Starting phenix.real_space_refine on Sun Jul 5 03:39:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qdh_13919/07_2026/7qdh_13919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdh_13919/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qdh_13919/07_2026/7qdh_13919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdh_13919/07_2026/7qdh_13919.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qdh_13919/07_2026/7qdh_13919.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qdh_13919/07_2026/7qdh_13919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qdh_13919/07_2026/7qdh_13919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdh_13919/07_2026/7qdh_13919.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 5.73, per 1000 atoms: 0.22 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: 2.45 Conformation dependent library (CDL) restraints added in 985.5 milliseconds 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: 1.09 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: 6.33 Time building geometry restraints manager: 3.20 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 - 17.36: 13722 17.36 - 34.72: 1255 34.72 - 52.08: 244 52.08 - 69.44: 55 69.44 - 86.80: 25 Dihedral angle restraints: 15301 sinusoidal: 5934 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 15298 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: 1.790 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.660 Find NCS groups from input model: 0.750 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 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 : 13.720 86.795 9153 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/Z covalent geometry : bond 0.01085 / 0.71 (26300) covalent geometry : angle 1.49889 / 0.94 (35807) SS BOND : bond 0.35443 / 22.75 ( 42) SS BOND : angle 13.24096 / 9.89 ( 84) hydrogen bonds : bond 0.28264 / 18.78 ( 872) hydrogen bonds : angle 9.68542 / 6.67 ( 2433) Misc. bond : bond 0.32817 / 15.80 ( 2) link_BETA1-4 : bond 0.00312 / 0.24 ( 10) link_BETA1-4 : angle 2.00118 / 1.37 ( 30) link_NAG-ASN : bond 0.01451 / 0.92 ( 32) link_NAG-ASN : angle 7.39878 / 5.39 ( 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 : 0.949 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: 0.1837 time to fit residues: 241.1285 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 : 0.937 ------------------------------------------------------------------------------- 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... 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4674 r_free = 0.4674 target = 0.182262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.136073 restraints weight = 67109.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.141178 restraints weight = 47022.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.144861 restraints weight = 35801.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.147554 restraints weight = 28946.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.149500 restraints weight = 24550.493| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 26386 Z= 0.229 Angle : 0.903 21.970 36017 Z= 0.452 Chirality : 0.055 0.668 4182 Planarity : 0.006 0.061 4587 Dihedral : 5.597 31.099 3449 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 0.54 % Allowed : 5.69 % Favored : 93.77 % 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: -0.46 (0.14), residues: 3187 helix: 1.16 (0.19), residues: 684 sheet: 0.08 (0.20), residues: 655 loop : -1.03 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B1107 TYR 0.036 0.002 TYR C 904 PHE 0.030 0.003 PHE B 823 TRP 0.050 0.003 TRP A 64 HIS 0.016 0.003 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (26300) covalent geometry : angle 0.85607 / 0.44 (35807) SS BOND : bond 0.00639 / 0.41 ( 42) SS BOND : angle 2.91436 / 1.94 ( 84) hydrogen bonds : bond 0.06556 / 4.46 ( 872) hydrogen bonds : angle 7.21284 / 4.89 ( 2433) Misc. bond : bond 0.00553 / 0.29 ( 2) link_BETA1-4 : bond 0.00482 / 0.37 ( 10) link_BETA1-4 : angle 1.61701 / 1.05 ( 30) link_NAG-ASN : bond 0.00987 / 0.63 ( 32) link_NAG-ASN : angle 4.91829 / 3.48 ( 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 580 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 565 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8533 (mmtt) cc_final: 0.7827 (ttpt) REVERT: A 53 ASP cc_start: 0.8447 (t0) cc_final: 0.8052 (t0) REVERT: A 65 PHE cc_start: 0.7667 (m-80) cc_final: 0.7121 (m-80) REVERT: A 104 TRP cc_start: 0.6155 (m-90) cc_final: 0.5442 (m-90) REVERT: A 128 ILE cc_start: 0.8554 (mt) cc_final: 0.7481 (mt) REVERT: A 170 TYR cc_start: 0.7451 (t80) cc_final: 0.6965 (t80) REVERT: A 189 LEU cc_start: 0.8355 (tp) cc_final: 0.8044 (tp) REVERT: A 194 PHE cc_start: 0.9049 (m-80) cc_final: 0.8137 (m-80) REVERT: A 195 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8465 (ttpp) REVERT: A 202 LYS cc_start: 0.7858 (mttt) cc_final: 0.7273 (mttp) REVERT: A 275 PHE cc_start: 0.6760 (m-10) cc_final: 0.5802 (m-10) REVERT: A 304 LYS cc_start: 0.8825 (tppp) cc_final: 0.8468 (tptt) REVERT: A 312 ILE cc_start: 0.8402 (tt) cc_final: 0.8141 (tt) REVERT: A 313 TYR cc_start: 0.8294 (m-10) cc_final: 0.7921 (m-10) REVERT: A 380 TYR cc_start: 0.7847 (m-80) cc_final: 0.7414 (m-80) REVERT: A 386 LYS cc_start: 0.8675 (mttp) cc_final: 0.8413 (mmmm) REVERT: A 421 TYR cc_start: 0.8499 (m-10) cc_final: 0.7940 (m-10) REVERT: A 462 LYS cc_start: 0.7905 (mmtm) cc_final: 0.6915 (ttpp) REVERT: A 535 LYS cc_start: 0.7948 (mttm) cc_final: 0.7657 (ttmm) REVERT: A 562 PHE cc_start: 0.7968 (p90) cc_final: 0.7660 (p90) REVERT: A 585 LEU cc_start: 0.8497 (mt) cc_final: 0.7971 (tt) REVERT: A 586 ASP cc_start: 0.7217 (p0) cc_final: 0.6918 (p0) REVERT: A 751 ASN cc_start: 0.8829 (m110) cc_final: 0.8583 (m110) REVERT: A 752 LEU cc_start: 0.8815 (mt) cc_final: 0.8420 (tt) REVERT: A 755 GLN cc_start: 0.8155 (mp10) cc_final: 0.7659 (tt0) REVERT: A 759 PHE cc_start: 0.8690 (m-80) cc_final: 0.8448 (m-80) REVERT: A 762 GLN cc_start: 0.8949 (pt0) cc_final: 0.8665 (pt0) REVERT: A 764 ASN cc_start: 0.8806 (m110) cc_final: 0.8397 (m110) REVERT: A 796 ASP cc_start: 0.7779 (m-30) cc_final: 0.7288 (p0) REVERT: A 867 ASP cc_start: 0.7604 (m-30) cc_final: 0.7201 (p0) REVERT: A 900 MET cc_start: 0.7540 (tmm) cc_final: 0.7179 (tmm) REVERT: A 917 TYR cc_start: 0.8674 (m-80) cc_final: 0.8213 (m-80) REVERT: A 927 PHE cc_start: 0.7604 (t80) cc_final: 0.7295 (t80) REVERT: A 947 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7488 (pttt) REVERT: A 954 GLN cc_start: 0.9088 (tp40) cc_final: 0.8572 (tm-30) REVERT: A 965 GLN cc_start: 0.8521 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 968 SER cc_start: 0.8456 (m) cc_final: 0.7679 (t) REVERT: A 983 ARG cc_start: 0.8890 (ptt90) cc_final: 0.8518 (ttp80) REVERT: A 990 GLU cc_start: 0.8796 (tt0) cc_final: 0.8452 (mt-10) REVERT: A 993 ILE cc_start: 0.8900 (mt) cc_final: 0.8591 (pt) REVERT: A 994 ASP cc_start: 0.8719 (m-30) cc_final: 0.8078 (m-30) REVERT: A 1001 LEU cc_start: 0.9343 (mt) cc_final: 0.8822 (pp) REVERT: A 1002 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 1018 ILE cc_start: 0.8797 (mm) cc_final: 0.8442 (tt) REVERT: A 1019 ARG cc_start: 0.8948 (ttt180) cc_final: 0.8177 (ttm110) REVERT: A 1109 PHE cc_start: 0.7319 (t80) cc_final: 0.6972 (t80) REVERT: B 44 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7101 (mtm-85) REVERT: B 48 LEU cc_start: 0.8498 (mp) cc_final: 0.7636 (mt) REVERT: B 58 PHE cc_start: 0.8039 (m-80) cc_final: 0.7275 (m-80) REVERT: B 59 PHE cc_start: 0.7226 (t80) cc_final: 0.6966 (t80) REVERT: B 63 THR cc_start: 0.7949 (p) cc_final: 0.6709 (t) REVERT: B 64 TRP cc_start: 0.8773 (t60) cc_final: 0.8548 (t-100) REVERT: B 65 PHE cc_start: 0.8247 (m-80) cc_final: 0.7592 (m-80) REVERT: B 194 PHE cc_start: 0.7750 (m-80) cc_final: 0.6994 (m-10) REVERT: B 212 LEU cc_start: 0.8567 (tp) cc_final: 0.8321 (tp) REVERT: B 223 LEU cc_start: 0.8532 (mt) cc_final: 0.8233 (mm) REVERT: B 276 LEU cc_start: 0.8695 (tt) cc_final: 0.8327 (tt) REVERT: B 300 LYS cc_start: 0.8234 (mttt) cc_final: 0.7836 (mtmm) REVERT: B 304 LYS cc_start: 0.8569 (ptpp) cc_final: 0.7984 (tppt) REVERT: B 306 PHE cc_start: 0.6820 (m-80) cc_final: 0.5502 (m-80) REVERT: B 313 TYR cc_start: 0.7332 (m-10) cc_final: 0.6888 (m-80) REVERT: B 396 TYR cc_start: 0.8197 (m-80) cc_final: 0.7865 (m-80) REVERT: B 560 LEU cc_start: 0.8834 (mt) cc_final: 0.8489 (mt) REVERT: B 603 ASN cc_start: 0.9218 (t0) cc_final: 0.8792 (p0) REVERT: B 612 TYR cc_start: 0.7290 (m-10) cc_final: 0.6837 (m-10) REVERT: B 656 VAL cc_start: 0.8120 (m) cc_final: 0.7909 (m) REVERT: B 748 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8753 (pp20) REVERT: B 764 ASN cc_start: 0.9033 (m-40) cc_final: 0.8767 (m-40) REVERT: B 775 ASP cc_start: 0.8327 (m-30) cc_final: 0.7659 (m-30) REVERT: B 819 GLU cc_start: 0.8897 (pt0) cc_final: 0.8407 (pt0) REVERT: B 822 LEU cc_start: 0.9132 (tp) cc_final: 0.8680 (mt) REVERT: B 824 ASN cc_start: 0.8537 (m110) cc_final: 0.8332 (m110) REVERT: B 869 MET cc_start: 0.8502 (mtt) cc_final: 0.8221 (mmp) REVERT: B 927 PHE cc_start: 0.8601 (t80) cc_final: 0.7973 (t80) REVERT: B 954 GLN cc_start: 0.9027 (mt0) cc_final: 0.8193 (tm-30) REVERT: B 955 ASN cc_start: 0.8778 (m110) cc_final: 0.8486 (t0) REVERT: B 957 GLN cc_start: 0.9225 (pt0) cc_final: 0.8624 (pp30) REVERT: B 960 ASN cc_start: 0.8880 (m-40) cc_final: 0.8297 (t0) REVERT: B 964 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8824 (pttp) REVERT: B 965 GLN cc_start: 0.9280 (mm110) cc_final: 0.8566 (mm110) REVERT: B 969 ASN cc_start: 0.8899 (p0) cc_final: 0.8288 (t0) REVERT: B 978 ASN cc_start: 0.8753 (t160) cc_final: 0.8544 (t0) REVERT: B 981 LEU cc_start: 0.8600 (tp) cc_final: 0.8391 (tt) REVERT: B 998 THR cc_start: 0.9025 (p) cc_final: 0.8664 (p) REVERT: B 1002 GLN cc_start: 0.8941 (tp40) cc_final: 0.8737 (mp10) REVERT: B 1010 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8660 (mm-40) REVERT: B 1012 LEU cc_start: 0.9388 (mt) cc_final: 0.9156 (mt) REVERT: B 1019 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8282 (ptm160) REVERT: B 1021 SER cc_start: 0.8742 (t) cc_final: 0.8439 (p) REVERT: B 1028 LYS cc_start: 0.7260 (tptt) cc_final: 0.6997 (tptt) REVERT: B 1050 MET cc_start: 0.7262 (tpt) cc_final: 0.6597 (mtp) REVERT: C 33 THR cc_start: 0.6419 (p) cc_final: 0.6118 (t) REVERT: C 59 PHE cc_start: 0.7511 (m-80) cc_final: 0.7224 (m-10) REVERT: C 91 TYR cc_start: 0.7642 (t80) cc_final: 0.6654 (t80) REVERT: C 104 TRP cc_start: 0.5616 (m-90) cc_final: 0.5286 (m-90) REVERT: C 117 LEU cc_start: 0.8677 (tt) cc_final: 0.8147 (pt) REVERT: C 192 PHE cc_start: 0.8524 (m-80) cc_final: 0.8239 (m-80) REVERT: C 194 PHE cc_start: 0.8003 (m-80) cc_final: 0.7584 (m-80) REVERT: C 235 ILE cc_start: 0.7032 (mt) cc_final: 0.6700 (mm) REVERT: C 281 GLU cc_start: 0.8204 (tp30) cc_final: 0.7905 (tp30) REVERT: C 324 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8084 (mp0) REVERT: C 338 PHE cc_start: 0.8912 (m-80) cc_final: 0.8521 (m-10) REVERT: C 342 PHE cc_start: 0.8799 (m-80) cc_final: 0.8464 (m-10) REVERT: C 365 TYR cc_start: 0.8776 (m-10) cc_final: 0.8518 (m-80) REVERT: C 386 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8110 (mttt) REVERT: C 417 LYS cc_start: 0.9092 (tppp) cc_final: 0.8871 (tppt) REVERT: C 425 LEU cc_start: 0.8192 (mt) cc_final: 0.7929 (tp) REVERT: C 517 LEU cc_start: 0.6750 (pp) cc_final: 0.6144 (pp) REVERT: C 562 PHE cc_start: 0.8781 (p90) cc_final: 0.8261 (p90) REVERT: C 563 GLN cc_start: 0.8306 (mt0) cc_final: 0.7973 (mt0) REVERT: C 588 THR cc_start: 0.8437 (m) cc_final: 0.8177 (p) REVERT: C 737 ASP cc_start: 0.8819 (t0) cc_final: 0.8569 (t0) REVERT: C 738 CYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6505 (p) REVERT: C 748 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8341 (tm-30) REVERT: C 752 LEU cc_start: 0.8599 (pp) cc_final: 0.7951 (pp) REVERT: C 759 PHE cc_start: 0.8601 (m-80) cc_final: 0.7948 (m-10) REVERT: C 765 ARG cc_start: 0.9042 (ptp-170) cc_final: 0.8746 (ptp-170) REVERT: C 770 ILE cc_start: 0.9287 (mm) cc_final: 0.9003 (mm) REVERT: C 773 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7642 (tm-30) REVERT: C 776 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8346 (tmtt) REVERT: C 869 MET cc_start: 0.9049 (mtm) cc_final: 0.8094 (tmm) REVERT: C 917 TYR cc_start: 0.8114 (m-80) cc_final: 0.7859 (m-10) REVERT: C 954 GLN cc_start: 0.9057 (mt0) cc_final: 0.8411 (pp30) REVERT: C 955 ASN cc_start: 0.7927 (p0) cc_final: 0.7416 (p0) REVERT: C 957 GLN cc_start: 0.8916 (tt0) cc_final: 0.8591 (pp30) REVERT: C 959 LEU cc_start: 0.9342 (mp) cc_final: 0.9061 (pp) REVERT: C 964 LYS cc_start: 0.9182 (tttt) cc_final: 0.8891 (tmtt) REVERT: C 965 GLN cc_start: 0.9290 (mm110) cc_final: 0.8563 (mm110) REVERT: C 969 ASN cc_start: 0.7747 (p0) cc_final: 0.6627 (p0) REVERT: C 979 ASP cc_start: 0.9032 (m-30) cc_final: 0.8730 (m-30) REVERT: C 983 ARG cc_start: 0.8995 (tmt-80) cc_final: 0.8751 (tpt90) REVERT: C 1000 ARG cc_start: 0.9060 (mmm160) cc_final: 0.8785 (mmm160) REVERT: C 1001 LEU cc_start: 0.9580 (tt) cc_final: 0.9245 (tt) REVERT: C 1002 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8570 (mm110) REVERT: C 1010 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8299 (tm-30) REVERT: C 1012 LEU cc_start: 0.9202 (mt) cc_final: 0.8964 (mt) REVERT: C 1014 ARG cc_start: 0.8608 (mmp80) cc_final: 0.8288 (mmt-90) REVERT: C 1017 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8096 (mp0) REVERT: C 1019 ARG cc_start: 0.8889 (ptp-170) cc_final: 0.8368 (ptp90) REVERT: C 1028 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7585 (ttmt) outliers start: 15 outliers final: 1 residues processed: 577 average time/residue: 0.1882 time to fit residues: 167.5098 Evaluate side-chains 485 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 483 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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: 0.0270 chunk 169 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 563 GLN A 564 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 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 = 0.4665 r_free = 0.4665 target = 0.180755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.135117 restraints weight = 67265.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.140325 restraints weight = 46808.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.144103 restraints weight = 35537.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.146873 restraints weight = 28650.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.148882 restraints weight = 24214.823| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26386 Z= 0.175 Angle : 0.770 16.456 36017 Z= 0.384 Chirality : 0.051 0.562 4182 Planarity : 0.005 0.066 4587 Dihedral : 5.326 30.763 3449 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.95 % 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: -0.63 (0.14), residues: 3187 helix: 1.01 (0.19), residues: 698 sheet: 0.01 (0.19), residues: 653 loop : -1.18 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 457 TYR 0.019 0.002 TYR A 674 PHE 0.022 0.002 PHE C 797 TRP 0.023 0.002 TRP A 64 HIS 0.007 0.002 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (26300) covalent geometry : angle 0.73064 / 0.37 (35807) SS BOND : bond 0.00508 / 0.30 ( 42) SS BOND : angle 2.16420 / 1.48 ( 84) hydrogen bonds : bond 0.05335 / 3.63 ( 872) hydrogen bonds : angle 6.59594 / 4.46 ( 2433) Misc. bond : bond 0.00259 / 0.14 ( 2) link_BETA1-4 : bond 0.00652 / 0.46 ( 10) link_BETA1-4 : angle 1.20646 / 0.85 ( 30) link_NAG-ASN : bond 0.00776 / 0.47 ( 32) link_NAG-ASN : angle 4.33094 / 3.10 ( 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 544 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 542 time to evaluate : 0.907 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: 0.8410 (t0) cc_final: 0.8057 (t0) REVERT: A 65 PHE cc_start: 0.7806 (m-80) cc_final: 0.7274 (m-80) REVERT: A 128 ILE cc_start: 0.8574 (mt) cc_final: 0.7633 (mt) REVERT: A 170 TYR cc_start: 0.7373 (t80) cc_final: 0.6906 (t80) REVERT: A 189 LEU cc_start: 0.8629 (tp) cc_final: 0.8273 (tp) REVERT: A 194 PHE cc_start: 0.8680 (m-80) cc_final: 0.8159 (m-80) REVERT: A 202 LYS cc_start: 0.7378 (mttt) cc_final: 0.6814 (mttt) REVERT: A 275 PHE cc_start: 0.6875 (m-10) cc_final: 0.6274 (m-10) REVERT: A 312 ILE cc_start: 0.8395 (tt) cc_final: 0.8194 (tt) REVERT: A 313 TYR cc_start: 0.8345 (m-10) cc_final: 0.7993 (m-10) REVERT: A 380 TYR cc_start: 0.7941 (m-80) cc_final: 0.7462 (m-80) REVERT: A 386 LYS cc_start: 0.8699 (mttp) cc_final: 0.8077 (mmmm) REVERT: A 400 PHE cc_start: 0.5983 (p90) cc_final: 0.5243 (p90) REVERT: A 414 GLN cc_start: 0.6402 (pt0) cc_final: 0.5876 (pm20) REVERT: A 461 LEU cc_start: 0.8093 (mt) cc_final: 0.6931 (mt) REVERT: A 462 LYS cc_start: 0.7777 (mmtm) cc_final: 0.7024 (ttpp) REVERT: A 529 LYS cc_start: 0.8820 (tttm) cc_final: 0.8478 (tmtt) REVERT: A 731 MET cc_start: 0.8719 (ppp) cc_final: 0.8430 (ppp) REVERT: A 752 LEU cc_start: 0.8820 (mt) cc_final: 0.8604 (tt) REVERT: A 755 GLN cc_start: 0.8413 (mp10) cc_final: 0.8030 (tt0) REVERT: A 759 PHE cc_start: 0.8806 (m-80) cc_final: 0.8538 (m-80) REVERT: A 762 GLN cc_start: 0.8912 (pt0) cc_final: 0.8572 (pt0) REVERT: A 764 ASN cc_start: 0.8939 (m110) cc_final: 0.8629 (m110) REVERT: A 796 ASP cc_start: 0.7702 (m-30) cc_final: 0.7183 (p0) REVERT: A 819 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7507 (mp0) REVERT: A 867 ASP cc_start: 0.7466 (m-30) cc_final: 0.7027 (p0) REVERT: A 917 TYR cc_start: 0.8036 (m-80) cc_final: 0.7633 (m-80) REVERT: A 927 PHE cc_start: 0.7700 (t80) cc_final: 0.7293 (t80) REVERT: A 947 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7518 (pttt) REVERT: A 949 GLN cc_start: 0.8144 (pp30) cc_final: 0.7876 (pp30) REVERT: A 954 GLN cc_start: 0.9042 (tp40) cc_final: 0.8567 (tm-30) REVERT: A 964 LYS cc_start: 0.9335 (ttmm) cc_final: 0.8946 (mmtt) REVERT: A 965 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 968 SER cc_start: 0.8319 (m) cc_final: 0.7898 (t) REVERT: A 979 ASP cc_start: 0.9044 (m-30) cc_final: 0.8500 (t0) REVERT: A 990 GLU cc_start: 0.8787 (tt0) cc_final: 0.8476 (mt-10) REVERT: A 993 ILE cc_start: 0.8874 (mt) cc_final: 0.8140 (tp) REVERT: A 994 ASP cc_start: 0.8744 (m-30) cc_final: 0.8150 (m-30) REVERT: A 995 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8329 (ptp-110) REVERT: A 997 ILE cc_start: 0.9482 (mt) cc_final: 0.9174 (pt) REVERT: A 1001 LEU cc_start: 0.9224 (mt) cc_final: 0.8819 (mm) REVERT: A 1002 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 1005 GLN cc_start: 0.8970 (mt0) cc_final: 0.8706 (mm-40) REVERT: A 1014 ARG cc_start: 0.8798 (mmp-170) cc_final: 0.8417 (mmm160) REVERT: A 1060 VAL cc_start: 0.6484 (t) cc_final: 0.6182 (p) REVERT: B 37 TYR cc_start: 0.8483 (p90) cc_final: 0.8247 (p90) REVERT: B 41 LYS cc_start: 0.8766 (tppt) cc_final: 0.8452 (tppt) REVERT: B 44 ARG cc_start: 0.7819 (mtt90) cc_final: 0.6826 (ptp-170) REVERT: B 47 VAL cc_start: 0.8741 (p) cc_final: 0.8492 (p) REVERT: B 58 PHE cc_start: 0.7917 (m-80) cc_final: 0.6593 (m-80) REVERT: B 63 THR cc_start: 0.7963 (p) cc_final: 0.6754 (t) REVERT: B 65 PHE cc_start: 0.8216 (m-80) cc_final: 0.7620 (m-80) REVERT: B 129 LYS cc_start: 0.7948 (tptt) cc_final: 0.7714 (tppt) REVERT: B 170 TYR cc_start: 0.8425 (t80) cc_final: 0.7592 (t80) REVERT: B 194 PHE cc_start: 0.7745 (m-80) cc_final: 0.7157 (m-10) REVERT: B 212 LEU cc_start: 0.8556 (tp) cc_final: 0.8175 (tt) REVERT: B 266 TYR cc_start: 0.7218 (m-10) cc_final: 0.6864 (m-10) REVERT: B 275 PHE cc_start: 0.6434 (m-10) cc_final: 0.5504 (m-10) REVERT: B 276 LEU cc_start: 0.8950 (tt) cc_final: 0.7948 (mp) REVERT: B 287 ASP cc_start: 0.8007 (m-30) cc_final: 0.7486 (t70) REVERT: B 300 LYS cc_start: 0.8072 (mttt) cc_final: 0.7645 (mtmm) REVERT: B 313 TYR cc_start: 0.7716 (m-10) cc_final: 0.7173 (m-10) REVERT: B 396 TYR cc_start: 0.8157 (m-80) cc_final: 0.7863 (m-80) REVERT: B 603 ASN cc_start: 0.9253 (t0) cc_final: 0.8830 (p0) REVERT: B 753 LEU cc_start: 0.9049 (tp) cc_final: 0.8694 (pp) REVERT: B 754 LEU cc_start: 0.9016 (mt) cc_final: 0.8808 (mt) REVERT: B 777 ASN cc_start: 0.8158 (m110) cc_final: 0.7956 (m110) REVERT: B 819 GLU cc_start: 0.8898 (pt0) cc_final: 0.8341 (pt0) REVERT: B 822 LEU cc_start: 0.9111 (tp) cc_final: 0.8663 (mt) REVERT: B 867 ASP cc_start: 0.8417 (p0) cc_final: 0.8143 (p0) REVERT: B 869 MET cc_start: 0.8500 (mtt) cc_final: 0.8198 (mmp) REVERT: B 927 PHE cc_start: 0.8557 (t80) cc_final: 0.7881 (t80) REVERT: B 954 GLN cc_start: 0.9009 (mt0) cc_final: 0.8621 (pp30) REVERT: B 955 ASN cc_start: 0.8862 (m110) cc_final: 0.8519 (t0) REVERT: B 957 GLN cc_start: 0.9190 (pt0) cc_final: 0.8638 (pp30) REVERT: B 959 LEU cc_start: 0.8613 (pp) cc_final: 0.8346 (pp) REVERT: B 960 ASN cc_start: 0.8775 (m-40) cc_final: 0.8419 (m-40) REVERT: B 964 LYS cc_start: 0.9065 (ttmm) cc_final: 0.7896 (tptp) REVERT: B 965 GLN cc_start: 0.9213 (mm110) cc_final: 0.8583 (mm110) REVERT: B 969 ASN cc_start: 0.8617 (p0) cc_final: 0.8319 (m110) REVERT: B 979 ASP cc_start: 0.8583 (t0) cc_final: 0.8284 (t0) REVERT: B 983 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7089 (tmm-80) REVERT: B 984 LEU cc_start: 0.8426 (mt) cc_final: 0.7900 (tp) REVERT: B 995 ARG cc_start: 0.8445 (ptt180) cc_final: 0.7960 (ptt-90) REVERT: B 1000 ARG cc_start: 0.8451 (ptp-110) cc_final: 0.8102 (ptp-110) REVERT: B 1009 THR cc_start: 0.9206 (p) cc_final: 0.8955 (p) REVERT: B 1010 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8635 (mm-40) REVERT: B 1011 GLN cc_start: 0.8556 (mm110) cc_final: 0.8215 (mp10) REVERT: B 1017 GLU cc_start: 0.8636 (pp20) cc_final: 0.8198 (pp20) REVERT: B 1018 ILE cc_start: 0.9123 (pt) cc_final: 0.8879 (pt) REVERT: B 1019 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8111 (ptm160) REVERT: B 1021 SER cc_start: 0.8603 (t) cc_final: 0.8340 (p) REVERT: B 1028 LYS cc_start: 0.7240 (tptm) cc_final: 0.6983 (tptt) REVERT: C 37 TYR cc_start: 0.8129 (p90) cc_final: 0.7753 (p90) REVERT: C 59 PHE cc_start: 0.7570 (m-80) cc_final: 0.7168 (m-10) REVERT: C 65 PHE cc_start: 0.7531 (m-80) cc_final: 0.7101 (m-80) REVERT: C 160 TYR cc_start: 0.8324 (p90) cc_final: 0.7202 (p90) REVERT: C 194 PHE cc_start: 0.7886 (m-80) cc_final: 0.7558 (m-80) REVERT: C 237 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8464 (mmm-85) REVERT: C 281 GLU cc_start: 0.8288 (tp30) cc_final: 0.7805 (tp30) REVERT: C 289 VAL cc_start: 0.8739 (t) cc_final: 0.8532 (p) REVERT: C 313 TYR cc_start: 0.7525 (m-10) cc_final: 0.7233 (m-10) REVERT: C 324 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8069 (pm20) REVERT: C 338 PHE cc_start: 0.8915 (m-80) cc_final: 0.8555 (m-10) REVERT: C 342 PHE cc_start: 0.8847 (m-80) cc_final: 0.8478 (m-10) REVERT: C 354 ASN cc_start: 0.9025 (t0) cc_final: 0.8814 (t0) REVERT: C 356 LYS cc_start: 0.8442 (tptp) cc_final: 0.7795 (tmmt) REVERT: C 365 TYR cc_start: 0.8791 (m-10) cc_final: 0.8383 (m-80) REVERT: C 380 TYR cc_start: 0.7802 (m-10) cc_final: 0.7546 (m-80) REVERT: C 386 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8053 (mttm) REVERT: C 409 GLN cc_start: 0.8249 (mp10) cc_final: 0.8032 (mp10) REVERT: C 417 LYS cc_start: 0.9085 (tppp) cc_final: 0.8834 (tppt) REVERT: C 425 LEU cc_start: 0.8322 (mt) cc_final: 0.7991 (tp) REVERT: C 516 GLU cc_start: 0.6308 (mp0) cc_final: 0.5820 (mp0) REVERT: C 562 PHE cc_start: 0.8782 (p90) cc_final: 0.8574 (p90) REVERT: C 563 GLN cc_start: 0.8293 (mt0) cc_final: 0.8074 (mt0) REVERT: C 571 ASP cc_start: 0.9141 (t0) cc_final: 0.8835 (t0) REVERT: C 747 THR cc_start: 0.9200 (p) cc_final: 0.8957 (p) REVERT: C 748 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8698 (mp0) REVERT: C 759 PHE cc_start: 0.8643 (m-80) cc_final: 0.8062 (m-10) REVERT: C 762 GLN cc_start: 0.9069 (mt0) cc_final: 0.8775 (mt0) REVERT: C 763 LEU cc_start: 0.9107 (mt) cc_final: 0.8857 (mt) REVERT: C 764 ASN cc_start: 0.9005 (m110) cc_final: 0.8623 (m110) REVERT: C 765 ARG cc_start: 0.9105 (ptp-170) cc_final: 0.8601 (ptt-90) REVERT: C 770 ILE cc_start: 0.9216 (mm) cc_final: 0.9014 (mm) REVERT: C 773 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 776 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8363 (tmtt) REVERT: C 858 LEU cc_start: 0.8827 (mp) cc_final: 0.8553 (mm) REVERT: C 869 MET cc_start: 0.9004 (mtm) cc_final: 0.8152 (tmm) REVERT: C 900 MET cc_start: 0.8023 (ppp) cc_final: 0.7722 (ppp) REVERT: C 917 TYR cc_start: 0.7993 (m-80) cc_final: 0.7754 (m-10) REVERT: C 936 ASP cc_start: 0.8425 (m-30) cc_final: 0.8138 (m-30) REVERT: C 954 GLN cc_start: 0.9042 (mt0) cc_final: 0.8713 (pp30) REVERT: C 955 ASN cc_start: 0.8148 (p0) cc_final: 0.7807 (p0) REVERT: C 957 GLN cc_start: 0.9043 (tt0) cc_final: 0.8585 (pp30) REVERT: C 959 LEU cc_start: 0.9258 (mp) cc_final: 0.9052 (pp) REVERT: C 964 LYS cc_start: 0.9255 (tttt) cc_final: 0.8885 (ptmm) REVERT: C 965 GLN cc_start: 0.9232 (mm110) cc_final: 0.8687 (mm110) REVERT: C 969 ASN cc_start: 0.7991 (p0) cc_final: 0.7327 (p0) REVERT: C 970 PHE cc_start: 0.8009 (m-80) cc_final: 0.7637 (m-10) REVERT: C 978 ASN cc_start: 0.9482 (m110) cc_final: 0.9178 (m110) REVERT: C 981 LEU cc_start: 0.8893 (mp) cc_final: 0.8522 (pp) REVERT: C 983 ARG cc_start: 0.9021 (tmt-80) cc_final: 0.8725 (tpt90) REVERT: C 1000 ARG cc_start: 0.9178 (mtt-85) cc_final: 0.8594 (mmm160) REVERT: C 1001 LEU cc_start: 0.9562 (tt) cc_final: 0.9273 (tp) REVERT: C 1002 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8592 (mm110) REVERT: C 1010 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8124 (tm-30) REVERT: C 1012 LEU cc_start: 0.9233 (mt) cc_final: 0.8971 (mt) REVERT: C 1019 ARG cc_start: 0.8880 (ptp-170) cc_final: 0.8566 (ptt-90) outliers start: 2 outliers final: 0 residues processed: 544 average time/residue: 0.1898 time to fit residues: 158.1133 Evaluate side-chains 476 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 301 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** 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 953 ASN C1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.180132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.132185 restraints weight = 62371.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136750 restraints weight = 45303.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.140043 restraints weight = 35493.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.142480 restraints weight = 29437.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.144248 restraints weight = 25500.434| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 26386 Z= 0.253 Angle : 0.790 13.400 36017 Z= 0.408 Chirality : 0.050 0.486 4182 Planarity : 0.006 0.074 4587 Dihedral : 5.607 32.707 3449 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % 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: -1.03 (0.14), residues: 3187 helix: 0.53 (0.19), residues: 704 sheet: -0.51 (0.19), residues: 674 loop : -1.25 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 44 TYR 0.029 0.002 TYR B 266 PHE 0.032 0.002 PHE B 175 TRP 0.019 0.002 TRP A 64 HIS 0.012 0.002 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 (26300) covalent geometry : angle 0.76153 / 0.40 (35807) SS BOND : bond 0.00403 / 0.28 ( 42) SS BOND : angle 1.99586 / 1.37 ( 84) hydrogen bonds : bond 0.05547 / 3.78 ( 872) hydrogen bonds : angle 6.55463 / 4.43 ( 2433) Misc. bond : bond 0.00060 / 0.03 ( 2) link_BETA1-4 : bond 0.00416 / 0.24 ( 10) link_BETA1-4 : angle 1.22403 / 0.83 ( 30) link_NAG-ASN : bond 0.00662 / 0.40 ( 32) link_NAG-ASN : angle 3.73146 / 2.61 ( 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 539 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 536 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8489 (t0) cc_final: 0.8106 (t0) REVERT: A 65 PHE cc_start: 0.8032 (m-80) cc_final: 0.7398 (m-80) REVERT: A 99 ASN cc_start: 0.9326 (t0) cc_final: 0.9010 (t0) REVERT: A 128 ILE cc_start: 0.8687 (mt) cc_final: 0.7853 (mt) REVERT: A 170 TYR cc_start: 0.7745 (t80) cc_final: 0.7088 (t80) REVERT: A 177 MET cc_start: 0.1635 (mpp) cc_final: 0.1161 (mmp) REVERT: A 275 PHE cc_start: 0.7057 (m-10) cc_final: 0.6307 (m-10) REVERT: A 313 TYR cc_start: 0.8212 (m-80) cc_final: 0.7896 (m-10) REVERT: A 317 ASN cc_start: 0.7547 (t0) cc_final: 0.7339 (t0) REVERT: A 321 GLN cc_start: 0.9413 (pm20) cc_final: 0.9128 (pm20) REVERT: A 350 VAL cc_start: 0.8555 (p) cc_final: 0.8221 (p) REVERT: A 365 TYR cc_start: 0.8114 (m-80) cc_final: 0.7800 (m-80) REVERT: A 380 TYR cc_start: 0.8116 (m-80) cc_final: 0.7716 (m-80) REVERT: A 389 ASP cc_start: 0.8770 (m-30) cc_final: 0.8223 (p0) REVERT: A 400 PHE cc_start: 0.6559 (p90) cc_final: 0.5881 (p90) REVERT: A 433 VAL cc_start: 0.8510 (m) cc_final: 0.8138 (m) REVERT: A 461 LEU cc_start: 0.8201 (mt) cc_final: 0.7731 (mt) REVERT: A 557 LYS cc_start: 0.8233 (mttt) cc_final: 0.7437 (tptp) REVERT: A 585 LEU cc_start: 0.8672 (mp) cc_final: 0.8385 (mp) REVERT: A 751 ASN cc_start: 0.8853 (m110) cc_final: 0.8431 (p0) REVERT: A 752 LEU cc_start: 0.8866 (mt) cc_final: 0.8476 (tt) REVERT: A 759 PHE cc_start: 0.8798 (m-80) cc_final: 0.8103 (m-80) REVERT: A 762 GLN cc_start: 0.8891 (pt0) cc_final: 0.8559 (pp30) REVERT: A 776 LYS cc_start: 0.8999 (tptm) cc_final: 0.8467 (tptp) REVERT: A 867 ASP cc_start: 0.7784 (m-30) cc_final: 0.7501 (p0) REVERT: A 917 TYR cc_start: 0.8067 (m-80) cc_final: 0.7556 (m-80) REVERT: A 927 PHE cc_start: 0.7840 (t80) cc_final: 0.7425 (t80) REVERT: A 947 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7725 (pttt) REVERT: A 949 GLN cc_start: 0.8242 (pp30) cc_final: 0.7938 (pp30) REVERT: A 954 GLN cc_start: 0.9061 (tp40) cc_final: 0.8536 (tm-30) REVERT: A 960 ASN cc_start: 0.8810 (t0) cc_final: 0.8250 (m110) REVERT: A 964 LYS cc_start: 0.9293 (ttmm) cc_final: 0.8824 (ptpp) REVERT: A 979 ASP cc_start: 0.9088 (m-30) cc_final: 0.8546 (t0) REVERT: A 990 GLU cc_start: 0.8812 (tt0) cc_final: 0.8490 (mt-10) REVERT: A 993 ILE cc_start: 0.9041 (mt) cc_final: 0.8361 (tp) REVERT: A 994 ASP cc_start: 0.8771 (m-30) cc_final: 0.8185 (m-30) REVERT: A 995 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8077 (ptm160) REVERT: A 996 LEU cc_start: 0.9345 (mt) cc_final: 0.9133 (mt) REVERT: A 1000 ARG cc_start: 0.9102 (mmt180) cc_final: 0.8731 (mmt180) REVERT: A 1001 LEU cc_start: 0.9089 (mt) cc_final: 0.8670 (mm) REVERT: A 1002 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8520 (tm-30) REVERT: A 1014 ARG cc_start: 0.8898 (mmp-170) cc_final: 0.8597 (mmp80) REVERT: A 1050 MET cc_start: 0.5603 (ttt) cc_final: 0.5332 (ttt) REVERT: A 1053 PRO cc_start: 0.8206 (Cg_endo) cc_final: 0.7881 (Cg_exo) REVERT: B 37 TYR cc_start: 0.8717 (p90) cc_final: 0.8162 (p90) REVERT: B 41 LYS cc_start: 0.8767 (tppt) cc_final: 0.8301 (tppt) REVERT: B 44 ARG cc_start: 0.7993 (mtt90) cc_final: 0.6872 (ptp90) REVERT: B 48 LEU cc_start: 0.8470 (mt) cc_final: 0.7865 (mt) REVERT: B 58 PHE cc_start: 0.7807 (m-80) cc_final: 0.6739 (m-80) REVERT: B 65 PHE cc_start: 0.8372 (m-80) cc_final: 0.7913 (m-80) REVERT: B 86 PHE cc_start: 0.7873 (t80) cc_final: 0.7577 (t80) REVERT: B 128 ILE cc_start: 0.8870 (mt) cc_final: 0.8506 (mm) REVERT: B 170 TYR cc_start: 0.8521 (t80) cc_final: 0.7692 (t80) REVERT: B 194 PHE cc_start: 0.7881 (m-80) cc_final: 0.7282 (m-10) REVERT: B 229 LEU cc_start: 0.9508 (mm) cc_final: 0.8787 (pp) REVERT: B 275 PHE cc_start: 0.6747 (m-10) cc_final: 0.5509 (m-10) REVERT: B 276 LEU cc_start: 0.9008 (tt) cc_final: 0.8187 (mp) REVERT: B 294 ASP cc_start: 0.8871 (m-30) cc_final: 0.8224 (m-30) REVERT: B 298 GLU cc_start: 0.8601 (tt0) cc_final: 0.7881 (mm-30) REVERT: B 313 TYR cc_start: 0.7681 (m-10) cc_final: 0.7022 (m-10) REVERT: B 396 TYR cc_start: 0.8118 (m-80) cc_final: 0.7840 (m-80) REVERT: B 562 PHE cc_start: 0.8855 (p90) cc_final: 0.8397 (p90) REVERT: B 586 ASP cc_start: 0.8324 (t0) cc_final: 0.7632 (p0) REVERT: B 587 ILE cc_start: 0.8907 (mp) cc_final: 0.8622 (mp) REVERT: B 603 ASN cc_start: 0.9325 (t0) cc_final: 0.8932 (p0) REVERT: B 658 ASN cc_start: 0.8338 (t0) cc_final: 0.8137 (t0) REVERT: B 748 GLU cc_start: 0.8890 (pp20) cc_final: 0.8630 (pp20) REVERT: B 753 LEU cc_start: 0.9096 (tp) cc_final: 0.8837 (tp) REVERT: B 759 PHE cc_start: 0.8449 (m-80) cc_final: 0.8194 (m-80) REVERT: B 819 GLU cc_start: 0.8965 (pt0) cc_final: 0.8479 (pt0) REVERT: B 822 LEU cc_start: 0.9057 (tp) cc_final: 0.8609 (mt) REVERT: B 824 ASN cc_start: 0.8814 (m110) cc_final: 0.8543 (m110) REVERT: B 877 LEU cc_start: 0.8317 (mt) cc_final: 0.8054 (tt) REVERT: B 917 TYR cc_start: 0.8229 (m-10) cc_final: 0.7905 (m-10) REVERT: B 927 PHE cc_start: 0.8587 (t80) cc_final: 0.7902 (t80) REVERT: B 954 GLN cc_start: 0.9033 (mt0) cc_final: 0.8552 (tm-30) REVERT: B 955 ASN cc_start: 0.8920 (m110) cc_final: 0.8634 (t0) REVERT: B 957 GLN cc_start: 0.9127 (pt0) cc_final: 0.8865 (pp30) REVERT: B 964 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8936 (ptmm) REVERT: B 969 ASN cc_start: 0.8802 (p0) cc_final: 0.8493 (p0) REVERT: B 978 ASN cc_start: 0.8802 (p0) cc_final: 0.8160 (p0) REVERT: B 979 ASP cc_start: 0.8729 (t0) cc_final: 0.8188 (m-30) REVERT: B 983 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7445 (ttp-110) REVERT: B 1005 GLN cc_start: 0.8551 (pp30) cc_final: 0.7958 (pp30) REVERT: B 1010 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8488 (mm-40) REVERT: B 1011 GLN cc_start: 0.8700 (mm110) cc_final: 0.8266 (mm-40) REVERT: B 1014 ARG cc_start: 0.8854 (mtt90) cc_final: 0.8627 (mmt90) REVERT: B 1017 GLU cc_start: 0.8819 (pp20) cc_final: 0.8392 (pp20) REVERT: B 1019 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8102 (ttm-80) REVERT: B 1021 SER cc_start: 0.8823 (t) cc_final: 0.8584 (p) REVERT: B 1028 LYS cc_start: 0.7521 (tptm) cc_final: 0.7180 (tptt) REVERT: C 41 LYS cc_start: 0.8270 (tppt) cc_final: 0.7923 (tppt) REVERT: C 59 PHE cc_start: 0.8085 (m-80) cc_final: 0.7764 (m-10) REVERT: C 65 PHE cc_start: 0.8055 (m-80) cc_final: 0.7696 (m-80) REVERT: C 88 ASP cc_start: 0.9134 (p0) cc_final: 0.8932 (p0) REVERT: C 92 PHE cc_start: 0.8399 (t80) cc_final: 0.7410 (t80) REVERT: C 134 GLN cc_start: 0.8922 (tm130) cc_final: 0.8483 (mp10) REVERT: C 135 PHE cc_start: 0.9097 (m-10) cc_final: 0.8814 (m-10) REVERT: C 160 TYR cc_start: 0.8254 (p90) cc_final: 0.7920 (p90) REVERT: C 192 PHE cc_start: 0.8695 (m-80) cc_final: 0.8142 (m-80) REVERT: C 201 PHE cc_start: 0.8585 (t80) cc_final: 0.8343 (t80) REVERT: C 281 GLU cc_start: 0.8333 (tp30) cc_final: 0.7878 (tp30) REVERT: C 289 VAL cc_start: 0.8849 (t) cc_final: 0.8595 (p) REVERT: C 300 LYS cc_start: 0.8348 (mttt) cc_final: 0.7853 (mmtp) REVERT: C 324 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8203 (mp0) REVERT: C 338 PHE cc_start: 0.8995 (m-80) cc_final: 0.8605 (m-10) REVERT: C 342 PHE cc_start: 0.8816 (m-80) cc_final: 0.8410 (m-10) REVERT: C 354 ASN cc_start: 0.8996 (t0) cc_final: 0.8777 (t0) REVERT: C 365 TYR cc_start: 0.8966 (m-10) cc_final: 0.8455 (m-80) REVERT: C 386 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8104 (mtmm) REVERT: C 409 GLN cc_start: 0.8456 (mp10) cc_final: 0.8243 (mp10) REVERT: C 425 LEU cc_start: 0.8377 (mt) cc_final: 0.8085 (tp) REVERT: C 490 PHE cc_start: 0.8572 (t80) cc_final: 0.8317 (t80) REVERT: C 505 TYR cc_start: 0.8386 (t80) cc_final: 0.8037 (t80) REVERT: C 737 ASP cc_start: 0.8615 (t0) cc_final: 0.8323 (t0) REVERT: C 747 THR cc_start: 0.9127 (p) cc_final: 0.8889 (p) REVERT: C 748 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8814 (mp0) REVERT: C 759 PHE cc_start: 0.8654 (m-80) cc_final: 0.8151 (m-10) REVERT: C 761 THR cc_start: 0.9404 (m) cc_final: 0.8936 (p) REVERT: C 762 GLN cc_start: 0.9098 (mt0) cc_final: 0.8821 (mt0) REVERT: C 763 LEU cc_start: 0.9134 (mt) cc_final: 0.8927 (mt) REVERT: C 764 ASN cc_start: 0.8894 (m110) cc_final: 0.8514 (m110) REVERT: C 765 ARG cc_start: 0.9126 (ptp-170) cc_final: 0.8757 (ptp-170) REVERT: C 773 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7970 (mm-30) REVERT: C 776 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8416 (tmtt) REVERT: C 858 LEU cc_start: 0.8845 (mp) cc_final: 0.8551 (mm) REVERT: C 869 MET cc_start: 0.9175 (mtm) cc_final: 0.8188 (tmm) REVERT: C 898 PHE cc_start: 0.6227 (t80) cc_final: 0.5703 (t80) REVERT: C 900 MET cc_start: 0.8049 (ppp) cc_final: 0.7827 (ppp) REVERT: C 934 ILE cc_start: 0.7935 (tp) cc_final: 0.7504 (mm) REVERT: C 936 ASP cc_start: 0.8527 (m-30) cc_final: 0.8292 (m-30) REVERT: C 954 GLN cc_start: 0.9081 (mt0) cc_final: 0.8746 (tm-30) REVERT: C 959 LEU cc_start: 0.9285 (mp) cc_final: 0.9050 (pp) REVERT: C 970 PHE cc_start: 0.8078 (m-80) cc_final: 0.7590 (m-10) REVERT: C 978 ASN cc_start: 0.9526 (m110) cc_final: 0.9303 (m110) REVERT: C 979 ASP cc_start: 0.9048 (m-30) cc_final: 0.8762 (m-30) REVERT: C 981 LEU cc_start: 0.8963 (mp) cc_final: 0.8546 (pp) REVERT: C 994 ASP cc_start: 0.8698 (m-30) cc_final: 0.8413 (m-30) REVERT: C 1000 ARG cc_start: 0.9193 (mtt-85) cc_final: 0.8616 (mmm160) REVERT: C 1010 GLN cc_start: 0.8806 (tp-100) cc_final: 0.7622 (tm-30) REVERT: C 1012 LEU cc_start: 0.9384 (mt) cc_final: 0.9177 (mt) REVERT: C 1014 ARG cc_start: 0.8623 (mmp80) cc_final: 0.7571 (mmp80) REVERT: C 1017 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8549 (tm-30) REVERT: C 1018 ILE cc_start: 0.8807 (pt) cc_final: 0.8189 (pt) REVERT: C 1019 ARG cc_start: 0.8932 (ptp-170) cc_final: 0.8566 (ptt-90) REVERT: C 1054 GLN cc_start: 0.6924 (mp10) cc_final: 0.6649 (mp10) outliers start: 3 outliers final: 2 residues processed: 538 average time/residue: 0.1843 time to fit residues: 152.7481 Evaluate side-chains 478 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 476 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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: 0.6980 chunk 38 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 258 optimal weight: 0.0060 chunk 140 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 221 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 66 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.172527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.129405 restraints weight = 65334.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.134399 restraints weight = 45429.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.137978 restraints weight = 34361.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.140572 restraints weight = 27664.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.142435 restraints weight = 23360.741| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 26386 Z= 0.208 Angle : 0.754 12.115 36017 Z= 0.382 Chirality : 0.050 0.440 4182 Planarity : 0.005 0.076 4587 Dihedral : 5.443 30.954 3449 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % 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: -1.17 (0.14), residues: 3187 helix: 0.46 (0.19), residues: 700 sheet: -0.71 (0.19), residues: 678 loop : -1.31 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.022 0.002 TYR B 756 PHE 0.027 0.002 PHE A 782 TRP 0.029 0.002 TRP B 436 HIS 0.020 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 (26300) covalent geometry : angle 0.72565 / 0.38 (35807) SS BOND : bond 0.00367 / 0.25 ( 42) SS BOND : angle 1.94859 / 1.45 ( 84) hydrogen bonds : bond 0.05050 / 3.44 ( 872) hydrogen bonds : angle 6.37828 / 4.30 ( 2433) Misc. bond : bond 0.00264 / 0.13 ( 2) link_BETA1-4 : bond 0.00394 / 0.26 ( 10) link_BETA1-4 : angle 1.07655 / 0.74 ( 30) link_NAG-ASN : bond 0.00657 / 0.40 ( 32) link_NAG-ASN : angle 3.59816 / 2.53 ( 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 541 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 539 time to evaluate : 0.959 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 43 PHE cc_start: 0.8036 (t80) cc_final: 0.7757 (t80) REVERT: A 53 ASP cc_start: 0.8514 (t0) cc_final: 0.8091 (t0) REVERT: A 65 PHE cc_start: 0.8051 (m-80) cc_final: 0.7389 (m-80) REVERT: A 128 ILE cc_start: 0.8727 (mt) cc_final: 0.7737 (mt) REVERT: A 170 TYR cc_start: 0.7677 (t80) cc_final: 0.6970 (t80) REVERT: A 177 MET cc_start: 0.2371 (mpp) cc_final: 0.1623 (mmt) REVERT: A 189 LEU cc_start: 0.8516 (tp) cc_final: 0.8315 (tp) REVERT: A 275 PHE cc_start: 0.6753 (m-10) cc_final: 0.6405 (m-10) REVERT: A 313 TYR cc_start: 0.8273 (m-80) cc_final: 0.8007 (m-10) REVERT: A 365 TYR cc_start: 0.8238 (m-80) cc_final: 0.7735 (m-80) REVERT: A 380 TYR cc_start: 0.8120 (m-80) cc_final: 0.7682 (m-80) REVERT: A 389 ASP cc_start: 0.8645 (m-30) cc_final: 0.8294 (p0) REVERT: A 421 TYR cc_start: 0.8186 (m-10) cc_final: 0.7919 (m-10) REVERT: A 433 VAL cc_start: 0.8498 (m) cc_final: 0.8199 (m) REVERT: A 461 LEU cc_start: 0.8132 (mt) cc_final: 0.7713 (mt) REVERT: A 585 LEU cc_start: 0.8628 (mp) cc_final: 0.8399 (mp) REVERT: A 751 ASN cc_start: 0.9021 (m110) cc_final: 0.8673 (m110) REVERT: A 759 PHE cc_start: 0.8829 (m-80) cc_final: 0.8158 (m-80) REVERT: A 765 ARG cc_start: 0.8607 (ptp90) cc_final: 0.8097 (ptt-90) REVERT: A 776 LYS cc_start: 0.9020 (tptm) cc_final: 0.8469 (tptp) REVERT: A 856 ASN cc_start: 0.8217 (t0) cc_final: 0.7949 (p0) REVERT: A 867 ASP cc_start: 0.7887 (m-30) cc_final: 0.7546 (p0) REVERT: A 873 TYR cc_start: 0.8389 (m-10) cc_final: 0.8134 (m-80) REVERT: A 917 TYR cc_start: 0.8045 (m-80) cc_final: 0.7504 (m-10) REVERT: A 927 PHE cc_start: 0.8112 (t80) cc_final: 0.7588 (t80) REVERT: A 947 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7502 (mmmt) REVERT: A 954 GLN cc_start: 0.8993 (tp40) cc_final: 0.8500 (tm-30) REVERT: A 959 LEU cc_start: 0.9291 (mp) cc_final: 0.8956 (pp) REVERT: A 964 LYS cc_start: 0.9231 (ttmm) cc_final: 0.8428 (tppt) REVERT: A 974 SER cc_start: 0.8824 (t) cc_final: 0.8576 (t) REVERT: A 979 ASP cc_start: 0.8991 (m-30) cc_final: 0.8412 (t0) REVERT: A 983 ARG cc_start: 0.8843 (ptt90) cc_final: 0.7906 (ttp80) REVERT: A 990 GLU cc_start: 0.8834 (tt0) cc_final: 0.8504 (mt-10) REVERT: A 993 ILE cc_start: 0.9052 (mt) cc_final: 0.8317 (tp) REVERT: A 994 ASP cc_start: 0.8782 (m-30) cc_final: 0.8148 (m-30) REVERT: A 995 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8067 (ptm160) REVERT: A 996 LEU cc_start: 0.9362 (mt) cc_final: 0.9138 (mt) REVERT: A 1000 ARG cc_start: 0.9005 (mmt180) cc_final: 0.8801 (mmt180) REVERT: A 1001 LEU cc_start: 0.9302 (mt) cc_final: 0.8858 (pp) REVERT: A 1002 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 1014 ARG cc_start: 0.8808 (mmp-170) cc_final: 0.8444 (mmm160) REVERT: A 1023 ASN cc_start: 0.8672 (m-40) cc_final: 0.8455 (m-40) REVERT: A 1050 MET cc_start: 0.5656 (ttt) cc_final: 0.5207 (ttt) REVERT: A 1053 PRO cc_start: 0.8444 (Cg_endo) cc_final: 0.7787 (Cg_exo) REVERT: B 37 TYR cc_start: 0.8551 (p90) cc_final: 0.8080 (p90) REVERT: B 41 LYS cc_start: 0.8752 (tppt) cc_final: 0.8448 (tppt) REVERT: B 44 ARG cc_start: 0.8071 (mtt90) cc_final: 0.6981 (mtt90) REVERT: B 48 LEU cc_start: 0.8770 (mt) cc_final: 0.8318 (mt) REVERT: B 58 PHE cc_start: 0.7829 (m-80) cc_final: 0.7094 (m-80) REVERT: B 63 THR cc_start: 0.8054 (p) cc_final: 0.7696 (t) REVERT: B 65 PHE cc_start: 0.8385 (m-80) cc_final: 0.8013 (m-80) REVERT: B 86 PHE cc_start: 0.7881 (t80) cc_final: 0.7541 (t80) REVERT: B 128 ILE cc_start: 0.8871 (mt) cc_final: 0.8367 (mp) REVERT: B 170 TYR cc_start: 0.8494 (t80) cc_final: 0.7901 (t80) REVERT: B 194 PHE cc_start: 0.7764 (m-80) cc_final: 0.7044 (m-10) REVERT: B 265 TYR cc_start: 0.6996 (p90) cc_final: 0.6592 (p90) REVERT: B 276 LEU cc_start: 0.9057 (tt) cc_final: 0.8281 (mp) REVERT: B 298 GLU cc_start: 0.8593 (tt0) cc_final: 0.7809 (mm-30) REVERT: B 300 LYS cc_start: 0.8058 (mttt) cc_final: 0.7390 (mtmm) REVERT: B 313 TYR cc_start: 0.7605 (m-80) cc_final: 0.6974 (m-10) REVERT: B 318 PHE cc_start: 0.8197 (t80) cc_final: 0.7895 (t80) REVERT: B 543 PHE cc_start: 0.8435 (p90) cc_final: 0.8234 (p90) REVERT: B 562 PHE cc_start: 0.8833 (p90) cc_final: 0.8206 (p90) REVERT: B 586 ASP cc_start: 0.8365 (t0) cc_final: 0.7604 (p0) REVERT: B 587 ILE cc_start: 0.9003 (mp) cc_final: 0.8761 (mp) REVERT: B 603 ASN cc_start: 0.9309 (t0) cc_final: 0.9001 (p0) REVERT: B 612 TYR cc_start: 0.7587 (m-10) cc_final: 0.7295 (m-10) REVERT: B 741 TYR cc_start: 0.8852 (t80) cc_final: 0.8379 (t80) REVERT: B 753 LEU cc_start: 0.8925 (tp) cc_final: 0.8662 (tp) REVERT: B 777 ASN cc_start: 0.8271 (m110) cc_final: 0.8065 (m110) REVERT: B 802 PHE cc_start: 0.7890 (m-80) cc_final: 0.6736 (m-80) REVERT: B 819 GLU cc_start: 0.8972 (pt0) cc_final: 0.8471 (pt0) REVERT: B 822 LEU cc_start: 0.9078 (tp) cc_final: 0.8611 (mt) REVERT: B 824 ASN cc_start: 0.8754 (m110) cc_final: 0.8509 (m110) REVERT: B 867 ASP cc_start: 0.8399 (p0) cc_final: 0.8075 (p0) REVERT: B 877 LEU cc_start: 0.8295 (mt) cc_final: 0.8042 (tt) REVERT: B 917 TYR cc_start: 0.8121 (m-10) cc_final: 0.7734 (m-10) REVERT: B 927 PHE cc_start: 0.8589 (t80) cc_final: 0.7949 (t80) REVERT: B 937 SER cc_start: 0.8606 (t) cc_final: 0.8285 (p) REVERT: B 954 GLN cc_start: 0.8985 (mt0) cc_final: 0.8376 (tm-30) REVERT: B 955 ASN cc_start: 0.8887 (m110) cc_final: 0.7904 (m110) REVERT: B 957 GLN cc_start: 0.9106 (pt0) cc_final: 0.8851 (pp30) REVERT: B 965 GLN cc_start: 0.9075 (mm110) cc_final: 0.8871 (mm-40) REVERT: B 969 ASN cc_start: 0.8882 (p0) cc_final: 0.8636 (p0) REVERT: B 978 ASN cc_start: 0.8785 (p0) cc_final: 0.8059 (p0) REVERT: B 979 ASP cc_start: 0.8703 (t0) cc_final: 0.8233 (m-30) REVERT: B 983 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7453 (ttp-170) REVERT: B 1000 ARG cc_start: 0.8876 (ptp-110) cc_final: 0.7887 (ptm160) REVERT: B 1002 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 1010 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8355 (mm-40) REVERT: B 1011 GLN cc_start: 0.8629 (mm110) cc_final: 0.8359 (mp10) REVERT: B 1012 LEU cc_start: 0.9420 (mt) cc_final: 0.9213 (mt) REVERT: B 1014 ARG cc_start: 0.8765 (mtt90) cc_final: 0.8503 (mmt90) REVERT: B 1017 GLU cc_start: 0.8748 (pp20) cc_final: 0.8353 (pp20) REVERT: B 1021 SER cc_start: 0.8826 (t) cc_final: 0.8582 (p) REVERT: B 1028 LYS cc_start: 0.7514 (tptm) cc_final: 0.7138 (tptt) REVERT: C 41 LYS cc_start: 0.8288 (tppt) cc_final: 0.7862 (tppt) REVERT: C 65 PHE cc_start: 0.8124 (m-80) cc_final: 0.7415 (m-80) REVERT: C 66 HIS cc_start: 0.5781 (OUTLIER) cc_final: 0.3530 (t70) REVERT: C 88 ASP cc_start: 0.9143 (p0) cc_final: 0.8902 (p0) REVERT: C 92 PHE cc_start: 0.8197 (t80) cc_final: 0.7365 (t80) REVERT: C 117 LEU cc_start: 0.8802 (tt) cc_final: 0.8428 (pp) REVERT: C 177 MET cc_start: 0.3969 (mtm) cc_final: 0.3070 (mmm) REVERT: C 192 PHE cc_start: 0.8811 (m-80) cc_final: 0.8158 (m-80) REVERT: C 194 PHE cc_start: 0.7807 (m-80) cc_final: 0.7388 (m-80) REVERT: C 223 LEU cc_start: 0.8170 (pt) cc_final: 0.7702 (pt) REVERT: C 276 LEU cc_start: 0.7929 (tp) cc_final: 0.7709 (tp) REVERT: C 281 GLU cc_start: 0.8345 (tp30) cc_final: 0.7846 (tp30) REVERT: C 289 VAL cc_start: 0.8835 (t) cc_final: 0.8627 (p) REVERT: C 298 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7602 (mp0) REVERT: C 313 TYR cc_start: 0.7020 (m-10) cc_final: 0.6743 (m-10) REVERT: C 314 GLN cc_start: 0.7567 (tm-30) cc_final: 0.7349 (tm-30) REVERT: C 324 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8203 (mp0) REVERT: C 338 PHE cc_start: 0.9045 (m-80) cc_final: 0.8688 (m-10) REVERT: C 342 PHE cc_start: 0.8771 (m-80) cc_final: 0.8465 (m-80) REVERT: C 356 LYS cc_start: 0.8488 (tptp) cc_final: 0.7942 (tmmt) REVERT: C 365 TYR cc_start: 0.9072 (m-10) cc_final: 0.8504 (m-10) REVERT: C 380 TYR cc_start: 0.7539 (m-80) cc_final: 0.7212 (m-80) REVERT: C 386 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8139 (mtmm) REVERT: C 417 LYS cc_start: 0.9119 (tptt) cc_final: 0.8789 (tppt) REVERT: C 421 TYR cc_start: 0.8621 (m-10) cc_final: 0.8195 (m-10) REVERT: C 425 LEU cc_start: 0.8305 (mt) cc_final: 0.8028 (tp) REVERT: C 451 TYR cc_start: 0.6512 (m-80) cc_final: 0.6191 (m-80) REVERT: C 490 PHE cc_start: 0.8548 (t80) cc_final: 0.8241 (t80) REVERT: C 535 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8583 (mmmt) REVERT: C 571 ASP cc_start: 0.9139 (t0) cc_final: 0.8728 (t0) REVERT: C 737 ASP cc_start: 0.8501 (t0) cc_final: 0.7703 (p0) REVERT: C 740 MET cc_start: 0.8842 (tpt) cc_final: 0.8565 (tpp) REVERT: C 747 THR cc_start: 0.9089 (p) cc_final: 0.8866 (p) REVERT: C 748 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8831 (pm20) REVERT: C 761 THR cc_start: 0.9386 (m) cc_final: 0.9101 (p) REVERT: C 762 GLN cc_start: 0.9131 (mt0) cc_final: 0.8905 (mt0) REVERT: C 763 LEU cc_start: 0.9145 (mt) cc_final: 0.8931 (mt) REVERT: C 764 ASN cc_start: 0.8970 (m110) cc_final: 0.8700 (m110) REVERT: C 765 ARG cc_start: 0.9135 (ptp-170) cc_final: 0.8866 (ptp-110) REVERT: C 773 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 776 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8388 (tmtt) REVERT: C 858 LEU cc_start: 0.8799 (mp) cc_final: 0.8471 (mm) REVERT: C 869 MET cc_start: 0.9159 (mtm) cc_final: 0.8257 (mmt) REVERT: C 873 TYR cc_start: 0.8148 (m-10) cc_final: 0.7657 (m-80) REVERT: C 898 PHE cc_start: 0.6154 (t80) cc_final: 0.5797 (t80) REVERT: C 954 GLN cc_start: 0.9075 (mt0) cc_final: 0.8744 (tm-30) REVERT: C 964 LYS cc_start: 0.9422 (tttt) cc_final: 0.8938 (mmtt) REVERT: C 969 ASN cc_start: 0.8666 (p0) cc_final: 0.8443 (p0) REVERT: C 970 PHE cc_start: 0.8168 (m-80) cc_final: 0.7434 (m-10) REVERT: C 978 ASN cc_start: 0.9507 (m110) cc_final: 0.9295 (m110) REVERT: C 979 ASP cc_start: 0.9077 (m-30) cc_final: 0.8778 (m-30) REVERT: C 981 LEU cc_start: 0.8990 (mp) cc_final: 0.8722 (pp) REVERT: C 994 ASP cc_start: 0.8839 (m-30) cc_final: 0.8606 (m-30) REVERT: C 1000 ARG cc_start: 0.9174 (mtt-85) cc_final: 0.8558 (mmm-85) REVERT: C 1001 LEU cc_start: 0.9456 (tp) cc_final: 0.9126 (tp) REVERT: C 1002 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8543 (mm110) REVERT: C 1010 GLN cc_start: 0.8744 (tp-100) cc_final: 0.7568 (tm-30) REVERT: C 1011 GLN cc_start: 0.8927 (pt0) cc_final: 0.8448 (pt0) REVERT: C 1014 ARG cc_start: 0.8635 (mmp80) cc_final: 0.7543 (mmp80) REVERT: C 1017 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8505 (tm-30) REVERT: C 1018 ILE cc_start: 0.8773 (pt) cc_final: 0.8170 (pt) REVERT: C 1019 ARG cc_start: 0.8804 (ptp-170) cc_final: 0.8458 (ptt-90) REVERT: C 1054 GLN cc_start: 0.6967 (mp10) cc_final: 0.6624 (mp-120) outliers start: 2 outliers final: 1 residues processed: 540 average time/residue: 0.1927 time to fit residues: 159.9108 Evaluate side-chains 474 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 472 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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: 10.0000 chunk 142 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 111 optimal weight: 0.0050 chunk 225 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 12 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 928 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.172970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.124759 restraints weight = 63163.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.129178 restraints weight = 46498.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.132395 restraints weight = 36595.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.134651 restraints weight = 30541.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.136468 restraints weight = 26753.976| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 26386 Z= 0.244 Angle : 0.769 10.818 36017 Z= 0.398 Chirality : 0.050 0.388 4182 Planarity : 0.005 0.077 4587 Dihedral : 5.615 36.842 3449 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -1.37 (0.14), residues: 3187 helix: 0.23 (0.19), residues: 699 sheet: -0.76 (0.20), residues: 641 loop : -1.44 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 273 TYR 0.025 0.002 TYR B 904 PHE 0.032 0.002 PHE A 562 TRP 0.021 0.002 TRP C 64 HIS 0.017 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.24 (26300) covalent geometry : angle 0.74418 / 0.39 (35807) SS BOND : bond 0.00508 / 0.31 ( 42) SS BOND : angle 2.14259 / 1.58 ( 84) hydrogen bonds : bond 0.05254 / 3.56 ( 872) hydrogen bonds : angle 6.43367 / 4.35 ( 2433) Misc. bond : bond 0.02702 / 1.42 ( 2) link_BETA1-4 : bond 0.00346 / 0.23 ( 10) link_BETA1-4 : angle 1.07538 / 0.74 ( 30) link_NAG-ASN : bond 0.00612 / 0.36 ( 32) link_NAG-ASN : angle 3.27381 / 2.29 ( 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 541 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 0.917 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 41 LYS cc_start: 0.8579 (mmtt) cc_final: 0.7976 (mmtp) REVERT: A 43 PHE cc_start: 0.8025 (t80) cc_final: 0.7687 (t80) REVERT: A 53 ASP cc_start: 0.8498 (t0) cc_final: 0.8059 (t0) REVERT: A 65 PHE cc_start: 0.8128 (m-80) cc_final: 0.7501 (m-80) REVERT: A 99 ASN cc_start: 0.9502 (t0) cc_final: 0.9297 (t0) REVERT: A 106 PHE cc_start: 0.8167 (m-10) cc_final: 0.6370 (m-10) REVERT: A 128 ILE cc_start: 0.8664 (mt) cc_final: 0.7630 (mt) REVERT: A 170 TYR cc_start: 0.7515 (t80) cc_final: 0.6709 (t80) REVERT: A 177 MET cc_start: 0.3171 (mpp) cc_final: 0.2597 (mmt) REVERT: A 207 HIS cc_start: 0.9064 (p-80) cc_final: 0.8833 (p-80) REVERT: A 228 ASP cc_start: 0.8448 (m-30) cc_final: 0.8222 (m-30) REVERT: A 275 PHE cc_start: 0.6788 (m-10) cc_final: 0.6129 (m-10) REVERT: A 304 LYS cc_start: 0.8943 (mppt) cc_final: 0.8716 (mmtt) REVERT: A 321 GLN cc_start: 0.8890 (pm20) cc_final: 0.8638 (pm20) REVERT: A 365 TYR cc_start: 0.8171 (m-80) cc_final: 0.7719 (m-80) REVERT: A 380 TYR cc_start: 0.8061 (m-80) cc_final: 0.7723 (m-80) REVERT: A 389 ASP cc_start: 0.8816 (m-30) cc_final: 0.8381 (p0) REVERT: A 585 LEU cc_start: 0.8748 (mp) cc_final: 0.8511 (mp) REVERT: A 731 MET cc_start: 0.8388 (ppp) cc_final: 0.7882 (ppp) REVERT: A 751 ASN cc_start: 0.8988 (m110) cc_final: 0.8739 (m110) REVERT: A 752 LEU cc_start: 0.9009 (tt) cc_final: 0.8808 (tt) REVERT: A 755 GLN cc_start: 0.8716 (mp10) cc_final: 0.8437 (tt0) REVERT: A 759 PHE cc_start: 0.8813 (m-80) cc_final: 0.8029 (m-80) REVERT: A 776 LYS cc_start: 0.9010 (tptm) cc_final: 0.8451 (tptp) REVERT: A 869 MET cc_start: 0.8399 (ptp) cc_final: 0.7744 (ptp) REVERT: A 873 TYR cc_start: 0.8416 (m-10) cc_final: 0.8164 (m-80) REVERT: A 917 TYR cc_start: 0.8182 (m-80) cc_final: 0.7587 (m-10) REVERT: A 927 PHE cc_start: 0.7864 (t80) cc_final: 0.7460 (t80) REVERT: A 936 ASP cc_start: 0.8619 (m-30) cc_final: 0.8408 (m-30) REVERT: A 947 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7499 (mmmt) REVERT: A 954 GLN cc_start: 0.9076 (tp40) cc_final: 0.8599 (tm-30) REVERT: A 959 LEU cc_start: 0.9373 (mp) cc_final: 0.9106 (mm) REVERT: A 960 ASN cc_start: 0.8725 (t0) cc_final: 0.8097 (m110) REVERT: A 964 LYS cc_start: 0.9295 (ttmm) cc_final: 0.8815 (ptpp) REVERT: A 979 ASP cc_start: 0.9222 (m-30) cc_final: 0.8659 (t0) REVERT: A 983 ARG cc_start: 0.8766 (ptt90) cc_final: 0.7841 (ttp80) REVERT: A 990 GLU cc_start: 0.8763 (tt0) cc_final: 0.8444 (mt-10) REVERT: A 993 ILE cc_start: 0.9063 (mt) cc_final: 0.8525 (tp) REVERT: A 994 ASP cc_start: 0.8567 (m-30) cc_final: 0.8169 (m-30) REVERT: A 1000 ARG cc_start: 0.8963 (mmt180) cc_final: 0.8749 (mmt180) REVERT: A 1001 LEU cc_start: 0.9255 (mt) cc_final: 0.8873 (pp) REVERT: A 1002 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 1014 ARG cc_start: 0.8913 (mmp-170) cc_final: 0.8635 (mmm160) REVERT: A 1050 MET cc_start: 0.5855 (ttt) cc_final: 0.5240 (ttt) REVERT: A 1062 PHE cc_start: 0.6247 (m-80) cc_final: 0.5792 (m-80) REVERT: B 37 TYR cc_start: 0.8661 (p90) cc_final: 0.8138 (p90) REVERT: B 41 LYS cc_start: 0.8744 (tppt) cc_final: 0.8171 (tppp) REVERT: B 48 LEU cc_start: 0.8336 (mt) cc_final: 0.7898 (mt) REVERT: B 58 PHE cc_start: 0.7884 (m-80) cc_final: 0.7179 (m-10) REVERT: B 86 PHE cc_start: 0.8009 (t80) cc_final: 0.7535 (t80) REVERT: B 105 ILE cc_start: 0.8899 (mp) cc_final: 0.8675 (tp) REVERT: B 129 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8049 (mmmt) REVERT: B 170 TYR cc_start: 0.8281 (t80) cc_final: 0.8009 (t80) REVERT: B 177 MET cc_start: 0.4429 (mpp) cc_final: 0.4109 (mpp) REVERT: B 194 PHE cc_start: 0.7894 (m-80) cc_final: 0.7059 (m-10) REVERT: B 265 TYR cc_start: 0.6994 (p90) cc_final: 0.6692 (p90) REVERT: B 276 LEU cc_start: 0.9126 (tt) cc_final: 0.8518 (mp) REVERT: B 298 GLU cc_start: 0.8692 (tt0) cc_final: 0.8316 (tt0) REVERT: B 300 LYS cc_start: 0.8080 (mttt) cc_final: 0.7477 (mtmm) REVERT: B 313 TYR cc_start: 0.7740 (m-80) cc_final: 0.7090 (m-10) REVERT: B 317 ASN cc_start: 0.8573 (p0) cc_final: 0.8273 (t0) REVERT: B 543 PHE cc_start: 0.8494 (p90) cc_final: 0.8258 (p90) REVERT: B 562 PHE cc_start: 0.8963 (p90) cc_final: 0.8431 (p90) REVERT: B 603 ASN cc_start: 0.9373 (t0) cc_final: 0.9078 (p0) REVERT: B 759 PHE cc_start: 0.8337 (m-80) cc_final: 0.8056 (m-80) REVERT: B 777 ASN cc_start: 0.8452 (m110) cc_final: 0.8239 (m-40) REVERT: B 819 GLU cc_start: 0.8969 (pt0) cc_final: 0.8602 (pt0) REVERT: B 822 LEU cc_start: 0.9072 (tp) cc_final: 0.8665 (mt) REVERT: B 824 ASN cc_start: 0.8904 (m110) cc_final: 0.8677 (m110) REVERT: B 869 MET cc_start: 0.8524 (mpp) cc_final: 0.7524 (mmp) REVERT: B 873 TYR cc_start: 0.7971 (m-10) cc_final: 0.7596 (m-80) REVERT: B 917 TYR cc_start: 0.8469 (m-10) cc_final: 0.8080 (m-10) REVERT: B 927 PHE cc_start: 0.8507 (t80) cc_final: 0.7792 (t80) REVERT: B 937 SER cc_start: 0.8699 (t) cc_final: 0.8380 (p) REVERT: B 954 GLN cc_start: 0.9092 (mt0) cc_final: 0.8496 (tm-30) REVERT: B 955 ASN cc_start: 0.8933 (m110) cc_final: 0.8125 (m110) REVERT: B 957 GLN cc_start: 0.9129 (pt0) cc_final: 0.8919 (pp30) REVERT: B 965 GLN cc_start: 0.9000 (mm110) cc_final: 0.8787 (mm-40) REVERT: B 969 ASN cc_start: 0.8822 (p0) cc_final: 0.8604 (p0) REVERT: B 978 ASN cc_start: 0.8905 (p0) cc_final: 0.8669 (p0) REVERT: B 979 ASP cc_start: 0.8780 (t0) cc_final: 0.8552 (t0) REVERT: B 983 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7359 (ttp-170) REVERT: B 995 ARG cc_start: 0.8710 (ptt180) cc_final: 0.8132 (ptt180) REVERT: B 1000 ARG cc_start: 0.8930 (ptp-110) cc_final: 0.8389 (ptm160) REVERT: B 1002 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 1011 GLN cc_start: 0.8602 (mm110) cc_final: 0.7945 (mm-40) REVERT: B 1014 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8516 (mmt-90) REVERT: B 1017 GLU cc_start: 0.8763 (pp20) cc_final: 0.8249 (pp20) REVERT: B 1018 ILE cc_start: 0.9097 (pt) cc_final: 0.8891 (pt) REVERT: B 1019 ARG cc_start: 0.8888 (ptm-80) cc_final: 0.8396 (ptm-80) REVERT: B 1021 SER cc_start: 0.8967 (t) cc_final: 0.8739 (p) REVERT: B 1028 LYS cc_start: 0.7489 (tptm) cc_final: 0.7168 (tptt) REVERT: B 1107 ARG cc_start: 0.7289 (tmm160) cc_final: 0.6750 (ppt170) REVERT: C 41 LYS cc_start: 0.8215 (tppt) cc_final: 0.7710 (tppt) REVERT: C 65 PHE cc_start: 0.8284 (m-80) cc_final: 0.7834 (m-80) REVERT: C 88 ASP cc_start: 0.9183 (p0) cc_final: 0.8932 (p0) REVERT: C 92 PHE cc_start: 0.8453 (t80) cc_final: 0.7566 (t80) REVERT: C 117 LEU cc_start: 0.8837 (tt) cc_final: 0.8433 (pp) REVERT: C 129 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8514 (mmmt) REVERT: C 160 TYR cc_start: 0.8729 (p90) cc_final: 0.8448 (p90) REVERT: C 192 PHE cc_start: 0.8826 (m-80) cc_final: 0.8192 (m-80) REVERT: C 194 PHE cc_start: 0.7985 (m-80) cc_final: 0.7507 (m-80) REVERT: C 223 LEU cc_start: 0.8453 (pt) cc_final: 0.8032 (pt) REVERT: C 237 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8518 (mmm-85) REVERT: C 266 TYR cc_start: 0.7235 (m-80) cc_final: 0.6944 (m-10) REVERT: C 276 LEU cc_start: 0.7908 (tp) cc_final: 0.7706 (tp) REVERT: C 281 GLU cc_start: 0.8343 (tp30) cc_final: 0.7994 (tp30) REVERT: C 289 VAL cc_start: 0.8907 (t) cc_final: 0.8688 (p) REVERT: C 298 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7590 (mp0) REVERT: C 313 TYR cc_start: 0.7043 (m-10) cc_final: 0.6677 (m-10) REVERT: C 324 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8301 (mp0) REVERT: C 338 PHE cc_start: 0.9021 (m-80) cc_final: 0.8623 (m-10) REVERT: C 342 PHE cc_start: 0.8730 (m-80) cc_final: 0.8416 (m-80) REVERT: C 356 LYS cc_start: 0.8462 (tptp) cc_final: 0.7975 (tmmt) REVERT: C 365 TYR cc_start: 0.9046 (m-10) cc_final: 0.8512 (m-10) REVERT: C 377 PHE cc_start: 0.7783 (t80) cc_final: 0.7552 (t80) REVERT: C 380 TYR cc_start: 0.7405 (m-80) cc_final: 0.7130 (m-80) REVERT: C 386 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8231 (mtmm) REVERT: C 409 GLN cc_start: 0.8671 (mp10) cc_final: 0.8419 (mp10) REVERT: C 417 LYS cc_start: 0.9142 (tptt) cc_final: 0.8758 (tppt) REVERT: C 421 TYR cc_start: 0.8614 (m-10) cc_final: 0.8198 (m-80) REVERT: C 425 LEU cc_start: 0.8427 (mt) cc_final: 0.8040 (tp) REVERT: C 426 PRO cc_start: 0.8717 (Cg_exo) cc_final: 0.8151 (Cg_endo) REVERT: C 451 TYR cc_start: 0.6468 (m-80) cc_final: 0.6050 (m-80) REVERT: C 490 PHE cc_start: 0.8663 (t80) cc_final: 0.8392 (t80) REVERT: C 505 TYR cc_start: 0.8433 (t80) cc_final: 0.8167 (t80) REVERT: C 516 GLU cc_start: 0.7285 (mp0) cc_final: 0.6972 (mp0) REVERT: C 562 PHE cc_start: 0.8763 (p90) cc_final: 0.8364 (p90) REVERT: C 722 VAL cc_start: 0.4767 (p) cc_final: 0.4406 (p) REVERT: C 737 ASP cc_start: 0.8645 (t0) cc_final: 0.8328 (t0) REVERT: C 748 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8898 (mp0) REVERT: C 761 THR cc_start: 0.9314 (m) cc_final: 0.9061 (p) REVERT: C 762 GLN cc_start: 0.9086 (mt0) cc_final: 0.8511 (mt0) REVERT: C 764 ASN cc_start: 0.9073 (m110) cc_final: 0.8798 (m110) REVERT: C 765 ARG cc_start: 0.9140 (ptp-170) cc_final: 0.8611 (ptp90) REVERT: C 770 ILE cc_start: 0.9388 (mt) cc_final: 0.9152 (mm) REVERT: C 773 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 776 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8338 (tmtt) REVERT: C 858 LEU cc_start: 0.8755 (mp) cc_final: 0.8504 (mm) REVERT: C 869 MET cc_start: 0.9138 (mtm) cc_final: 0.8302 (mmt) REVERT: C 873 TYR cc_start: 0.8241 (m-10) cc_final: 0.7859 (m-80) REVERT: C 898 PHE cc_start: 0.6510 (t80) cc_final: 0.6114 (t80) REVERT: C 954 GLN cc_start: 0.9083 (mt0) cc_final: 0.8602 (tm-30) REVERT: C 957 GLN cc_start: 0.9240 (tt0) cc_final: 0.8805 (pp30) REVERT: C 964 LYS cc_start: 0.9425 (tttt) cc_final: 0.9058 (mmtt) REVERT: C 969 ASN cc_start: 0.8660 (p0) cc_final: 0.7984 (p0) REVERT: C 970 PHE cc_start: 0.8105 (m-80) cc_final: 0.7209 (m-10) REVERT: C 977 LEU cc_start: 0.9504 (mt) cc_final: 0.9276 (mp) REVERT: C 979 ASP cc_start: 0.9050 (m-30) cc_final: 0.8649 (m-30) REVERT: C 994 ASP cc_start: 0.8888 (m-30) cc_final: 0.8670 (m-30) REVERT: C 1000 ARG cc_start: 0.9148 (mtt-85) cc_final: 0.8696 (mmm160) REVERT: C 1001 LEU cc_start: 0.9444 (tp) cc_final: 0.9086 (tp) REVERT: C 1002 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8557 (mm110) REVERT: C 1010 GLN cc_start: 0.8813 (tp-100) cc_final: 0.7571 (tm-30) REVERT: C 1011 GLN cc_start: 0.8919 (pt0) cc_final: 0.8433 (pt0) REVERT: C 1014 ARG cc_start: 0.8667 (mmp80) cc_final: 0.7438 (mmp80) REVERT: C 1017 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8583 (tm-30) REVERT: C 1018 ILE cc_start: 0.8783 (pt) cc_final: 0.8198 (pt) REVERT: C 1052 PHE cc_start: 0.7769 (m-80) cc_final: 0.7499 (m-80) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.1937 time to fit residues: 161.0396 Evaluate side-chains 477 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 3.9990 chunk 271 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 265 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 218 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** A 409 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.180540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.135783 restraints weight = 65817.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.140658 restraints weight = 46626.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.144226 restraints weight = 35521.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.146888 restraints weight = 28756.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.148786 restraints weight = 24367.433| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26386 Z= 0.164 Angle : 0.719 11.613 36017 Z= 0.362 Chirality : 0.049 0.361 4182 Planarity : 0.005 0.071 4587 Dihedral : 5.360 35.708 3449 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % 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: -1.20 (0.14), residues: 3187 helix: 0.51 (0.19), residues: 688 sheet: -0.71 (0.20), residues: 611 loop : -1.35 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 319 TYR 0.023 0.001 TYR A 904 PHE 0.028 0.002 PHE A 562 TRP 0.018 0.002 TRP C 64 HIS 0.011 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (26300) covalent geometry : angle 0.69497 / 0.36 (35807) SS BOND : bond 0.00352 / 0.22 ( 42) SS BOND : angle 2.15295 / 1.58 ( 84) hydrogen bonds : bond 0.04623 / 3.16 ( 872) hydrogen bonds : angle 6.19141 / 4.17 ( 2433) Misc. bond : bond 0.00525 / 0.28 ( 2) link_BETA1-4 : bond 0.00378 / 0.26 ( 10) link_BETA1-4 : angle 1.00147 / 0.69 ( 30) link_NAG-ASN : bond 0.00560 / 0.33 ( 32) link_NAG-ASN : angle 3.03990 / 2.13 ( 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 529 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 528 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7869 (t80) cc_final: 0.7495 (t80) REVERT: A 53 ASP cc_start: 0.8577 (t0) cc_final: 0.8056 (t0) REVERT: A 65 PHE cc_start: 0.8125 (m-80) cc_final: 0.7478 (m-80) REVERT: A 106 PHE cc_start: 0.7474 (m-10) cc_final: 0.6621 (m-80) REVERT: A 128 ILE cc_start: 0.8717 (mt) cc_final: 0.7750 (mm) REVERT: A 170 TYR cc_start: 0.7526 (t80) cc_final: 0.7154 (t80) REVERT: A 177 MET cc_start: 0.3080 (mpp) cc_final: 0.2331 (mmp) REVERT: A 194 PHE cc_start: 0.7601 (t80) cc_final: 0.7216 (t80) REVERT: A 201 PHE cc_start: 0.8101 (m-80) cc_final: 0.7532 (m-80) REVERT: A 238 PHE cc_start: 0.7435 (m-10) cc_final: 0.7025 (m-10) REVERT: A 240 THR cc_start: 0.8328 (m) cc_final: 0.8107 (m) REVERT: A 275 PHE cc_start: 0.6622 (m-10) cc_final: 0.6060 (m-10) REVERT: A 310 LYS cc_start: 0.8558 (tptt) cc_final: 0.8173 (tppt) REVERT: A 323 THR cc_start: 0.8672 (p) cc_final: 0.7984 (p) REVERT: A 324 GLU cc_start: 0.7955 (mp0) cc_final: 0.7516 (mp0) REVERT: A 355 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.7962 (tpp80) REVERT: A 365 TYR cc_start: 0.8207 (m-80) cc_final: 0.7718 (m-80) REVERT: A 380 TYR cc_start: 0.8076 (m-80) cc_final: 0.7799 (m-80) REVERT: A 389 ASP cc_start: 0.8874 (m-30) cc_final: 0.8414 (p0) REVERT: A 421 TYR cc_start: 0.8059 (m-10) cc_final: 0.7837 (m-10) REVERT: A 461 LEU cc_start: 0.7917 (mt) cc_final: 0.7463 (mt) REVERT: A 557 LYS cc_start: 0.8316 (mttt) cc_final: 0.7493 (tptp) REVERT: A 562 PHE cc_start: 0.8346 (p90) cc_final: 0.8046 (p90) REVERT: A 567 ARG cc_start: 0.8329 (mtp180) cc_final: 0.7862 (mtt180) REVERT: A 585 LEU cc_start: 0.8674 (mp) cc_final: 0.8443 (mp) REVERT: A 755 GLN cc_start: 0.8690 (mp10) cc_final: 0.8367 (tt0) REVERT: A 759 PHE cc_start: 0.8848 (m-80) cc_final: 0.8005 (m-80) REVERT: A 776 LYS cc_start: 0.8977 (tptm) cc_final: 0.8389 (tptp) REVERT: A 869 MET cc_start: 0.8394 (ptp) cc_final: 0.8160 (ptp) REVERT: A 873 TYR cc_start: 0.8398 (m-10) cc_final: 0.8107 (m-80) REVERT: A 917 TYR cc_start: 0.7964 (m-80) cc_final: 0.7381 (m-10) REVERT: A 927 PHE cc_start: 0.7916 (t80) cc_final: 0.7397 (t80) REVERT: A 936 ASP cc_start: 0.8662 (m-30) cc_final: 0.8318 (m-30) REVERT: A 947 LYS cc_start: 0.7735 (mtpt) cc_final: 0.7504 (mmmt) REVERT: A 954 GLN cc_start: 0.9034 (tp40) cc_final: 0.8583 (tm-30) REVERT: A 959 LEU cc_start: 0.9346 (mp) cc_final: 0.9053 (mm) REVERT: A 960 ASN cc_start: 0.8643 (t0) cc_final: 0.7953 (m-40) REVERT: A 964 LYS cc_start: 0.9188 (ttmm) cc_final: 0.8706 (ptpp) REVERT: A 965 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 979 ASP cc_start: 0.9065 (m-30) cc_final: 0.8519 (t0) REVERT: A 983 ARG cc_start: 0.8734 (ptt90) cc_final: 0.7827 (ttp80) REVERT: A 990 GLU cc_start: 0.8746 (tt0) cc_final: 0.8449 (mt-10) REVERT: A 994 ASP cc_start: 0.8687 (m-30) cc_final: 0.8157 (m-30) REVERT: A 995 ARG cc_start: 0.8809 (ttm110) cc_final: 0.8218 (ptp-170) REVERT: A 1000 ARG cc_start: 0.8984 (mmt180) cc_final: 0.8645 (mmt180) REVERT: A 1001 LEU cc_start: 0.9221 (mt) cc_final: 0.8800 (pp) REVERT: A 1002 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8420 (tm-30) REVERT: A 1011 GLN cc_start: 0.8985 (tp40) cc_final: 0.8594 (tt0) REVERT: A 1014 ARG cc_start: 0.8875 (mmp-170) cc_final: 0.8560 (mmm160) REVERT: A 1023 ASN cc_start: 0.8787 (m110) cc_final: 0.8586 (m-40) REVERT: A 1050 MET cc_start: 0.5592 (ttt) cc_final: 0.5036 (ttt) REVERT: B 37 TYR cc_start: 0.8507 (p90) cc_final: 0.8092 (p90) REVERT: B 41 LYS cc_start: 0.8747 (tppt) cc_final: 0.8200 (mmmm) REVERT: B 58 PHE cc_start: 0.7885 (m-80) cc_final: 0.7331 (m-10) REVERT: B 65 PHE cc_start: 0.8127 (m-10) cc_final: 0.7867 (m-80) REVERT: B 86 PHE cc_start: 0.7764 (t80) cc_final: 0.7271 (t80) REVERT: B 105 ILE cc_start: 0.8827 (mp) cc_final: 0.8577 (tp) REVERT: B 129 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8072 (mmmt) REVERT: B 177 MET cc_start: 0.4658 (mpp) cc_final: 0.4179 (mpp) REVERT: B 194 PHE cc_start: 0.7901 (m-80) cc_final: 0.7363 (m-10) REVERT: B 265 TYR cc_start: 0.7004 (p90) cc_final: 0.6735 (p90) REVERT: B 275 PHE cc_start: 0.7444 (m-10) cc_final: 0.5980 (m-10) REVERT: B 276 LEU cc_start: 0.9170 (tt) cc_final: 0.8523 (mp) REVERT: B 287 ASP cc_start: 0.8256 (m-30) cc_final: 0.7433 (p0) REVERT: B 298 GLU cc_start: 0.8679 (tt0) cc_final: 0.8248 (tt0) REVERT: B 313 TYR cc_start: 0.7636 (m-80) cc_final: 0.7057 (m-10) REVERT: B 317 ASN cc_start: 0.8533 (p0) cc_final: 0.8277 (t0) REVERT: B 543 PHE cc_start: 0.8512 (p90) cc_final: 0.8144 (p90) REVERT: B 562 PHE cc_start: 0.8946 (p90) cc_final: 0.8461 (p90) REVERT: B 586 ASP cc_start: 0.8383 (t0) cc_final: 0.7826 (p0) REVERT: B 587 ILE cc_start: 0.8906 (mp) cc_final: 0.8590 (mp) REVERT: B 603 ASN cc_start: 0.9342 (t0) cc_final: 0.9137 (p0) REVERT: B 754 LEU cc_start: 0.8870 (mt) cc_final: 0.8662 (mt) REVERT: B 777 ASN cc_start: 0.8393 (m110) cc_final: 0.8123 (m-40) REVERT: B 819 GLU cc_start: 0.8979 (pt0) cc_final: 0.8382 (tm-30) REVERT: B 820 ASP cc_start: 0.8699 (t0) cc_final: 0.8454 (t0) REVERT: B 822 LEU cc_start: 0.9023 (tp) cc_final: 0.8552 (mt) REVERT: B 824 ASN cc_start: 0.8819 (m110) cc_final: 0.8566 (m110) REVERT: B 869 MET cc_start: 0.8572 (mpp) cc_final: 0.8333 (mmp) REVERT: B 917 TYR cc_start: 0.8369 (m-10) cc_final: 0.8109 (m-10) REVERT: B 927 PHE cc_start: 0.8602 (t80) cc_final: 0.7827 (t80) REVERT: B 937 SER cc_start: 0.8649 (t) cc_final: 0.8337 (p) REVERT: B 954 GLN cc_start: 0.9079 (mt0) cc_final: 0.8506 (tm-30) REVERT: B 955 ASN cc_start: 0.8955 (m110) cc_final: 0.8130 (m110) REVERT: B 957 GLN cc_start: 0.9113 (pt0) cc_final: 0.8878 (pp30) REVERT: B 978 ASN cc_start: 0.8806 (p0) cc_final: 0.8523 (p0) REVERT: B 979 ASP cc_start: 0.8680 (t0) cc_final: 0.8239 (t0) REVERT: B 983 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7069 (ttp-110) REVERT: B 995 ARG cc_start: 0.8503 (ptt180) cc_final: 0.8033 (ptt180) REVERT: B 1000 ARG cc_start: 0.8969 (ptp-110) cc_final: 0.8072 (ptm160) REVERT: B 1002 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 1011 GLN cc_start: 0.8634 (mm110) cc_final: 0.8299 (mp10) REVERT: B 1014 ARG cc_start: 0.8726 (mtt90) cc_final: 0.8398 (mmt-90) REVERT: B 1017 GLU cc_start: 0.8742 (pp20) cc_final: 0.8225 (pp20) REVERT: B 1018 ILE cc_start: 0.9091 (pt) cc_final: 0.8876 (pt) REVERT: B 1019 ARG cc_start: 0.8890 (ptm-80) cc_final: 0.8340 (ptm-80) REVERT: B 1028 LYS cc_start: 0.7301 (tptm) cc_final: 0.6956 (tptt) REVERT: B 1052 PHE cc_start: 0.8027 (m-10) cc_final: 0.7749 (m-80) REVERT: B 1107 ARG cc_start: 0.7127 (tmm160) cc_final: 0.6628 (ppt170) REVERT: C 41 LYS cc_start: 0.8299 (tppt) cc_final: 0.7741 (tppt) REVERT: C 65 PHE cc_start: 0.8256 (m-80) cc_final: 0.7779 (m-80) REVERT: C 88 ASP cc_start: 0.9118 (p0) cc_final: 0.8858 (p0) REVERT: C 92 PHE cc_start: 0.8377 (t80) cc_final: 0.7481 (t80) REVERT: C 117 LEU cc_start: 0.8774 (tt) cc_final: 0.8333 (pp) REVERT: C 129 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8652 (mmmt) REVERT: C 160 TYR cc_start: 0.8768 (p90) cc_final: 0.8274 (p90) REVERT: C 192 PHE cc_start: 0.8836 (m-80) cc_final: 0.8196 (m-80) REVERT: C 194 PHE cc_start: 0.7918 (m-80) cc_final: 0.7408 (m-80) REVERT: C 223 LEU cc_start: 0.8215 (pt) cc_final: 0.7871 (pt) REVERT: C 237 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8449 (mmm-85) REVERT: C 266 TYR cc_start: 0.7092 (m-80) cc_final: 0.6857 (m-10) REVERT: C 276 LEU cc_start: 0.7965 (tp) cc_final: 0.7742 (tp) REVERT: C 281 GLU cc_start: 0.8309 (tp30) cc_final: 0.7978 (tm-30) REVERT: C 289 VAL cc_start: 0.8836 (t) cc_final: 0.8635 (p) REVERT: C 298 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7485 (mp0) REVERT: C 313 TYR cc_start: 0.6885 (m-10) cc_final: 0.6552 (m-10) REVERT: C 324 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8223 (mp0) REVERT: C 338 PHE cc_start: 0.9044 (m-80) cc_final: 0.8629 (m-10) REVERT: C 342 PHE cc_start: 0.8819 (m-80) cc_final: 0.8439 (m-80) REVERT: C 354 ASN cc_start: 0.8871 (t0) cc_final: 0.8636 (t0) REVERT: C 356 LYS cc_start: 0.8495 (tptp) cc_final: 0.8000 (tmmt) REVERT: C 365 TYR cc_start: 0.9006 (m-10) cc_final: 0.8443 (m-10) REVERT: C 380 TYR cc_start: 0.7423 (m-80) cc_final: 0.7040 (m-80) REVERT: C 386 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8196 (mtmt) REVERT: C 409 GLN cc_start: 0.8559 (mp10) cc_final: 0.8088 (mp10) REVERT: C 417 LYS cc_start: 0.9130 (tptt) cc_final: 0.8830 (tppt) REVERT: C 421 TYR cc_start: 0.8602 (m-10) cc_final: 0.8333 (m-10) REVERT: C 425 LEU cc_start: 0.8270 (mt) cc_final: 0.7943 (tp) REVERT: C 426 PRO cc_start: 0.8673 (Cg_exo) cc_final: 0.8096 (Cg_endo) REVERT: C 451 TYR cc_start: 0.6320 (m-80) cc_final: 0.5829 (m-80) REVERT: C 490 PHE cc_start: 0.8712 (t80) cc_final: 0.8399 (t80) REVERT: C 505 TYR cc_start: 0.8453 (t80) cc_final: 0.8088 (t80) REVERT: C 722 VAL cc_start: 0.4914 (p) cc_final: 0.4544 (p) REVERT: C 737 ASP cc_start: 0.8636 (t0) cc_final: 0.8246 (t0) REVERT: C 761 THR cc_start: 0.9254 (m) cc_final: 0.9021 (p) REVERT: C 762 GLN cc_start: 0.9032 (mt0) cc_final: 0.8735 (mt0) REVERT: C 763 LEU cc_start: 0.9024 (mt) cc_final: 0.8727 (mt) REVERT: C 765 ARG cc_start: 0.9153 (ptp-170) cc_final: 0.8851 (ptp-110) REVERT: C 770 ILE cc_start: 0.9345 (mt) cc_final: 0.9072 (mm) REVERT: C 773 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 776 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8267 (tmtt) REVERT: C 802 PHE cc_start: 0.6415 (m-80) cc_final: 0.5536 (m-80) REVERT: C 858 LEU cc_start: 0.8774 (mp) cc_final: 0.8542 (mm) REVERT: C 869 MET cc_start: 0.9119 (mtm) cc_final: 0.8269 (mmt) REVERT: C 873 TYR cc_start: 0.8245 (m-10) cc_final: 0.7658 (m-80) REVERT: C 954 GLN cc_start: 0.9027 (mt0) cc_final: 0.8593 (tm-30) REVERT: C 957 GLN cc_start: 0.9239 (tt0) cc_final: 0.8693 (pp30) REVERT: C 964 LYS cc_start: 0.9391 (tttt) cc_final: 0.9051 (mmtt) REVERT: C 969 ASN cc_start: 0.8630 (p0) cc_final: 0.7945 (p0) REVERT: C 970 PHE cc_start: 0.8023 (m-80) cc_final: 0.7259 (m-10) REVERT: C 978 ASN cc_start: 0.9509 (m110) cc_final: 0.9308 (m110) REVERT: C 979 ASP cc_start: 0.9016 (m-30) cc_final: 0.8637 (m-30) REVERT: C 981 LEU cc_start: 0.9300 (mt) cc_final: 0.8813 (pp) REVERT: C 994 ASP cc_start: 0.8787 (m-30) cc_final: 0.8577 (m-30) REVERT: C 1000 ARG cc_start: 0.9103 (mtt-85) cc_final: 0.8530 (mmm160) REVERT: C 1005 GLN cc_start: 0.8797 (pp30) cc_final: 0.8476 (pp30) REVERT: C 1010 GLN cc_start: 0.8778 (tp-100) cc_final: 0.7561 (tm-30) REVERT: C 1011 GLN cc_start: 0.8827 (pt0) cc_final: 0.8332 (pt0) REVERT: C 1014 ARG cc_start: 0.8679 (mmp80) cc_final: 0.7361 (mmp80) REVERT: C 1017 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8595 (tm-30) REVERT: C 1018 ILE cc_start: 0.8768 (pt) cc_final: 0.8147 (pt) REVERT: C 1019 ARG cc_start: 0.8826 (ptp-170) cc_final: 0.8287 (ptt180) REVERT: C 1050 MET cc_start: 0.2577 (ttt) cc_final: 0.1939 (ttt) REVERT: C 1052 PHE cc_start: 0.7735 (m-80) cc_final: 0.7104 (m-80) outliers start: 1 outliers final: 0 residues processed: 529 average time/residue: 0.1928 time to fit residues: 156.9101 Evaluate side-chains 471 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 0.7980 chunk 181 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** A 409 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 207 HIS B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** 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 = 0.4564 r_free = 0.4564 target = 0.184827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.138544 restraints weight = 60060.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.142809 restraints weight = 44301.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.145925 restraints weight = 35059.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.148339 restraints weight = 29337.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.150134 restraints weight = 25483.087| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 26386 Z= 0.214 Angle : 0.745 13.187 36017 Z= 0.383 Chirality : 0.049 0.340 4182 Planarity : 0.005 0.073 4587 Dihedral : 5.501 36.114 3449 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -1.38 (0.14), residues: 3187 helix: 0.27 (0.19), residues: 683 sheet: -0.79 (0.21), residues: 570 loop : -1.44 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 319 TYR 0.024 0.002 TYR C 904 PHE 0.023 0.002 PHE A 86 TRP 0.018 0.002 TRP A 64 HIS 0.019 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (26300) covalent geometry : angle 0.72345 / 0.38 (35807) SS BOND : bond 0.00519 / 0.33 ( 42) SS BOND : angle 2.22408 / 1.58 ( 84) hydrogen bonds : bond 0.04926 / 3.38 ( 872) hydrogen bonds : angle 6.35259 / 4.30 ( 2433) Misc. bond : bond 0.01447 / 0.76 ( 2) link_BETA1-4 : bond 0.00478 / 0.33 ( 10) link_BETA1-4 : angle 1.11459 / 0.75 ( 30) link_NAG-ASN : bond 0.00570 / 0.33 ( 32) link_NAG-ASN : angle 2.90833 / 2.03 ( 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 528 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.944 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: 0.7886 (t80) cc_final: 0.7440 (t80) REVERT: A 53 ASP cc_start: 0.8600 (t0) cc_final: 0.8355 (m-30) REVERT: A 65 PHE cc_start: 0.8113 (m-80) cc_final: 0.7557 (m-80) REVERT: A 106 PHE cc_start: 0.7437 (m-10) cc_final: 0.6949 (m-10) REVERT: A 128 ILE cc_start: 0.8593 (mt) cc_final: 0.7630 (mm) REVERT: A 170 TYR cc_start: 0.7624 (t80) cc_final: 0.7210 (t80) REVERT: A 177 MET cc_start: 0.2873 (mpp) cc_final: 0.1846 (mmp) REVERT: A 195 LYS cc_start: 0.8866 (pttp) cc_final: 0.8521 (tptp) REVERT: A 201 PHE cc_start: 0.7983 (m-80) cc_final: 0.7472 (m-80) REVERT: A 240 THR cc_start: 0.8338 (m) cc_final: 0.8117 (m) REVERT: A 275 PHE cc_start: 0.6685 (m-10) cc_final: 0.6107 (m-10) REVERT: A 304 LYS cc_start: 0.8882 (mppt) cc_final: 0.8627 (mmtt) REVERT: A 355 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7929 (tpp80) REVERT: A 365 TYR cc_start: 0.8106 (m-80) cc_final: 0.7698 (m-80) REVERT: A 389 ASP cc_start: 0.8929 (m-30) cc_final: 0.8475 (p0) REVERT: A 408 ARG cc_start: 0.8993 (pmt-80) cc_final: 0.8744 (pmt-80) REVERT: A 557 LYS cc_start: 0.8389 (mttt) cc_final: 0.7462 (tptp) REVERT: A 562 PHE cc_start: 0.8325 (p90) cc_final: 0.7933 (p90) REVERT: A 585 LEU cc_start: 0.8669 (mp) cc_final: 0.8433 (mp) REVERT: A 731 MET cc_start: 0.8491 (ppp) cc_final: 0.8074 (ppp) REVERT: A 755 GLN cc_start: 0.8723 (mp10) cc_final: 0.8392 (tt0) REVERT: A 759 PHE cc_start: 0.8975 (m-80) cc_final: 0.8096 (m-80) REVERT: A 776 LYS cc_start: 0.9021 (tptm) cc_final: 0.8393 (tptp) REVERT: A 869 MET cc_start: 0.8320 (ptp) cc_final: 0.8069 (ptp) REVERT: A 873 TYR cc_start: 0.8519 (m-10) cc_final: 0.8209 (m-80) REVERT: A 917 TYR cc_start: 0.7974 (m-80) cc_final: 0.7547 (m-10) REVERT: A 927 PHE cc_start: 0.7779 (t80) cc_final: 0.7389 (t80) REVERT: A 936 ASP cc_start: 0.8759 (m-30) cc_final: 0.8448 (m-30) REVERT: A 947 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7515 (mmmt) REVERT: A 954 GLN cc_start: 0.9079 (tp40) cc_final: 0.8639 (tm-30) REVERT: A 959 LEU cc_start: 0.9387 (mp) cc_final: 0.9107 (mm) REVERT: A 960 ASN cc_start: 0.8816 (t0) cc_final: 0.8140 (m-40) REVERT: A 964 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8790 (ptpp) REVERT: A 979 ASP cc_start: 0.9085 (m-30) cc_final: 0.8522 (t0) REVERT: A 983 ARG cc_start: 0.8670 (ptt90) cc_final: 0.7815 (ttp80) REVERT: A 990 GLU cc_start: 0.8737 (tt0) cc_final: 0.8391 (mt-10) REVERT: A 994 ASP cc_start: 0.8742 (m-30) cc_final: 0.8270 (m-30) REVERT: A 1000 ARG cc_start: 0.8837 (mmt180) cc_final: 0.8577 (mmt180) REVERT: A 1001 LEU cc_start: 0.9292 (mt) cc_final: 0.8751 (pp) REVERT: A 1002 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 1011 GLN cc_start: 0.9070 (tp40) cc_final: 0.8556 (tt0) REVERT: A 1014 ARG cc_start: 0.8882 (mmp-170) cc_final: 0.8568 (mmm160) REVERT: A 1023 ASN cc_start: 0.8775 (m110) cc_final: 0.8571 (m-40) REVERT: A 1050 MET cc_start: 0.6102 (ttt) cc_final: 0.5541 (ttt) REVERT: B 37 TYR cc_start: 0.8650 (p90) cc_final: 0.8113 (p90) REVERT: B 41 LYS cc_start: 0.8738 (tppt) cc_final: 0.8178 (mmmm) REVERT: B 48 LEU cc_start: 0.8830 (mt) cc_final: 0.8320 (mt) REVERT: B 58 PHE cc_start: 0.7816 (m-80) cc_final: 0.6878 (m-10) REVERT: B 65 PHE cc_start: 0.8457 (m-10) cc_final: 0.8127 (m-80) REVERT: B 86 PHE cc_start: 0.7887 (t80) cc_final: 0.7352 (t80) REVERT: B 105 ILE cc_start: 0.8804 (mp) cc_final: 0.8498 (tp) REVERT: B 129 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8056 (mmmt) REVERT: B 177 MET cc_start: 0.5007 (mpp) cc_final: 0.4358 (mpp) REVERT: B 194 PHE cc_start: 0.7929 (m-80) cc_final: 0.7412 (m-10) REVERT: B 220 PHE cc_start: 0.7210 (m-10) cc_final: 0.6732 (m-10) REVERT: B 275 PHE cc_start: 0.7400 (m-10) cc_final: 0.5865 (m-10) REVERT: B 276 LEU cc_start: 0.9113 (tt) cc_final: 0.8570 (mp) REVERT: B 287 ASP cc_start: 0.8271 (m-30) cc_final: 0.7535 (p0) REVERT: B 298 GLU cc_start: 0.8671 (tt0) cc_final: 0.8327 (tt0) REVERT: B 300 LYS cc_start: 0.8090 (mttt) cc_final: 0.7426 (mtmm) REVERT: B 313 TYR cc_start: 0.7584 (m-80) cc_final: 0.7041 (m-10) REVERT: B 543 PHE cc_start: 0.8357 (p90) cc_final: 0.8091 (p90) REVERT: B 562 PHE cc_start: 0.8908 (p90) cc_final: 0.8363 (p90) REVERT: B 577 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7777 (tpt170) REVERT: B 586 ASP cc_start: 0.8428 (t0) cc_final: 0.7713 (p0) REVERT: B 587 ILE cc_start: 0.8912 (mp) cc_final: 0.8616 (mp) REVERT: B 731 MET cc_start: 0.8199 (tmm) cc_final: 0.7726 (tmm) REVERT: B 754 LEU cc_start: 0.8929 (mt) cc_final: 0.8713 (mt) REVERT: B 777 ASN cc_start: 0.8481 (m110) cc_final: 0.8214 (m-40) REVERT: B 819 GLU cc_start: 0.8956 (pt0) cc_final: 0.8398 (tm-30) REVERT: B 820 ASP cc_start: 0.8766 (t0) cc_final: 0.8527 (t0) REVERT: B 822 LEU cc_start: 0.9104 (tp) cc_final: 0.8654 (mt) REVERT: B 824 ASN cc_start: 0.8888 (m110) cc_final: 0.8643 (m110) REVERT: B 917 TYR cc_start: 0.8574 (m-10) cc_final: 0.8335 (m-10) REVERT: B 927 PHE cc_start: 0.8533 (t80) cc_final: 0.7770 (t80) REVERT: B 937 SER cc_start: 0.8879 (t) cc_final: 0.8516 (p) REVERT: B 954 GLN cc_start: 0.9022 (mt0) cc_final: 0.8572 (tm-30) REVERT: B 960 ASN cc_start: 0.8736 (t0) cc_final: 0.7845 (t0) REVERT: B 965 GLN cc_start: 0.8931 (mp-120) cc_final: 0.8636 (mm-40) REVERT: B 978 ASN cc_start: 0.8742 (p0) cc_final: 0.8459 (p0) REVERT: B 983 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7078 (ttp-170) REVERT: B 995 ARG cc_start: 0.8529 (ptt180) cc_final: 0.8233 (ptt180) REVERT: B 1011 GLN cc_start: 0.8551 (mm110) cc_final: 0.7877 (mm-40) REVERT: B 1014 ARG cc_start: 0.8675 (mtt90) cc_final: 0.8395 (mmt-90) REVERT: B 1017 GLU cc_start: 0.8761 (pp20) cc_final: 0.8207 (pp20) REVERT: B 1019 ARG cc_start: 0.8920 (ptm-80) cc_final: 0.8302 (ptm-80) REVERT: B 1028 LYS cc_start: 0.7348 (tptm) cc_final: 0.7070 (tptt) REVERT: B 1048 HIS cc_start: 0.6784 (p-80) cc_final: 0.6567 (p-80) REVERT: B 1052 PHE cc_start: 0.7922 (m-10) cc_final: 0.7655 (m-80) REVERT: B 1107 ARG cc_start: 0.7460 (tmm160) cc_final: 0.7133 (ppt170) REVERT: C 41 LYS cc_start: 0.8318 (tppt) cc_final: 0.7858 (tppt) REVERT: C 65 PHE cc_start: 0.8442 (m-80) cc_final: 0.7893 (m-80) REVERT: C 92 PHE cc_start: 0.8349 (t80) cc_final: 0.7438 (t80) REVERT: C 117 LEU cc_start: 0.8849 (tt) cc_final: 0.8389 (pp) REVERT: C 129 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8617 (mmmt) REVERT: C 160 TYR cc_start: 0.8791 (p90) cc_final: 0.8295 (p90) REVERT: C 177 MET cc_start: 0.5383 (mpp) cc_final: 0.4807 (mpp) REVERT: C 192 PHE cc_start: 0.8823 (m-80) cc_final: 0.8188 (m-80) REVERT: C 194 PHE cc_start: 0.7842 (m-80) cc_final: 0.7429 (m-80) REVERT: C 223 LEU cc_start: 0.8497 (pt) cc_final: 0.8165 (pt) REVERT: C 237 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8413 (mmm-85) REVERT: C 266 TYR cc_start: 0.7348 (m-80) cc_final: 0.6936 (m-10) REVERT: C 276 LEU cc_start: 0.8030 (tp) cc_final: 0.7782 (tp) REVERT: C 281 GLU cc_start: 0.8297 (tp30) cc_final: 0.7933 (tp30) REVERT: C 313 TYR cc_start: 0.7005 (m-10) cc_final: 0.6651 (m-10) REVERT: C 324 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8389 (mp0) REVERT: C 338 PHE cc_start: 0.9035 (m-80) cc_final: 0.8566 (m-10) REVERT: C 342 PHE cc_start: 0.8730 (m-80) cc_final: 0.8362 (m-80) REVERT: C 356 LYS cc_start: 0.8561 (tptp) cc_final: 0.8010 (tmmt) REVERT: C 365 TYR cc_start: 0.8960 (m-10) cc_final: 0.8457 (m-10) REVERT: C 380 TYR cc_start: 0.7394 (m-80) cc_final: 0.7100 (m-80) REVERT: C 386 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8341 (mtmt) REVERT: C 417 LYS cc_start: 0.9153 (tptt) cc_final: 0.8859 (tppt) REVERT: C 425 LEU cc_start: 0.8563 (mt) cc_final: 0.8184 (tp) REVERT: C 426 PRO cc_start: 0.8675 (Cg_exo) cc_final: 0.8065 (Cg_endo) REVERT: C 464 PHE cc_start: 0.7708 (p90) cc_final: 0.7495 (p90) REVERT: C 490 PHE cc_start: 0.8775 (t80) cc_final: 0.8149 (t80) REVERT: C 654 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 737 ASP cc_start: 0.8325 (t0) cc_final: 0.7566 (p0) REVERT: C 740 MET cc_start: 0.8847 (tpt) cc_final: 0.8519 (tpp) REVERT: C 762 GLN cc_start: 0.8887 (mt0) cc_final: 0.8620 (mt0) REVERT: C 763 LEU cc_start: 0.9167 (mt) cc_final: 0.8878 (mt) REVERT: C 764 ASN cc_start: 0.9276 (m-40) cc_final: 0.9016 (m-40) REVERT: C 765 ARG cc_start: 0.9068 (ptp-170) cc_final: 0.8778 (ptp90) REVERT: C 770 ILE cc_start: 0.9369 (mt) cc_final: 0.9124 (mm) REVERT: C 773 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 776 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8238 (tmtt) REVERT: C 869 MET cc_start: 0.9103 (mtm) cc_final: 0.8327 (tmm) REVERT: C 954 GLN cc_start: 0.8985 (mt0) cc_final: 0.8609 (tm-30) REVERT: C 957 GLN cc_start: 0.9283 (tt0) cc_final: 0.8762 (pp30) REVERT: C 964 LYS cc_start: 0.9455 (tttt) cc_final: 0.9145 (mmtt) REVERT: C 969 ASN cc_start: 0.8636 (p0) cc_final: 0.8044 (p0) REVERT: C 970 PHE cc_start: 0.8107 (m-80) cc_final: 0.7331 (m-10) REVERT: C 979 ASP cc_start: 0.9006 (m-30) cc_final: 0.8626 (m-30) REVERT: C 983 ARG cc_start: 0.9015 (tmt170) cc_final: 0.8777 (tpt90) REVERT: C 1000 ARG cc_start: 0.9159 (mtt-85) cc_final: 0.8658 (mmm160) REVERT: C 1010 GLN cc_start: 0.8850 (tp-100) cc_final: 0.7629 (tm-30) REVERT: C 1011 GLN cc_start: 0.8878 (pt0) cc_final: 0.8461 (pt0) REVERT: C 1014 ARG cc_start: 0.8737 (mmp80) cc_final: 0.7489 (mmp80) REVERT: C 1017 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8606 (tm-30) REVERT: C 1018 ILE cc_start: 0.8821 (pt) cc_final: 0.8242 (pt) REVERT: C 1050 MET cc_start: 0.2368 (ttt) cc_final: 0.1612 (ttt) REVERT: C 1052 PHE cc_start: 0.7797 (m-80) cc_final: 0.7238 (m-80) REVERT: C 1062 PHE cc_start: 0.5249 (m-80) cc_final: 0.4984 (m-80) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.1960 time to fit residues: 158.2263 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 : 0.922 ------------------------------------------------------------------------------- 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: 0.8980 chunk 187 optimal weight: 4.9990 chunk 214 optimal weight: 40.0000 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 250 optimal weight: 0.0980 chunk 207 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** A 409 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS 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 764 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C1048 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.179841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.131613 restraints weight = 63776.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136202 restraints weight = 46487.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.139588 restraints weight = 36465.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.141860 restraints weight = 30283.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.143696 restraints weight = 26475.182| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.7659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26386 Z= 0.149 Angle : 0.723 10.291 36017 Z= 0.363 Chirality : 0.048 0.329 4182 Planarity : 0.005 0.130 4587 Dihedral : 5.299 34.079 3449 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.43 % 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: -1.27 (0.14), residues: 3187 helix: 0.55 (0.20), residues: 674 sheet: -0.77 (0.20), residues: 578 loop : -1.42 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 319 TYR 0.022 0.001 TYR A1047 PHE 0.024 0.002 PHE C 802 TRP 0.019 0.002 TRP B 104 HIS 0.017 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (26300) covalent geometry : angle 0.70042 / 0.36 (35807) SS BOND : bond 0.00410 / 0.26 ( 42) SS BOND : angle 2.32029 / 1.65 ( 84) hydrogen bonds : bond 0.04388 / 3.02 ( 872) hydrogen bonds : angle 6.13642 / 4.14 ( 2433) Misc. bond : bond 0.00394 / 0.21 ( 2) link_BETA1-4 : bond 0.00326 / 0.21 ( 10) link_BETA1-4 : angle 1.02627 / 0.69 ( 30) link_NAG-ASN : bond 0.00578 / 0.34 ( 32) link_NAG-ASN : angle 2.82039 / 1.97 ( 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 522 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 0.953 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: 0.8633 (t0) cc_final: 0.8398 (m-30) REVERT: A 65 PHE cc_start: 0.8171 (m-80) cc_final: 0.7573 (m-80) REVERT: A 128 ILE cc_start: 0.8534 (mt) cc_final: 0.7640 (mm) REVERT: A 170 TYR cc_start: 0.7510 (t80) cc_final: 0.7105 (t80) REVERT: A 177 MET cc_start: 0.2297 (mpp) cc_final: 0.1354 (mmp) REVERT: A 201 PHE cc_start: 0.7739 (m-80) cc_final: 0.7499 (m-80) REVERT: A 240 THR cc_start: 0.8386 (m) cc_final: 0.8179 (m) REVERT: A 275 PHE cc_start: 0.6562 (m-10) cc_final: 0.6022 (m-10) REVERT: A 355 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8140 (ttm110) REVERT: A 365 TYR cc_start: 0.8074 (m-80) cc_final: 0.7636 (m-80) REVERT: A 380 TYR cc_start: 0.7908 (m-80) cc_final: 0.7671 (m-80) REVERT: A 389 ASP cc_start: 0.8842 (m-30) cc_final: 0.8409 (p0) REVERT: A 408 ARG cc_start: 0.8848 (pmt-80) cc_final: 0.8555 (pmt-80) REVERT: A 562 PHE cc_start: 0.8241 (p90) cc_final: 0.7878 (p90) REVERT: A 585 LEU cc_start: 0.8735 (mp) cc_final: 0.8502 (mp) REVERT: A 755 GLN cc_start: 0.8730 (mp10) cc_final: 0.8403 (tt0) REVERT: A 759 PHE cc_start: 0.8734 (m-80) cc_final: 0.8005 (m-80) REVERT: A 869 MET cc_start: 0.8322 (ptp) cc_final: 0.8098 (ptp) REVERT: A 873 TYR cc_start: 0.8446 (m-10) cc_final: 0.8063 (m-80) REVERT: A 917 TYR cc_start: 0.8027 (m-80) cc_final: 0.7579 (m-10) REVERT: A 927 PHE cc_start: 0.7798 (t80) cc_final: 0.7419 (t80) REVERT: A 947 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7432 (mmmt) REVERT: A 954 GLN cc_start: 0.9034 (tp40) cc_final: 0.8521 (tm-30) REVERT: A 959 LEU cc_start: 0.9351 (mp) cc_final: 0.9074 (mm) REVERT: A 960 ASN cc_start: 0.8672 (t0) cc_final: 0.7912 (m-40) REVERT: A 964 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8681 (ptpp) REVERT: A 979 ASP cc_start: 0.9002 (m-30) cc_final: 0.8535 (t0) REVERT: A 983 ARG cc_start: 0.8624 (ptt90) cc_final: 0.8332 (ttp-170) REVERT: A 990 GLU cc_start: 0.8712 (tt0) cc_final: 0.8390 (mt-10) REVERT: A 994 ASP cc_start: 0.8733 (m-30) cc_final: 0.8222 (m-30) REVERT: A 1001 LEU cc_start: 0.9110 (mt) cc_final: 0.8886 (mm) REVERT: A 1002 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 1011 GLN cc_start: 0.9093 (tp40) cc_final: 0.8666 (tt0) REVERT: A 1014 ARG cc_start: 0.8860 (mmp-170) cc_final: 0.8573 (mmp80) REVERT: A 1023 ASN cc_start: 0.8766 (m110) cc_final: 0.8561 (m-40) REVERT: A 1029 MET cc_start: 0.7579 (ptp) cc_final: 0.7280 (ptp) REVERT: A 1050 MET cc_start: 0.5800 (ttt) cc_final: 0.5289 (ttt) REVERT: A 1062 PHE cc_start: 0.5893 (m-80) cc_final: 0.5228 (m-80) REVERT: B 37 TYR cc_start: 0.8400 (p90) cc_final: 0.8040 (p90) REVERT: B 41 LYS cc_start: 0.8724 (tppt) cc_final: 0.8030 (mmmm) REVERT: B 65 PHE cc_start: 0.8277 (m-10) cc_final: 0.8027 (m-10) REVERT: B 86 PHE cc_start: 0.7628 (t80) cc_final: 0.7209 (t80) REVERT: B 105 ILE cc_start: 0.8846 (mp) cc_final: 0.8554 (tp) REVERT: B 129 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8045 (mmmt) REVERT: B 177 MET cc_start: 0.4464 (mpp) cc_final: 0.3967 (mpp) REVERT: B 194 PHE cc_start: 0.7874 (m-80) cc_final: 0.7405 (m-10) REVERT: B 220 PHE cc_start: 0.7133 (m-10) cc_final: 0.6620 (m-10) REVERT: B 275 PHE cc_start: 0.7287 (m-10) cc_final: 0.5716 (m-10) REVERT: B 276 LEU cc_start: 0.9089 (tt) cc_final: 0.8568 (mp) REVERT: B 287 ASP cc_start: 0.8201 (m-30) cc_final: 0.7425 (p0) REVERT: B 298 GLU cc_start: 0.8674 (tt0) cc_final: 0.8309 (tt0) REVERT: B 313 TYR cc_start: 0.7578 (m-80) cc_final: 0.7005 (m-10) REVERT: B 321 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7817 (pp30) REVERT: B 543 PHE cc_start: 0.8473 (p90) cc_final: 0.8049 (p90) REVERT: B 562 PHE cc_start: 0.8991 (p90) cc_final: 0.8523 (p90) REVERT: B 577 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7737 (tpt170) REVERT: B 586 ASP cc_start: 0.8339 (t0) cc_final: 0.7642 (p0) REVERT: B 587 ILE cc_start: 0.8852 (mp) cc_final: 0.8575 (mp) REVERT: B 592 PHE cc_start: 0.7534 (p90) cc_final: 0.7298 (p90) REVERT: B 759 PHE cc_start: 0.8067 (m-80) cc_final: 0.7849 (m-80) REVERT: B 777 ASN cc_start: 0.8394 (m110) cc_final: 0.8143 (m-40) REVERT: B 819 GLU cc_start: 0.8931 (pt0) cc_final: 0.8344 (tm-30) REVERT: B 820 ASP cc_start: 0.8701 (t0) cc_final: 0.8442 (t0) REVERT: B 822 LEU cc_start: 0.9011 (tp) cc_final: 0.8542 (mt) REVERT: B 824 ASN cc_start: 0.8825 (m110) cc_final: 0.8557 (m110) REVERT: B 868 GLU cc_start: 0.8702 (mp0) cc_final: 0.8479 (pp20) REVERT: B 927 PHE cc_start: 0.8509 (t80) cc_final: 0.7779 (t80) REVERT: B 937 SER cc_start: 0.8754 (t) cc_final: 0.8356 (p) REVERT: B 954 GLN cc_start: 0.9029 (mt0) cc_final: 0.8602 (tm-30) REVERT: B 964 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8490 (ptpp) REVERT: B 965 GLN cc_start: 0.8898 (mp-120) cc_final: 0.8425 (mm-40) REVERT: B 978 ASN cc_start: 0.8721 (p0) cc_final: 0.8365 (p0) REVERT: B 979 ASP cc_start: 0.8724 (t0) cc_final: 0.8431 (t0) REVERT: B 983 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7267 (ttp-170) REVERT: B 995 ARG cc_start: 0.8572 (ptt180) cc_final: 0.7981 (ptt-90) REVERT: B 1002 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8176 (tm-30) REVERT: B 1011 GLN cc_start: 0.8615 (mm110) cc_final: 0.8272 (mp10) REVERT: B 1014 ARG cc_start: 0.8729 (mtt90) cc_final: 0.8339 (mmt-90) REVERT: B 1017 GLU cc_start: 0.8768 (pp20) cc_final: 0.8220 (pp20) REVERT: B 1019 ARG cc_start: 0.9000 (ptm-80) cc_final: 0.8332 (ptm-80) REVERT: B 1028 LYS cc_start: 0.7335 (tptm) cc_final: 0.7073 (tptt) REVERT: B 1052 PHE cc_start: 0.8020 (m-10) cc_final: 0.7722 (m-80) REVERT: B 1107 ARG cc_start: 0.7385 (tmm160) cc_final: 0.7094 (tmt170) REVERT: C 41 LYS cc_start: 0.8256 (tppt) cc_final: 0.7756 (tppt) REVERT: C 65 PHE cc_start: 0.8373 (m-80) cc_final: 0.7889 (m-80) REVERT: C 92 PHE cc_start: 0.8277 (t80) cc_final: 0.7338 (t80) REVERT: C 117 LEU cc_start: 0.8833 (tt) cc_final: 0.8386 (pp) REVERT: C 129 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8613 (mmmt) REVERT: C 160 TYR cc_start: 0.8769 (p90) cc_final: 0.8277 (p90) REVERT: C 177 MET cc_start: 0.5474 (mpp) cc_final: 0.4973 (mpp) REVERT: C 192 PHE cc_start: 0.8826 (m-80) cc_final: 0.8199 (m-80) REVERT: C 194 PHE cc_start: 0.7857 (m-80) cc_final: 0.7445 (m-80) REVERT: C 223 LEU cc_start: 0.8292 (pt) cc_final: 0.7962 (pt) REVERT: C 237 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8299 (mmm-85) REVERT: C 266 TYR cc_start: 0.7241 (m-80) cc_final: 0.6817 (m-10) REVERT: C 276 LEU cc_start: 0.8094 (tp) cc_final: 0.7882 (tp) REVERT: C 281 GLU cc_start: 0.8257 (tp30) cc_final: 0.7981 (tm-30) REVERT: C 298 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7512 (mp0) REVERT: C 300 LYS cc_start: 0.8154 (mttt) cc_final: 0.7695 (mmtp) REVERT: C 313 TYR cc_start: 0.7005 (m-10) cc_final: 0.6672 (m-10) REVERT: C 324 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8330 (mp0) REVERT: C 338 PHE cc_start: 0.9019 (m-80) cc_final: 0.8523 (m-10) REVERT: C 342 PHE cc_start: 0.8678 (m-80) cc_final: 0.8286 (m-80) REVERT: C 356 LYS cc_start: 0.8527 (tptp) cc_final: 0.8040 (tmmt) REVERT: C 365 TYR cc_start: 0.8995 (m-10) cc_final: 0.8481 (m-10) REVERT: C 377 PHE cc_start: 0.7586 (t80) cc_final: 0.7343 (t80) REVERT: C 380 TYR cc_start: 0.7325 (m-80) cc_final: 0.6932 (m-80) REVERT: C 386 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8300 (mtmt) REVERT: C 417 LYS cc_start: 0.9123 (tptt) cc_final: 0.8828 (tppt) REVERT: C 425 LEU cc_start: 0.8461 (mt) cc_final: 0.8138 (tp) REVERT: C 426 PRO cc_start: 0.8689 (Cg_exo) cc_final: 0.8059 (Cg_endo) REVERT: C 490 PHE cc_start: 0.8542 (t80) cc_final: 0.8275 (t80) REVERT: C 505 TYR cc_start: 0.8360 (t80) cc_final: 0.8047 (t80) REVERT: C 562 PHE cc_start: 0.8757 (p90) cc_final: 0.8479 (p90) REVERT: C 654 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6846 (mm-30) REVERT: C 737 ASP cc_start: 0.8251 (t0) cc_final: 0.7523 (p0) REVERT: C 740 MET cc_start: 0.8644 (tpt) cc_final: 0.8296 (tpp) REVERT: C 762 GLN cc_start: 0.8862 (mt0) cc_final: 0.8278 (mp10) REVERT: C 763 LEU cc_start: 0.9208 (mt) cc_final: 0.8983 (mt) REVERT: C 764 ASN cc_start: 0.9262 (m-40) cc_final: 0.8961 (m110) REVERT: C 765 ARG cc_start: 0.8917 (ptp-170) cc_final: 0.8657 (ptp-110) REVERT: C 770 ILE cc_start: 0.9335 (mt) cc_final: 0.8983 (mm) REVERT: C 773 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7924 (mm-30) REVERT: C 776 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8223 (tmtt) REVERT: C 869 MET cc_start: 0.9158 (mtm) cc_final: 0.8369 (mmt) REVERT: C 873 TYR cc_start: 0.8199 (m-10) cc_final: 0.7746 (m-80) REVERT: C 954 GLN cc_start: 0.8991 (mt0) cc_final: 0.8731 (tm-30) REVERT: C 964 LYS cc_start: 0.9405 (tttt) cc_final: 0.9116 (mmtt) REVERT: C 969 ASN cc_start: 0.8570 (p0) cc_final: 0.7993 (p0) REVERT: C 970 PHE cc_start: 0.7989 (m-80) cc_final: 0.7393 (m-10) REVERT: C 979 ASP cc_start: 0.8874 (m-30) cc_final: 0.8479 (m-30) REVERT: C 983 ARG cc_start: 0.8930 (tmt170) cc_final: 0.8693 (tpt90) REVERT: C 994 ASP cc_start: 0.8878 (m-30) cc_final: 0.8668 (m-30) REVERT: C 1000 ARG cc_start: 0.9042 (mtt-85) cc_final: 0.8642 (mmm-85) REVERT: C 1010 GLN cc_start: 0.8815 (tp-100) cc_final: 0.7568 (tm-30) REVERT: C 1011 GLN cc_start: 0.8815 (pt0) cc_final: 0.8327 (pt0) REVERT: C 1014 ARG cc_start: 0.8692 (mmp80) cc_final: 0.7472 (mmp80) REVERT: C 1017 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8593 (tm-30) REVERT: C 1018 ILE cc_start: 0.8693 (pt) cc_final: 0.8188 (pt) REVERT: C 1019 ARG cc_start: 0.8879 (ptp-170) cc_final: 0.8299 (ptt180) REVERT: C 1050 MET cc_start: 0.2628 (ttt) cc_final: 0.1981 (ttt) REVERT: C 1052 PHE cc_start: 0.7661 (m-80) cc_final: 0.7148 (m-80) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.1931 time to fit residues: 154.5136 Evaluate side-chains 468 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 40.0000 chunk 267 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 304 optimal weight: 0.0050 chunk 187 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN B 207 HIS ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1064 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.169044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.126657 restraints weight = 68853.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.131869 restraints weight = 47052.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.135638 restraints weight = 35101.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.138401 restraints weight = 27811.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.140362 restraints weight = 23147.308| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26386 Z= 0.147 Angle : 0.725 15.728 36017 Z= 0.363 Chirality : 0.048 0.321 4182 Planarity : 0.005 0.111 4587 Dihedral : 5.221 33.608 3449 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.25 (0.14), residues: 3187 helix: 0.59 (0.20), residues: 673 sheet: -0.82 (0.20), residues: 605 loop : -1.39 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.026 0.001 TYR C 904 PHE 0.022 0.002 PHE A 86 TRP 0.018 0.002 TRP B 104 HIS 0.013 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (26300) covalent geometry : angle 0.70242 / 0.36 (35807) SS BOND : bond 0.00355 / 0.22 ( 42) SS BOND : angle 2.40904 / 1.79 ( 84) hydrogen bonds : bond 0.04359 / 3.01 ( 872) hydrogen bonds : angle 6.07724 / 4.09 ( 2433) Misc. bond : bond 0.00392 / 0.21 ( 2) link_BETA1-4 : bond 0.00352 / 0.23 ( 10) link_BETA1-4 : angle 1.00770 / 0.68 ( 30) link_NAG-ASN : bond 0.00568 / 0.33 ( 32) link_NAG-ASN : angle 2.75649 / 1.92 ( 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 521 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.033 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: 0.8311 (t80) cc_final: 0.7902 (t80) REVERT: A 65 PHE cc_start: 0.8132 (m-80) cc_final: 0.7548 (m-80) REVERT: A 106 PHE cc_start: 0.7618 (m-10) cc_final: 0.6570 (m-10) REVERT: A 128 ILE cc_start: 0.8571 (mt) cc_final: 0.7626 (mm) REVERT: A 170 TYR cc_start: 0.7727 (t80) cc_final: 0.7233 (t80) REVERT: A 177 MET cc_start: 0.2363 (mpp) cc_final: 0.1422 (mmp) REVERT: A 207 HIS cc_start: 0.9012 (p-80) cc_final: 0.8794 (p-80) REVERT: A 240 THR cc_start: 0.8459 (m) cc_final: 0.8221 (m) REVERT: A 275 PHE cc_start: 0.6441 (m-10) cc_final: 0.5871 (m-10) REVERT: A 365 TYR cc_start: 0.8112 (m-80) cc_final: 0.7663 (m-80) REVERT: A 380 TYR cc_start: 0.7961 (m-80) cc_final: 0.7683 (m-80) REVERT: A 389 ASP cc_start: 0.8827 (m-30) cc_final: 0.8400 (p0) REVERT: A 408 ARG cc_start: 0.8844 (pmt-80) cc_final: 0.8501 (pmt-80) REVERT: A 461 LEU cc_start: 0.7978 (mt) cc_final: 0.7564 (mt) REVERT: A 562 PHE cc_start: 0.8254 (p90) cc_final: 0.7324 (p90) REVERT: A 577 ARG cc_start: 0.7381 (tmt170) cc_final: 0.7119 (tmm160) REVERT: A 585 LEU cc_start: 0.8741 (mp) cc_final: 0.8502 (mp) REVERT: A 755 GLN cc_start: 0.8695 (mp10) cc_final: 0.8354 (tt0) REVERT: A 759 PHE cc_start: 0.8732 (m-80) cc_final: 0.7943 (m-80) REVERT: A 776 LYS cc_start: 0.8955 (tptm) cc_final: 0.8397 (tptp) REVERT: A 824 ASN cc_start: 0.8406 (m-40) cc_final: 0.8183 (m-40) REVERT: A 873 TYR cc_start: 0.8489 (m-10) cc_final: 0.8120 (m-80) REVERT: A 917 TYR cc_start: 0.8012 (m-80) cc_final: 0.7574 (m-10) REVERT: A 927 PHE cc_start: 0.7922 (t80) cc_final: 0.7386 (t80) REVERT: A 947 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7405 (mmmt) REVERT: A 954 GLN cc_start: 0.8969 (tp40) cc_final: 0.8515 (tm-30) REVERT: A 959 LEU cc_start: 0.9268 (mp) cc_final: 0.9003 (mm) REVERT: A 960 ASN cc_start: 0.8583 (t0) cc_final: 0.7956 (m-40) REVERT: A 964 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8661 (ptpp) REVERT: A 979 ASP cc_start: 0.9006 (m-30) cc_final: 0.8538 (t0) REVERT: A 983 ARG cc_start: 0.8680 (ptt90) cc_final: 0.8342 (ttp-170) REVERT: A 990 GLU cc_start: 0.8686 (tt0) cc_final: 0.8290 (mt-10) REVERT: A 994 ASP cc_start: 0.8660 (m-30) cc_final: 0.8138 (m-30) REVERT: A 1002 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 1006 THR cc_start: 0.9017 (m) cc_final: 0.8737 (p) REVERT: A 1014 ARG cc_start: 0.8778 (mmp-170) cc_final: 0.8412 (mmp-170) REVERT: A 1029 MET cc_start: 0.7635 (ptp) cc_final: 0.7404 (ptp) REVERT: A 1050 MET cc_start: 0.5932 (ttt) cc_final: 0.5506 (ttt) REVERT: A 1062 PHE cc_start: 0.5786 (m-80) cc_final: 0.5273 (m-80) REVERT: B 37 TYR cc_start: 0.8376 (p90) cc_final: 0.8101 (p90) REVERT: B 41 LYS cc_start: 0.8845 (tppt) cc_final: 0.8106 (tppt) REVERT: B 65 PHE cc_start: 0.8358 (m-10) cc_final: 0.8025 (m-10) REVERT: B 86 PHE cc_start: 0.7621 (t80) cc_final: 0.7379 (t80) REVERT: B 105 ILE cc_start: 0.8842 (mp) cc_final: 0.8580 (tp) REVERT: B 129 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8033 (mmmt) REVERT: B 177 MET cc_start: 0.4857 (mpp) cc_final: 0.4343 (mpp) REVERT: B 194 PHE cc_start: 0.7866 (m-80) cc_final: 0.7396 (m-10) REVERT: B 266 TYR cc_start: 0.7531 (m-80) cc_final: 0.7276 (m-80) REVERT: B 275 PHE cc_start: 0.6851 (m-10) cc_final: 0.5314 (m-10) REVERT: B 276 LEU cc_start: 0.9161 (tt) cc_final: 0.8578 (mp) REVERT: B 287 ASP cc_start: 0.8240 (m-30) cc_final: 0.7458 (p0) REVERT: B 294 ASP cc_start: 0.8994 (m-30) cc_final: 0.8361 (m-30) REVERT: B 298 GLU cc_start: 0.8621 (tt0) cc_final: 0.8079 (mp0) REVERT: B 313 TYR cc_start: 0.7587 (m-80) cc_final: 0.7025 (m-10) REVERT: B 543 PHE cc_start: 0.8431 (p90) cc_final: 0.8175 (p90) REVERT: B 562 PHE cc_start: 0.9002 (p90) cc_final: 0.8558 (p90) REVERT: B 577 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7729 (tpt170) REVERT: B 586 ASP cc_start: 0.8388 (t0) cc_final: 0.7660 (p0) REVERT: B 587 ILE cc_start: 0.8854 (mp) cc_final: 0.8581 (mp) REVERT: B 592 PHE cc_start: 0.7330 (p90) cc_final: 0.7091 (p90) REVERT: B 754 LEU cc_start: 0.8883 (mt) cc_final: 0.8580 (tp) REVERT: B 777 ASN cc_start: 0.8354 (m110) cc_final: 0.8074 (m-40) REVERT: B 819 GLU cc_start: 0.8917 (pt0) cc_final: 0.8337 (tm-30) REVERT: B 820 ASP cc_start: 0.8701 (t0) cc_final: 0.8433 (t0) REVERT: B 822 LEU cc_start: 0.9028 (tp) cc_final: 0.8543 (mt) REVERT: B 824 ASN cc_start: 0.8816 (m110) cc_final: 0.8536 (m110) REVERT: B 877 LEU cc_start: 0.8378 (mt) cc_final: 0.8140 (tt) REVERT: B 917 TYR cc_start: 0.8360 (m-80) cc_final: 0.7626 (m-10) REVERT: B 927 PHE cc_start: 0.8601 (t80) cc_final: 0.7844 (t80) REVERT: B 937 SER cc_start: 0.8733 (t) cc_final: 0.8341 (p) REVERT: B 954 GLN cc_start: 0.9008 (mt0) cc_final: 0.8611 (tm-30) REVERT: B 965 GLN cc_start: 0.8955 (mp-120) cc_final: 0.7961 (mm-40) REVERT: B 978 ASN cc_start: 0.8692 (p0) cc_final: 0.8347 (p0) REVERT: B 979 ASP cc_start: 0.8718 (t0) cc_final: 0.8429 (t0) REVERT: B 983 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7262 (ttp-170) REVERT: B 995 ARG cc_start: 0.8550 (ptt180) cc_final: 0.8143 (ptt-90) REVERT: B 1002 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8115 (tm-30) REVERT: B 1011 GLN cc_start: 0.8594 (mm110) cc_final: 0.8163 (mp10) REVERT: B 1017 GLU cc_start: 0.8744 (pp20) cc_final: 0.8185 (pp20) REVERT: B 1019 ARG cc_start: 0.8922 (ptm-80) cc_final: 0.8412 (ptm-80) REVERT: B 1028 LYS cc_start: 0.7381 (tptm) cc_final: 0.7076 (tptt) REVERT: B 1052 PHE cc_start: 0.8014 (m-10) cc_final: 0.7743 (m-80) REVERT: B 1107 ARG cc_start: 0.7374 (tmm160) cc_final: 0.7032 (ppt170) REVERT: C 41 LYS cc_start: 0.8309 (tppt) cc_final: 0.7880 (tppt) REVERT: C 65 PHE cc_start: 0.8343 (m-80) cc_final: 0.7812 (m-80) REVERT: C 92 PHE cc_start: 0.8364 (t80) cc_final: 0.7363 (t80) REVERT: C 117 LEU cc_start: 0.8682 (tt) cc_final: 0.8025 (pt) REVERT: C 129 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8614 (mmmt) REVERT: C 160 TYR cc_start: 0.8749 (p90) cc_final: 0.8277 (p90) REVERT: C 192 PHE cc_start: 0.8843 (m-80) cc_final: 0.8206 (m-80) REVERT: C 194 PHE cc_start: 0.7906 (m-80) cc_final: 0.7427 (m-80) REVERT: C 223 LEU cc_start: 0.8245 (pt) cc_final: 0.7900 (pt) REVERT: C 235 ILE cc_start: 0.7105 (mm) cc_final: 0.6897 (mm) REVERT: C 237 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8311 (mmm-85) REVERT: C 276 LEU cc_start: 0.8244 (tp) cc_final: 0.8024 (tp) REVERT: C 281 GLU cc_start: 0.8279 (tp30) cc_final: 0.7999 (tm-30) REVERT: C 298 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7507 (mp0) REVERT: C 300 LYS cc_start: 0.8262 (mttt) cc_final: 0.7770 (mmtp) REVERT: C 313 TYR cc_start: 0.7112 (m-10) cc_final: 0.6803 (m-10) REVERT: C 324 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8279 (mp0) REVERT: C 338 PHE cc_start: 0.9125 (m-80) cc_final: 0.8630 (m-10) REVERT: C 342 PHE cc_start: 0.8745 (m-80) cc_final: 0.8361 (m-80) REVERT: C 353 TRP cc_start: 0.7310 (p-90) cc_final: 0.6976 (p90) REVERT: C 354 ASN cc_start: 0.8878 (t0) cc_final: 0.8641 (t0) REVERT: C 356 LYS cc_start: 0.8567 (tptp) cc_final: 0.8068 (ttpt) REVERT: C 365 TYR cc_start: 0.9012 (m-10) cc_final: 0.8489 (m-10) REVERT: C 377 PHE cc_start: 0.7727 (t80) cc_final: 0.7522 (t80) REVERT: C 380 TYR cc_start: 0.7508 (m-80) cc_final: 0.7027 (m-80) REVERT: C 386 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8283 (mtmt) REVERT: C 417 LYS cc_start: 0.9068 (tptt) cc_final: 0.8724 (tppt) REVERT: C 418 ILE cc_start: 0.9567 (pt) cc_final: 0.9157 (mp) REVERT: C 421 TYR cc_start: 0.8585 (m-10) cc_final: 0.8178 (m-10) REVERT: C 425 LEU cc_start: 0.8421 (mt) cc_final: 0.8059 (tp) REVERT: C 471 GLU cc_start: 0.8268 (pm20) cc_final: 0.8020 (mp0) REVERT: C 490 PHE cc_start: 0.8620 (t80) cc_final: 0.8304 (t80) REVERT: C 505 TYR cc_start: 0.8578 (t80) cc_final: 0.8268 (t80) REVERT: C 516 GLU cc_start: 0.7614 (mp0) cc_final: 0.7157 (pm20) REVERT: C 563 GLN cc_start: 0.7637 (mm-40) cc_final: 0.6922 (mm-40) REVERT: C 654 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6884 (mm-30) REVERT: C 731 MET cc_start: 0.8207 (ppp) cc_final: 0.7983 (ppp) REVERT: C 737 ASP cc_start: 0.8273 (t0) cc_final: 0.7512 (p0) REVERT: C 740 MET cc_start: 0.8663 (tpt) cc_final: 0.8237 (tpp) REVERT: C 762 GLN cc_start: 0.8881 (mt0) cc_final: 0.8421 (mp10) REVERT: C 763 LEU cc_start: 0.9188 (mt) cc_final: 0.8946 (mt) REVERT: C 764 ASN cc_start: 0.9269 (m-40) cc_final: 0.8991 (m110) REVERT: C 770 ILE cc_start: 0.9252 (mt) cc_final: 0.8935 (mm) REVERT: C 773 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7842 (mm-30) REVERT: C 776 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8224 (tmtt) REVERT: C 869 MET cc_start: 0.9123 (mtm) cc_final: 0.8388 (mmt) REVERT: C 873 TYR cc_start: 0.8205 (m-10) cc_final: 0.7813 (m-80) REVERT: C 902 MET cc_start: 0.4872 (ptm) cc_final: 0.3570 (mmt) REVERT: C 954 GLN cc_start: 0.9023 (mt0) cc_final: 0.8732 (tm-30) REVERT: C 966 LEU cc_start: 0.9321 (mm) cc_final: 0.9057 (mt) REVERT: C 969 ASN cc_start: 0.8581 (p0) cc_final: 0.7942 (p0) REVERT: C 970 PHE cc_start: 0.7993 (m-80) cc_final: 0.7392 (m-10) REVERT: C 979 ASP cc_start: 0.8891 (m-30) cc_final: 0.8495 (m-30) REVERT: C 994 ASP cc_start: 0.8853 (m-30) cc_final: 0.8642 (m-30) REVERT: C 995 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8202 (mtm180) REVERT: C 1000 ARG cc_start: 0.9078 (mtt-85) cc_final: 0.8720 (mmm160) REVERT: C 1010 GLN cc_start: 0.8788 (tp-100) cc_final: 0.7569 (tm-30) REVERT: C 1011 GLN cc_start: 0.8827 (pt0) cc_final: 0.8342 (pt0) REVERT: C 1012 LEU cc_start: 0.9286 (mt) cc_final: 0.9080 (mt) REVERT: C 1014 ARG cc_start: 0.8675 (mmp80) cc_final: 0.7331 (mmp80) REVERT: C 1017 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8558 (tm-30) REVERT: C 1018 ILE cc_start: 0.8780 (pt) cc_final: 0.8148 (pt) REVERT: C 1019 ARG cc_start: 0.8760 (ptp-170) cc_final: 0.8160 (ptt180) REVERT: C 1050 MET cc_start: 0.2573 (ttt) cc_final: 0.1717 (ttt) REVERT: C 1052 PHE cc_start: 0.7714 (m-80) cc_final: 0.7215 (m-80) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.1934 time to fit residues: 154.4912 Evaluate side-chains 471 residues out of total 2812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 0.8980 chunk 223 optimal weight: 0.5980 chunk 196 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 777 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 764 ASN B 935 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.172605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.128003 restraints weight = 66155.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.132938 restraints weight = 46485.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.136475 restraints weight = 35470.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.139084 restraints weight = 28770.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.141032 restraints weight = 24428.526| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26386 Z= 0.150 Angle : 0.723 13.673 36017 Z= 0.364 Chirality : 0.048 0.318 4182 Planarity : 0.005 0.070 4587 Dihedral : 5.204 33.448 3449 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % 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 : 0.07 % 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: -1.27 (0.14), residues: 3187 helix: 0.55 (0.20), residues: 673 sheet: -0.79 (0.20), residues: 592 loop : -1.41 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 319 TYR 0.023 0.001 TYR B 917 PHE 0.026 0.002 PHE C 592 TRP 0.020 0.002 TRP C 64 HIS 0.011 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (26300) covalent geometry : angle 0.70187 / 0.36 (35807) SS BOND : bond 0.00387 / 0.22 ( 42) SS BOND : angle 2.39356 / 1.76 ( 84) hydrogen bonds : bond 0.04357 / 3.02 ( 872) hydrogen bonds : angle 6.04573 / 4.07 ( 2433) Misc. bond : bond 0.00413 / 0.22 ( 2) link_BETA1-4 : bond 0.00353 / 0.24 ( 10) link_BETA1-4 : angle 0.98998 / 0.67 ( 30) link_NAG-ASN : bond 0.00548 / 0.33 ( 32) link_NAG-ASN : angle 2.68721 / 1.88 ( 96) =============================================================================== Job complete usr+sys time: 6039.41 seconds wall clock time: 105 minutes 6.04 seconds (6306.04 seconds total)