) cc_final: 0.8492 (mt-10) REVERT: A 994 ASP cc_start: 0.8836 (m-30) cc_final: 0.8365 (m-30) REVERT: A 995 ARG cc_start: 0.8911 (ttm110) cc_final: 0.8273 (ttm-80) REVERT: A 998 THR cc_start: 0.9337 (m) cc_final: 0.9079 (p) REVERT: A 1000 ARG cc_start: 0.9082 (mmt180) cc_final: 0.8390 (mmt180) REVERT: A 1001 LEU cc_start: 0.9124 (mt) cc_final: 0.8715 (mm) REVERT: A 1002 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 1005 GLN cc_start: 0.9017 (mt0) cc_final: 0.8729 (mm-40) REVERT: A 1011 GLN cc_start: 0.9043 (tp40) cc_final: 0.8026 (mm-40) REVERT: A 1014 ARG cc_start: 0.8871 (mmp-170) cc_final: 0.8587 (mmp80) REVERT: A 1019 ARG cc_start: 0.9007 (ttt180) cc_final: 0.8374 (ttm110) REVERT: A 1023 ASN cc_start: 0.8909 (m110) cc_final: 0.8620 (m-40) REVERT: A 1050 MET cc_start: 0.6110 (ttt) cc_final: 0.5492 (ttt) REVERT: A 1053 PRO cc_start: 0.8990 (Cg_endo) cc_final: 0.8482 (Cg_exo) REVERT: A 1062 PHE cc_start: 0.5935 (m-80) cc_final: 0.5604 (m-80) REVERT: B 37 TYR cc_start: 0.8567 (p90) cc_final: 0.8062 (p90) REVERT: B 41 LYS cc_start: 0.8689 (tppt) cc_final: 0.8178 (tmmt) REVERT: B 56 LEU cc_start: 0.9050 (tp) cc_final: 0.8570 (pp) REVERT: B 104 TRP cc_start: 0.6048 (m-10) cc_final: 0.5411 (m-10) REVERT: B 105 ILE cc_start: 0.8916 (mp) cc_final: 0.8536 (tp) REVERT: B 265 TYR cc_start: 0.7423 (p90) cc_final: 0.7108 (p90) REVERT: B 276 LEU cc_start: 0.8789 (tt) cc_final: 0.8287 (mp) REVERT: B 298 GLU cc_start: 0.8535 (tt0) cc_final: 0.8176 (tt0) REVERT: B 313 TYR cc_start: 0.7609 (m-80) cc_final: 0.6909 (m-10) REVERT: B 321 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7800 (pp30) REVERT: B 543 PHE cc_start: 0.8634 (p90) cc_final: 0.8268 (p90) REVERT: B 562 PHE cc_start: 0.9017 (p90) cc_final: 0.8516 (p90) REVERT: B 577 ARG cc_start: 0.8069 (ttm170) cc_final: 0.7599 (tpt170) REVERT: B 586 ASP cc_start: 0.8447 (t0) cc_final: 0.7655 (p0) REVERT: B 587 ILE cc_start: 0.8883 (mp) cc_final: 0.8664 (mp) REVERT: B 753 LEU cc_start: 0.8782 (tp) cc_final: 0.8481 (tp) REVERT: B 754 LEU cc_start: 0.8861 (mt) cc_final: 0.8619 (tp) REVERT: B 819 GLU cc_start: 0.8864 (pt0) cc_final: 0.8318 (tm-30) REVERT: B 820 ASP cc_start: 0.8772 (t0) cc_final: 0.8524 (t0) REVERT: B 824 ASN cc_start: 0.9093 (m110) cc_final: 0.8856 (m-40) REVERT: B 869 MET cc_start: 0.9021 (mpp) cc_final: 0.8050 (mpp) REVERT: B 873 TYR cc_start: 0.7841 (m-10) cc_final: 0.7586 (m-80) REVERT: B 877 LEU cc_start: 0.8323 (tt) cc_final: 0.8059 (mt) REVERT: B 917 TYR cc_start: 0.8742 (m-10) cc_final: 0.8472 (m-10) REVERT: B 927 PHE cc_start: 0.8473 (t80) cc_final: 0.7735 (t80) REVERT: B 937 SER cc_start: 0.8843 (t) cc_final: 0.8503 (p) REVERT: B 947 LYS cc_start: 0.7325 (mttt) cc_final: 0.7026 (mttt) REVERT: B 954 GLN cc_start: 0.9084 (mt0) cc_final: 0.8738 (tm-30) REVERT: B 960 ASN cc_start: 0.9034 (t0) cc_final: 0.8492 (t0) REVERT: B 964 LYS cc_start: 0.9296 (pttt) cc_final: 0.8966 (pttm) REVERT: B 979 ASP cc_start: 0.8813 (t0) cc_final: 0.8570 (t0) REVERT: B 983 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7553 (ttp-170) REVERT: B 995 ARG cc_start: 0.8777 (ptt-90) cc_final: 0.8520 (ptt-90) REVERT: B 1000 ARG cc_start: 0.9068 (ptp-110) cc_final: 0.8389 (mtp-110) REVERT: B 1002 GLN cc_start: 0.8747 (mp10) cc_final: 0.8338 (pm20) REVERT: B 1010 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8551 (mm-40) REVERT: B 1011 GLN cc_start: 0.8947 (mm110) cc_final: 0.8277 (mm-40) REVERT: B 1014 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8401 (mmp80) REVERT: B 1017 GLU cc_start: 0.8799 (pp20) cc_final: 0.8264 (pp20) REVERT: B 1019 ARG cc_start: 0.8925 (ptm-80) cc_final: 0.8352 (ptm-80) REVERT: B 1028 LYS cc_start: 0.7299 (tptt) cc_final: 0.6985 (tmtt) REVERT: B 1048 HIS cc_start: 0.7094 (p-80) cc_final: 0.6793 (p-80) REVERT: C 34 ARG cc_start: 0.8576 (mmm160) cc_final: 0.8120 (mmm160) REVERT: C 41 LYS cc_start: 0.8218 (tppt) cc_final: 0.7726 (tppt) REVERT: C 65 PHE cc_start: 0.8250 (m-80) cc_final: 0.7660 (m-80) REVERT: C 91 TYR cc_start: 0.7622 (t80) cc_final: 0.7082 (t80) REVERT: C 92 PHE cc_start: 0.8378 (t80) cc_final: 0.7663 (t80) REVERT: C 117 LEU cc_start: 0.8778 (tt) cc_final: 0.8335 (pp) REVERT: C 129 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8492 (tptp) REVERT: C 133 PHE cc_start: 0.8308 (m-80) cc_final: 0.7690 (m-80) REVERT: C 160 TYR cc_start: 0.8793 (p90) cc_final: 0.8510 (p90) REVERT: C 194 PHE cc_start: 0.7860 (m-80) cc_final: 0.7156 (m-80) REVERT: C 223 LEU cc_start: 0.8485 (pt) cc_final: 0.8110 (pt) REVERT: C 276 LEU cc_start: 0.8515 (tp) cc_final: 0.8260 (tp) REVERT: C 281 GLU cc_start: 0.8179 (tp30) cc_final: 0.7917 (tp30) REVERT: C 300 LYS cc_start: 0.8425 (mttt) cc_final: 0.7931 (mmtt) REVERT: C 313 TYR cc_start: 0.7605 (m-10) cc_final: 0.7076 (m-10) REVERT: C 324 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8526 (mp0) REVERT: C 338 PHE cc_start: 0.9112 (m-80) cc_final: 0.8511 (m-10) REVERT: C 342 PHE cc_start: 0.8762 (m-80) cc_final: 0.8374 (m-80) REVERT: C 353 TRP cc_start: 0.7298 (p-90) cc_final: 0.6968 (p90) REVERT: C 354 ASN cc_start: 0.8865 (t0) cc_final: 0.8609 (t0) REVERT: C 365 TYR cc_start: 0.9145 (m-10) cc_final: 0.8506 (m-10) REVERT: C 377 PHE cc_start: 0.7961 (t80) cc_final: 0.7647 (t80) REVERT: C 380 TYR cc_start: 0.7624 (m-80) cc_final: 0.7215 (m-80) REVERT: C 386 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8271 (mtmt) REVERT: C 417 LYS cc_start: 0.9088 (tptt) cc_final: 0.8790 (tppt) REVERT: C 418 ILE cc_start: 0.9443 (pt) cc_final: 0.8930 (mt) REVERT: C 421 TYR cc_start: 0.8792 (m-10) cc_final: 0.8256 (m-10) REVERT: C 425 LEU cc_start: 0.8509 (mt) cc_final: 0.8105 (tp) REVERT: C 426 PRO cc_start: 0.8613 (Cg_exo) cc_final: 0.7887 (Cg_endo) REVERT: C 451 TYR cc_start: 0.6589 (m-80) cc_final: 0.6295 (m-80) REVERT: C 464 PHE cc_start: 0.7918 (p90) cc_final: 0.7479 (p90) REVERT: C 490 PHE cc_start: 0.8762 (t80) cc_final: 0.8353 (t80) REVERT: C 505 TYR cc_start: 0.8704 (t80) cc_final: 0.8242 (t80) REVERT: C 516 GLU cc_start: 0.7807 (mp0) cc_final: 0.7536 (mp0) REVERT: C 535 LYS cc_start: 0.8956 (mmpt) cc_final: 0.8741 (mmmt) REVERT: C 543 PHE cc_start: 0.8599 (m-80) cc_final: 0.8385 (m-80) REVERT: C 558 LYS cc_start: 0.8782 (tmtt) cc_final: 0.8570 (tptp) REVERT: C 562 PHE cc_start: 0.8673 (p90) cc_final: 0.8448 (p90) REVERT: C 563 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7016 (mm-40) REVERT: C 737 ASP cc_start: 0.8738 (t0) cc_final: 0.7724 (p0) REVERT: C 740 MET cc_start: 0.8824 (tpt) cc_final: 0.8616 (tpp) REVERT: C 755 GLN cc_start: 0.9260 (pt0) cc_final: 0.9027 (pt0) REVERT: C 761 THR cc_start: 0.9266 (p) cc_final: 0.8797 (p) REVERT: C 763 LEU cc_start: 0.9099 (mt) cc_final: 0.8867 (mt) REVERT: C 764 ASN cc_start: 0.8873 (m110) cc_final: 0.8523 (m110) REVERT: C 765 ARG cc_start: 0.9135 (ptp-170) cc_final: 0.8542 (ptp-170) REVERT: C 773 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7996 (mm-30) REVERT: C 776 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8246 (tmtt) REVERT: C 802 PHE cc_start: 0.5355 (m-80) cc_final: 0.5005 (m-80) REVERT: C 869 MET cc_start: 0.9148 (mtm) cc_final: 0.8177 (tmm) REVERT: C 954 GLN cc_start: 0.8999 (mt0) cc_final: 0.8760 (tm-30) REVERT: C 959 LEU cc_start: 0.9220 (mp) cc_final: 0.8946 (pp) REVERT: C 960 ASN cc_start: 0.8871 (m110) cc_final: 0.8495 (m110) REVERT: C 969 ASN cc_start: 0.8731 (p0) cc_final: 0.8432 (p0) REVERT: C 970 PHE cc_start: 0.8154 (m-80) cc_final: 0.7483 (m-10) REVERT: C 979 ASP cc_start: 0.9177 (m-30) cc_final: 0.8830 (m-30) REVERT: C 981 LEU cc_start: 0.9240 (mp) cc_final: 0.8947 (pp) REVERT: C 983 ARG cc_start: 0.9009 (tmt-80) cc_final: 0.8793 (tpt90) REVERT: C 984 LEU cc_start: 0.8767 (tp) cc_final: 0.8527 (tp) REVERT: C 994 ASP cc_start: 0.8929 (m-30) cc_final: 0.8678 (m-30) REVERT: C 995 ARG cc_start: 0.8891 (mtt180) cc_final: 0.8229 (mtm180) REVERT: C 1000 ARG cc_start: 0.9349 (mtt-85) cc_final: 0.8938 (mmm160) REVERT: C 1010 GLN cc_start: 0.8805 (tp-100) cc_final: 0.7654 (tm-30) REVERT: C 1011 GLN cc_start: 0.8976 (pt0) cc_final: 0.8370 (pt0) REVERT: C 1014 ARG cc_start: 0.8670 (mmp80) cc_final: 0.7381 (mmp80) REVERT: C 1017 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8612 (tm-30) REVERT: C 1018 ILE cc_start: 0.8744 (pt) cc_final: 0.8312 (pt) REVERT: C 1019 ARG cc_start: 0.8963 (ptp90) cc_final: 0.8594 (ptt-90) REVERT: C 1028 LYS cc_start: 0.6603 (tttt) cc_final: 0.6220 (tttp) REVERT: C 1050 MET cc_start: 0.3923 (ttt) cc_final: 0.3128 (ttt) outliers start: 1 outliers final: 0 residues processed: 532 average time/residue: 0.1844 time to fit residues: 150.3172 Evaluate side-chains 473 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 46 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 223 optimal weight: 0.0070 chunk 196 optimal weight: 0.0470 chunk 40 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 164 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1036 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 935 GLN C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1088 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 = 0.4554 r_free = 0.4554 target = 0.171919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.125531 restraints weight = 64659.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.130248 restraints weight = 46140.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.133725 restraints weight = 35759.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.136321 restraints weight = 29326.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.138235 restraints weight = 25112.068| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.8174 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= 0.147 Angle : 0.758 14.547 36017 Z= 0.379 Chirality : 0.050 0.487 4182 Planarity : 0.005 0.079 4587 Dihedral : 7.982 93.342 4373 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3187 helix: 0.29 (0.19), residues: 672 sheet: -0.87 (0.20), residues: 614 loop : -1.50 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 815 TYR 0.029 0.002 TYR C 453 PHE 0.061 0.002 PHE A1109 TRP 0.024 0.002 TRP B 436 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00322 (26300) covalent geometry : angle 0.73201 (35807) SS BOND : bond 0.00293 ( 42) SS BOND : angle 2.18820 ( 84) hydrogen bonds : bond 0.04422 ( 872) hydrogen bonds : angle 6.23885 ( 2433) Misc. bond : bond 0.00529 ( 2) link_BETA1-4 : bond 0.00424 ( 10) link_BETA1-4 : angle 1.33537 ( 30) link_NAG-ASN : bond 0.00666 ( 32) link_NAG-ASN : angle 3.35031 ( 96) =============================================================================== Job complete usr+sys time: 5847.42 seconds wall clock time: 101 minutes 36.31 seconds (6096.31 seconds total)