Starting phenix.real_space_refine on Sat Jul 4 18:09:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dm1_27523/07_2026/8dm1_27523.cif" } resolution = 3.04 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 101 5.16 5 C 14181 2.51 5 N 3631 2.21 5 O 4363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 22276 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6641 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 43, 'TRANS': 807} Chain breaks: 8 Chain: "B" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6650 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 43, 'TRANS': 808} Chain breaks: 8 Chain: "C" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "D" 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: "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: "F" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 Chain: "B" 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 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.16, per 1000 atoms: 0.19 Number of scatterers: 22276 At special positions: 0 Unit cell: (138, 149, 173, 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 101 16.00 O 4363 8.00 N 3631 7.00 C 14181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 917.7 milliseconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 41 sheets defined 26.9% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.022A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.598A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.880A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.997A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.145A 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 616 through 620 removed outlier: 3.976A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.558A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.698A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.930A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.156A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.044A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.926A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.841A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.564A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.730A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.752A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.936A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.052A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.197A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.617A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.553A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.015A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.765A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.853A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.740A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.916A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.630A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.278A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.676A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.695A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.926A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.849A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.803A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.238A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.827A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.448A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.318A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.645A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.999A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.866A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.967A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.909A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.909A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.746A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.957A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.478A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.478A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.431A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 1032 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6879 1.34 - 1.46: 5361 1.46 - 1.58: 10384 1.58 - 1.70: 0 1.70 - 1.82: 131 Bond restraints: 22755 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.417 -0.082 1.38e-02 5.25e+03 3.56e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.87e+00 ... (remaining 22750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 29929 2.17 - 4.33: 953 4.33 - 6.50: 44 6.50 - 8.67: 23 8.67 - 10.83: 1 Bond angle restraints: 30950 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.46 129.76 -7.30 1.41e+00 5.03e-01 2.68e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.55 -7.09 1.41e+00 5.03e-01 2.53e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.42 -6.96 1.41e+00 5.03e-01 2.44e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.96 -5.26 1.22e+00 6.72e-01 1.86e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.93 -5.23 1.22e+00 6.72e-01 1.84e+01 ... (remaining 30945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12125 17.92 - 35.83: 808 35.83 - 53.75: 158 53.75 - 71.67: 43 71.67 - 89.58: 23 Dihedral angle restraints: 13157 sinusoidal: 5150 harmonic: 8007 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -55.09 -30.91 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -55.46 -30.54 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -56.42 -29.58 1 1.00e+01 1.00e-02 1.25e+01 ... (remaining 13154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2471 0.047 - 0.095: 806 0.095 - 0.142: 362 0.142 - 0.189: 56 0.189 - 0.237: 8 Chirality restraints: 3703 Sorted by residual: chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL B 227 " pdb=" CA VAL B 227 " pdb=" CG1 VAL B 227 " pdb=" CG2 VAL B 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3700 not shown) Planarity restraints: 3957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 953 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ASN C 953 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN C 953 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS C 954 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C VAL B 952 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL B 952 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 953 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 954 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C HIS B 954 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS B 954 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.022 2.00e-02 2.50e+03 ... (remaining 3954 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6584 2.82 - 3.34: 19060 3.34 - 3.86: 38323 3.86 - 4.38: 43747 4.38 - 4.90: 75829 Nonbonded interactions: 183543 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.354 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.360 3.040 ... (remaining 183538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 528 or resid 530 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.590 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22844 Z= 0.256 Angle : 0.853 10.833 31183 Z= 0.470 Chirality : 0.056 0.237 3703 Planarity : 0.007 0.067 3920 Dihedral : 13.273 89.584 7887 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.54 % Allowed : 4.22 % Favored : 95.24 % Cbeta Deviations : 0.00 % 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: 0.41 (0.15), residues: 2699 helix: 1.91 (0.18), residues: 653 sheet: 0.66 (0.19), residues: 611 loop : -0.68 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 273 TYR 0.032 0.002 TYR C1067 PHE 0.027 0.002 PHE C 371 TRP 0.022 0.002 TRP A 64 HIS 0.018 0.002 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 (22755) covalent geometry : angle 0.83752 / 0.47 (30950) SS BOND : bond 0.00309 / 0.21 ( 34) SS BOND : angle 1.46389 / 0.93 ( 68) hydrogen bonds : bond 0.11714 / 7.52 ( 985) hydrogen bonds : angle 7.20150 / 4.89 ( 2868) link_BETA1-4 : bond 0.00650 / 0.40 ( 18) link_BETA1-4 : angle 1.54008 / 1.05 ( 54) link_NAG-ASN : bond 0.00341 / 0.20 ( 37) link_NAG-ASN : angle 2.51792 / 1.77 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 558 time to evaluate : 0.806 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: A 36 VAL cc_start: 0.8202 (t) cc_final: 0.7581 (p) REVERT: A 137 ASN cc_start: 0.7473 (m110) cc_final: 0.6782 (p0) REVERT: A 201 PHE cc_start: 0.7456 (t80) cc_final: 0.7053 (t80) REVERT: A 615 VAL cc_start: 0.7793 (t) cc_final: 0.7571 (t) REVERT: A 858 LEU cc_start: 0.8335 (mt) cc_final: 0.8115 (mt) REVERT: B 42 VAL cc_start: 0.7924 (t) cc_final: 0.7352 (t) REVERT: B 55 PHE cc_start: 0.8208 (m-80) cc_final: 0.7670 (m-80) REVERT: B 177 MET cc_start: 0.7796 (pmm) cc_final: 0.7350 (pmm) REVERT: B 200 TYR cc_start: 0.8266 (m-80) cc_final: 0.7829 (m-80) REVERT: B 202 LYS cc_start: 0.8478 (mttm) cc_final: 0.8004 (mppt) REVERT: B 223 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6197 (mp) REVERT: B 226 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7841 (tp) REVERT: B 330 PRO cc_start: 0.8496 (Cg_exo) cc_final: 0.8003 (Cg_endo) REVERT: B 613 GLN cc_start: 0.8770 (mt0) cc_final: 0.8119 (mp10) REVERT: B 900 MET cc_start: 0.7762 (mtp) cc_final: 0.7456 (mtt) REVERT: B 902 MET cc_start: 0.8866 (tpp) cc_final: 0.8628 (tpt) REVERT: B 917 TYR cc_start: 0.7935 (m-80) cc_final: 0.7523 (m-80) REVERT: B 970 PHE cc_start: 0.8364 (m-80) cc_final: 0.8135 (m-10) REVERT: C 91 TYR cc_start: 0.7359 (t80) cc_final: 0.6939 (t80) REVERT: C 99 ASN cc_start: 0.7971 (p0) cc_final: 0.6938 (t0) REVERT: C 189 LEU cc_start: 0.9391 (tp) cc_final: 0.9176 (tt) REVERT: C 191 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7067 (mt-10) REVERT: C 202 LYS cc_start: 0.8072 (mttm) cc_final: 0.7681 (mppt) REVERT: C 220 PHE cc_start: 0.4280 (m-80) cc_final: 0.3868 (m-80) REVERT: C 235 ILE cc_start: 0.6789 (mt) cc_final: 0.6449 (mt) REVERT: C 238 PHE cc_start: 0.5644 (p90) cc_final: 0.5091 (p90) REVERT: C 302 THR cc_start: 0.8788 (m) cc_final: 0.8286 (p) REVERT: C 351 TYR cc_start: 0.8643 (p90) cc_final: 0.8168 (p90) REVERT: C 392 PHE cc_start: 0.6575 (m-80) cc_final: 0.6278 (m-80) REVERT: C 574 ASP cc_start: 0.7487 (t0) cc_final: 0.7224 (t0) REVERT: C 585 LEU cc_start: 0.9024 (mt) cc_final: 0.8607 (mm) outliers start: 13 outliers final: 3 residues processed: 565 average time/residue: 0.1433 time to fit residues: 127.8224 Evaluate side-chains 301 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 296 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 613 GLN A 710 ASN A 957 GLN B 115 GLN B 245 HIS B 641 ASN B 901 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 926 GLN C1002 GLN C1010 GLN C1011 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.108730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071373 restraints weight = 53532.061| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.32 r_work: 0.3022 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 22844 Z= 0.246 Angle : 0.761 17.253 31183 Z= 0.383 Chirality : 0.055 1.465 3703 Planarity : 0.006 0.089 3920 Dihedral : 5.120 57.088 2941 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.10 % Allowed : 11.13 % Favored : 85.77 % Cbeta Deviations : 0.00 % 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: 0.31 (0.15), residues: 2699 helix: 1.49 (0.19), residues: 668 sheet: 0.30 (0.19), residues: 602 loop : -0.42 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1107 TYR 0.041 0.002 TYR A 707 PHE 0.035 0.002 PHE A 543 TRP 0.024 0.002 TRP A 104 HIS 0.009 0.002 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.25 (22755) covalent geometry : angle 0.74246 / 0.38 (30950) SS BOND : bond 0.00523 / 0.36 ( 34) SS BOND : angle 1.39147 / 0.94 ( 68) hydrogen bonds : bond 0.04678 / 3.06 ( 985) hydrogen bonds : angle 5.82311 / 3.99 ( 2868) link_BETA1-4 : bond 0.00406 / 0.26 ( 18) link_BETA1-4 : angle 1.34738 / 1.00 ( 54) link_NAG-ASN : bond 0.00722 / 0.41 ( 37) link_NAG-ASN : angle 2.65181 / 1.87 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 297 time to evaluate : 0.819 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: A 104 TRP cc_start: 0.7734 (m-90) cc_final: 0.7464 (m-90) REVERT: A 137 ASN cc_start: 0.7547 (m110) cc_final: 0.6823 (p0) REVERT: A 177 MET cc_start: 0.7253 (pmm) cc_final: 0.7040 (pmm) REVERT: A 201 PHE cc_start: 0.8055 (t80) cc_final: 0.7709 (t80) REVERT: A 314 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 955 ASN cc_start: 0.8540 (m-40) cc_final: 0.8276 (t0) REVERT: A 990 GLU cc_start: 0.8579 (pp20) cc_final: 0.8302 (pp20) REVERT: B 55 PHE cc_start: 0.8347 (m-80) cc_final: 0.7583 (m-80) REVERT: B 177 MET cc_start: 0.7555 (pmm) cc_final: 0.7222 (pmm) REVERT: B 200 TYR cc_start: 0.8011 (m-80) cc_final: 0.7719 (m-80) REVERT: B 751 ASN cc_start: 0.9043 (m-40) cc_final: 0.8836 (m110) REVERT: B 779 GLN cc_start: 0.8667 (tp40) cc_final: 0.8446 (tp40) REVERT: B 970 PHE cc_start: 0.8905 (m-80) cc_final: 0.8550 (m-80) REVERT: B 979 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8436 (t0) REVERT: C 52 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7377 (tp40) REVERT: C 53 ASP cc_start: 0.7754 (t0) cc_final: 0.7426 (t0) REVERT: C 235 ILE cc_start: 0.6436 (mt) cc_final: 0.6222 (mt) REVERT: C 238 PHE cc_start: 0.6781 (p90) cc_final: 0.6291 (p90) REVERT: C 351 TYR cc_start: 0.8736 (p90) cc_final: 0.8264 (p90) REVERT: C 574 ASP cc_start: 0.7920 (t0) cc_final: 0.7654 (t0) REVERT: C 598 ILE cc_start: 0.9367 (mp) cc_final: 0.9154 (mp) REVERT: C 950 ASP cc_start: 0.8719 (m-30) cc_final: 0.8342 (m-30) REVERT: C 957 GLN cc_start: 0.8651 (tt0) cc_final: 0.8444 (tt0) REVERT: C 984 LEU cc_start: 0.7384 (tp) cc_final: 0.7093 (tt) REVERT: C 994 ASP cc_start: 0.8762 (m-30) cc_final: 0.8331 (m-30) REVERT: C 1142 GLN cc_start: 0.8687 (tp40) cc_final: 0.8399 (tm-30) outliers start: 75 outliers final: 41 residues processed: 349 average time/residue: 0.1371 time to fit residues: 77.4901 Evaluate side-chains 266 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 226 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 230 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN B1011 GLN B1058 HIS C 762 GLN C 965 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.108200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071005 restraints weight = 53241.875| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.30 r_work: 0.3017 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22844 Z= 0.149 Angle : 0.572 8.863 31183 Z= 0.293 Chirality : 0.045 0.198 3703 Planarity : 0.004 0.050 3920 Dihedral : 4.420 56.446 2934 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.36 % Allowed : 13.03 % Favored : 84.61 % Cbeta Deviations : 0.00 % 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: 0.68 (0.15), residues: 2699 helix: 2.12 (0.19), residues: 666 sheet: 0.33 (0.19), residues: 632 loop : -0.27 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.022 0.001 TYR A1067 PHE 0.028 0.001 PHE C 855 TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (22755) covalent geometry : angle 0.55896 / 0.29 (30950) SS BOND : bond 0.00271 / 0.19 ( 34) SS BOND : angle 1.17672 / 0.79 ( 68) hydrogen bonds : bond 0.04014 / 2.62 ( 985) hydrogen bonds : angle 5.44059 / 3.73 ( 2868) link_BETA1-4 : bond 0.00369 / 0.24 ( 18) link_BETA1-4 : angle 1.10883 / 0.75 ( 54) link_NAG-ASN : bond 0.00315 / 0.20 ( 37) link_NAG-ASN : angle 1.86560 / 1.29 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 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: A 314 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 866 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 955 ASN cc_start: 0.8575 (m-40) cc_final: 0.8273 (t0) REVERT: B 55 PHE cc_start: 0.8108 (m-80) cc_final: 0.7442 (m-80) REVERT: B 177 MET cc_start: 0.7345 (pmm) cc_final: 0.6940 (pmm) REVERT: B 242 LEU cc_start: 0.8011 (mm) cc_final: 0.7661 (mm) REVERT: B 309 GLU cc_start: 0.9033 (mp0) cc_final: 0.8802 (mp0) REVERT: B 330 PRO cc_start: 0.8610 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: B 902 MET cc_start: 0.9450 (tpt) cc_final: 0.9150 (tpt) REVERT: B 970 PHE cc_start: 0.8866 (m-80) cc_final: 0.8635 (m-80) REVERT: B 988 GLU cc_start: 0.9003 (tp30) cc_final: 0.8790 (tp30) REVERT: C 52 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7476 (tp40) REVERT: C 235 ILE cc_start: 0.6359 (mt) cc_final: 0.6141 (mt) REVERT: C 238 PHE cc_start: 0.6795 (p90) cc_final: 0.6341 (p90) REVERT: C 351 TYR cc_start: 0.8797 (p90) cc_final: 0.8237 (p90) REVERT: C 855 PHE cc_start: 0.8483 (m-80) cc_final: 0.7876 (m-80) REVERT: C 933 LYS cc_start: 0.8366 (mmtm) cc_final: 0.8022 (mttm) REVERT: C 950 ASP cc_start: 0.8785 (m-30) cc_final: 0.8298 (m-30) outliers start: 57 outliers final: 36 residues processed: 278 average time/residue: 0.1464 time to fit residues: 64.8400 Evaluate side-chains 241 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 84 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 75 optimal weight: 0.0170 chunk 146 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.108050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.070996 restraints weight = 53253.773| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.25 r_work: 0.3020 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22844 Z= 0.136 Angle : 0.549 9.406 31183 Z= 0.282 Chirality : 0.044 0.196 3703 Planarity : 0.004 0.045 3920 Dihedral : 4.305 59.595 2934 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.77 % Allowed : 13.74 % Favored : 83.49 % Cbeta Deviations : 0.00 % 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: 0.74 (0.16), residues: 2699 helix: 2.24 (0.20), residues: 661 sheet: 0.23 (0.18), residues: 651 loop : -0.18 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.021 0.001 TYR A1067 PHE 0.024 0.001 PHE B 823 TRP 0.013 0.001 TRP B 104 HIS 0.026 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (22755) covalent geometry : angle 0.53627 / 0.28 (30950) SS BOND : bond 0.00146 / 0.08 ( 34) SS BOND : angle 1.01506 / 0.69 ( 68) hydrogen bonds : bond 0.03744 / 2.45 ( 985) hydrogen bonds : angle 5.23518 / 3.59 ( 2868) link_BETA1-4 : bond 0.00274 / 0.17 ( 18) link_BETA1-4 : angle 0.99252 / 0.68 ( 54) link_NAG-ASN : bond 0.00298 / 0.20 ( 37) link_NAG-ASN : angle 1.80126 / 1.25 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 0.549 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: A 19 ILE cc_start: 0.8463 (mm) cc_final: 0.8055 (tp) REVERT: A 200 TYR cc_start: 0.8093 (m-80) cc_final: 0.7847 (m-80) REVERT: A 214 ARG cc_start: 0.7101 (tpt-90) cc_final: 0.6898 (tpt-90) REVERT: A 314 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 866 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 955 ASN cc_start: 0.8524 (m-40) cc_final: 0.8219 (t0) REVERT: A 995 ARG cc_start: 0.8974 (mtp-110) cc_final: 0.8142 (mtp85) REVERT: B 55 PHE cc_start: 0.8146 (m-80) cc_final: 0.7535 (m-80) REVERT: B 177 MET cc_start: 0.7229 (pmm) cc_final: 0.6668 (pmm) REVERT: B 242 LEU cc_start: 0.8109 (mm) cc_final: 0.7740 (mm) REVERT: B 330 PRO cc_start: 0.8622 (Cg_exo) cc_final: 0.8335 (Cg_endo) REVERT: B 768 THR cc_start: 0.9110 (m) cc_final: 0.8886 (p) REVERT: B 955 ASN cc_start: 0.8415 (m110) cc_final: 0.7931 (t0) REVERT: B 979 ASP cc_start: 0.8467 (t0) cc_final: 0.8182 (t0) REVERT: C 52 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7679 (tp40) REVERT: C 53 ASP cc_start: 0.7504 (t0) cc_final: 0.7243 (t0) REVERT: C 99 ASN cc_start: 0.8159 (p0) cc_final: 0.7212 (t0) REVERT: C 238 PHE cc_start: 0.6862 (p90) cc_final: 0.6374 (p90) REVERT: C 351 TYR cc_start: 0.8776 (p90) cc_final: 0.8303 (p90) REVERT: C 403 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7130 (tpp80) REVERT: C 572 THR cc_start: 0.7756 (m) cc_final: 0.7451 (p) REVERT: C 855 PHE cc_start: 0.8428 (m-80) cc_final: 0.7971 (m-80) REVERT: C 856 ASN cc_start: 0.9304 (m110) cc_final: 0.8985 (m-40) REVERT: C 900 MET cc_start: 0.9026 (mtp) cc_final: 0.8812 (mtm) REVERT: C 923 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9390 (mp) REVERT: C 933 LYS cc_start: 0.8499 (mmtm) cc_final: 0.8191 (mttm) REVERT: C 950 ASP cc_start: 0.8793 (m-30) cc_final: 0.8298 (m-30) REVERT: C 1145 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7102 (pp) outliers start: 67 outliers final: 42 residues processed: 271 average time/residue: 0.1355 time to fit residues: 59.9298 Evaluate side-chains 240 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 126 optimal weight: 0.5980 chunk 267 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 824 ASN A1142 GLN B 207 HIS B 824 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 394 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 960 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.104309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066605 restraints weight = 53042.825| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.29 r_work: 0.2914 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22844 Z= 0.242 Angle : 0.648 8.400 31183 Z= 0.331 Chirality : 0.047 0.231 3703 Planarity : 0.005 0.054 3920 Dihedral : 4.501 47.262 2934 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.85 % Allowed : 13.98 % Favored : 83.16 % Cbeta Deviations : 0.00 % 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: 0.48 (0.15), residues: 2699 helix: 1.89 (0.19), residues: 666 sheet: 0.12 (0.19), residues: 632 loop : -0.31 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 983 TYR 0.022 0.002 TYR A1067 PHE 0.037 0.002 PHE B 220 TRP 0.022 0.002 TRP B 104 HIS 0.008 0.002 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (22755) covalent geometry : angle 0.63538 / 0.33 (30950) SS BOND : bond 0.00351 / 0.23 ( 34) SS BOND : angle 1.18744 / 0.81 ( 68) hydrogen bonds : bond 0.04360 / 2.85 ( 985) hydrogen bonds : angle 5.54262 / 3.82 ( 2868) link_BETA1-4 : bond 0.00347 / 0.22 ( 18) link_BETA1-4 : angle 1.21584 / 0.82 ( 54) link_NAG-ASN : bond 0.00505 / 0.32 ( 37) link_NAG-ASN : angle 1.99151 / 1.39 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7831 (m-10) cc_final: 0.7578 (m-10) REVERT: A 200 TYR cc_start: 0.8085 (m-80) cc_final: 0.7426 (m-80) REVERT: A 214 ARG cc_start: 0.7182 (tpt-90) cc_final: 0.6961 (tpt-90) REVERT: A 314 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 955 ASN cc_start: 0.8761 (m-40) cc_final: 0.8286 (t0) REVERT: A 988 GLU cc_start: 0.9090 (mp0) cc_final: 0.8729 (pm20) REVERT: B 55 PHE cc_start: 0.8054 (m-80) cc_final: 0.7535 (m-80) REVERT: B 177 MET cc_start: 0.7280 (pmm) cc_final: 0.6890 (pmm) REVERT: B 242 LEU cc_start: 0.8057 (mm) cc_final: 0.7698 (mm) REVERT: B 764 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8602 (ttpp) REVERT: B 988 GLU cc_start: 0.9064 (tp30) cc_final: 0.8710 (tp30) REVERT: C 52 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 309 GLU cc_start: 0.8823 (mp0) cc_final: 0.8569 (mp0) REVERT: C 351 TYR cc_start: 0.8833 (p90) cc_final: 0.8484 (p90) REVERT: C 396 TYR cc_start: 0.7310 (m-80) cc_final: 0.6176 (m-80) REVERT: C 512 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7588 (p) REVERT: C 572 THR cc_start: 0.7774 (m) cc_final: 0.7482 (p) REVERT: C 758 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8739 (p) REVERT: C 773 GLU cc_start: 0.8719 (tt0) cc_final: 0.8292 (tt0) REVERT: C 855 PHE cc_start: 0.8566 (m-80) cc_final: 0.8081 (m-80) REVERT: C 923 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9369 (mp) REVERT: C 988 GLU cc_start: 0.8815 (mp0) cc_final: 0.8448 (tp30) REVERT: C 1017 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8920 (tm-30) outliers start: 69 outliers final: 46 residues processed: 262 average time/residue: 0.1360 time to fit residues: 58.8124 Evaluate side-chains 229 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 764 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 99 optimal weight: 8.9990 chunk 272 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 0.0970 chunk 183 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 264 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 960 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.105869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068860 restraints weight = 53191.614| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.30 r_work: 0.2955 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22844 Z= 0.143 Angle : 0.563 9.630 31183 Z= 0.287 Chirality : 0.044 0.180 3703 Planarity : 0.004 0.047 3920 Dihedral : 4.206 39.893 2932 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.65 % Allowed : 15.18 % Favored : 82.17 % Cbeta Deviations : 0.00 % 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: 0.65 (0.16), residues: 2699 helix: 2.19 (0.19), residues: 665 sheet: 0.08 (0.18), residues: 654 loop : -0.21 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.024 0.001 TYR B 170 PHE 0.036 0.001 PHE B 220 TRP 0.027 0.002 TRP A 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22755) covalent geometry : angle 0.55108 / 0.28 (30950) SS BOND : bond 0.00241 / 0.13 ( 34) SS BOND : angle 1.23774 / 0.83 ( 68) hydrogen bonds : bond 0.03801 / 2.51 ( 985) hydrogen bonds : angle 5.31078 / 3.66 ( 2868) link_BETA1-4 : bond 0.00283 / 0.19 ( 18) link_BETA1-4 : angle 0.90447 / 0.61 ( 54) link_NAG-ASN : bond 0.00263 / 0.18 ( 37) link_NAG-ASN : angle 1.73591 / 1.21 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 202 time to evaluate : 0.839 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: A 52 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 137 ASN cc_start: 0.7247 (m-40) cc_final: 0.6522 (p0) REVERT: A 157 PHE cc_start: 0.7752 (m-10) cc_final: 0.7537 (m-10) REVERT: A 200 TYR cc_start: 0.8112 (m-80) cc_final: 0.7682 (m-80) REVERT: A 314 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 571 ASP cc_start: 0.8418 (p0) cc_final: 0.8200 (p0) REVERT: A 955 ASN cc_start: 0.8768 (m-40) cc_final: 0.8323 (t0) REVERT: A 988 GLU cc_start: 0.9070 (mp0) cc_final: 0.8709 (pm20) REVERT: A 995 ARG cc_start: 0.9144 (mtp-110) cc_final: 0.8420 (mtp85) REVERT: B 55 PHE cc_start: 0.8161 (m-80) cc_final: 0.7605 (m-80) REVERT: B 177 MET cc_start: 0.7230 (pmm) cc_final: 0.6578 (pmm) REVERT: B 242 LEU cc_start: 0.8091 (mm) cc_final: 0.7478 (mp) REVERT: B 745 ASP cc_start: 0.8551 (p0) cc_final: 0.8155 (p0) REVERT: B 955 ASN cc_start: 0.8654 (m110) cc_final: 0.8325 (t0) REVERT: B 988 GLU cc_start: 0.9096 (tp30) cc_final: 0.8747 (tp30) REVERT: C 52 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7918 (tp40) REVERT: C 53 ASP cc_start: 0.7814 (t0) cc_final: 0.7399 (t0) REVERT: C 324 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: C 351 TYR cc_start: 0.8864 (p90) cc_final: 0.8501 (p90) REVERT: C 512 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7596 (p) REVERT: C 572 THR cc_start: 0.7770 (m) cc_final: 0.7403 (p) REVERT: C 773 GLU cc_start: 0.8665 (tt0) cc_final: 0.8290 (tt0) REVERT: C 855 PHE cc_start: 0.8524 (m-80) cc_final: 0.8175 (m-80) REVERT: C 856 ASN cc_start: 0.9223 (m110) cc_final: 0.8833 (m-40) REVERT: C 923 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9364 (mp) REVERT: C 994 ASP cc_start: 0.8645 (m-30) cc_final: 0.8308 (t70) REVERT: C 1017 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8873 (tm-30) outliers start: 64 outliers final: 45 residues processed: 247 average time/residue: 0.1331 time to fit residues: 54.9640 Evaluate side-chains 231 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.104227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067116 restraints weight = 53245.847| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.24 r_work: 0.2923 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22844 Z= 0.223 Angle : 0.599 9.702 31183 Z= 0.304 Chirality : 0.045 0.181 3703 Planarity : 0.004 0.046 3920 Dihedral : 4.117 17.927 2930 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.48 % Allowed : 15.43 % Favored : 82.09 % Cbeta Deviations : 0.00 % 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: 0.60 (0.16), residues: 2699 helix: 2.14 (0.19), residues: 667 sheet: 0.05 (0.18), residues: 674 loop : -0.25 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.021 0.001 TYR A1067 PHE 0.026 0.001 PHE B 220 TRP 0.023 0.002 TRP A 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (22755) covalent geometry : angle 0.58619 / 0.30 (30950) SS BOND : bond 0.00209 / 0.12 ( 34) SS BOND : angle 1.39711 / 0.90 ( 68) hydrogen bonds : bond 0.03973 / 2.62 ( 985) hydrogen bonds : angle 5.34807 / 3.69 ( 2868) link_BETA1-4 : bond 0.00209 / 0.14 ( 18) link_BETA1-4 : angle 0.98105 / 0.67 ( 54) link_NAG-ASN : bond 0.00374 / 0.24 ( 37) link_NAG-ASN : angle 1.82288 / 1.27 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 137 ASN cc_start: 0.7388 (m-40) cc_final: 0.6612 (p0) REVERT: A 173 GLN cc_start: 0.8637 (pm20) cc_final: 0.8305 (tp40) REVERT: A 200 TYR cc_start: 0.8149 (m-80) cc_final: 0.7648 (m-80) REVERT: A 314 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 955 ASN cc_start: 0.8712 (m-40) cc_final: 0.8419 (t0) REVERT: A 988 GLU cc_start: 0.9061 (mp0) cc_final: 0.8723 (pm20) REVERT: A 995 ARG cc_start: 0.9153 (mtp-110) cc_final: 0.8451 (mtp85) REVERT: B 55 PHE cc_start: 0.8191 (m-80) cc_final: 0.7645 (m-80) REVERT: B 177 MET cc_start: 0.7156 (pmm) cc_final: 0.6931 (pmm) REVERT: B 242 LEU cc_start: 0.8090 (mm) cc_final: 0.7470 (mp) REVERT: B 745 ASP cc_start: 0.8628 (p0) cc_final: 0.8246 (p0) REVERT: B 955 ASN cc_start: 0.8686 (m110) cc_final: 0.8338 (t0) REVERT: B 988 GLU cc_start: 0.9196 (tp30) cc_final: 0.8846 (tp30) REVERT: C 52 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 220 PHE cc_start: 0.6844 (t80) cc_final: 0.6604 (t80) REVERT: C 324 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: C 351 TYR cc_start: 0.8879 (p90) cc_final: 0.8563 (p90) REVERT: C 512 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7728 (p) REVERT: C 572 THR cc_start: 0.7792 (m) cc_final: 0.7507 (p) REVERT: C 773 GLU cc_start: 0.8716 (tt0) cc_final: 0.8336 (tt0) REVERT: C 855 PHE cc_start: 0.8545 (m-80) cc_final: 0.8162 (m-80) REVERT: C 923 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9379 (mp) REVERT: C 988 GLU cc_start: 0.8791 (mp0) cc_final: 0.8485 (tp30) REVERT: C 994 ASP cc_start: 0.8642 (m-30) cc_final: 0.8412 (t70) outliers start: 60 outliers final: 46 residues processed: 235 average time/residue: 0.1395 time to fit residues: 54.3098 Evaluate side-chains 228 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 50 optimal weight: 0.9980 chunk 132 optimal weight: 0.0970 chunk 61 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 250 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 960 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.106101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069425 restraints weight = 52711.515| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.28 r_work: 0.2972 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22844 Z= 0.117 Angle : 0.554 9.958 31183 Z= 0.282 Chirality : 0.044 0.193 3703 Planarity : 0.004 0.044 3920 Dihedral : 3.970 18.386 2930 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.32 % Allowed : 15.56 % Favored : 82.13 % Cbeta Deviations : 0.00 % 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: 0.77 (0.16), residues: 2699 helix: 2.32 (0.19), residues: 667 sheet: 0.16 (0.18), residues: 646 loop : -0.16 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.028 0.001 TYR B 170 PHE 0.022 0.001 PHE B 823 TRP 0.033 0.002 TRP A 104 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (22755) covalent geometry : angle 0.54420 / 0.28 (30950) SS BOND : bond 0.00174 / 0.10 ( 34) SS BOND : angle 1.16103 / 0.76 ( 68) hydrogen bonds : bond 0.03581 / 2.36 ( 985) hydrogen bonds : angle 5.11977 / 3.53 ( 2868) link_BETA1-4 : bond 0.00326 / 0.20 ( 18) link_BETA1-4 : angle 0.83523 / 0.57 ( 54) link_NAG-ASN : bond 0.00233 / 0.15 ( 37) link_NAG-ASN : angle 1.58577 / 1.10 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 0.807 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: A 52 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 99 ASN cc_start: 0.8316 (m-40) cc_final: 0.7640 (p0) REVERT: A 101 ILE cc_start: 0.8368 (mp) cc_final: 0.8151 (mm) REVERT: A 137 ASN cc_start: 0.7327 (m-40) cc_final: 0.6558 (p0) REVERT: A 200 TYR cc_start: 0.8112 (m-80) cc_final: 0.7694 (m-80) REVERT: A 214 ARG cc_start: 0.7073 (tpt-90) cc_final: 0.6796 (tpt-90) REVERT: A 269 TYR cc_start: 0.8807 (m-80) cc_final: 0.7747 (m-80) REVERT: A 314 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 955 ASN cc_start: 0.8699 (m-40) cc_final: 0.8298 (t0) REVERT: A 988 GLU cc_start: 0.9036 (mp0) cc_final: 0.8672 (pm20) REVERT: A 995 ARG cc_start: 0.9139 (mtp-110) cc_final: 0.8536 (mtp85) REVERT: B 55 PHE cc_start: 0.8255 (m-80) cc_final: 0.7667 (m-80) REVERT: B 66 HIS cc_start: 0.5572 (OUTLIER) cc_final: 0.5128 (t-90) REVERT: B 177 MET cc_start: 0.7172 (pmm) cc_final: 0.6914 (pmm) REVERT: B 242 LEU cc_start: 0.8105 (mm) cc_final: 0.7542 (mp) REVERT: B 755 GLN cc_start: 0.9126 (mt0) cc_final: 0.8793 (tt0) REVERT: B 955 ASN cc_start: 0.8677 (m110) cc_final: 0.8311 (t0) REVERT: B 988 GLU cc_start: 0.9163 (tp30) cc_final: 0.8794 (tp30) REVERT: B 995 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8466 (ptm160) REVERT: C 52 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8242 (tm-30) REVERT: C 324 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: C 351 TYR cc_start: 0.8912 (p90) cc_final: 0.8601 (p90) REVERT: C 512 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7745 (p) REVERT: C 572 THR cc_start: 0.7746 (m) cc_final: 0.7494 (p) REVERT: C 773 GLU cc_start: 0.8673 (tt0) cc_final: 0.8294 (tt0) REVERT: C 855 PHE cc_start: 0.8502 (m-10) cc_final: 0.8168 (m-80) REVERT: C 856 ASN cc_start: 0.9177 (m110) cc_final: 0.8773 (m-40) REVERT: C 923 ILE cc_start: 0.9563 (OUTLIER) cc_final: 0.9304 (mp) REVERT: C 950 ASP cc_start: 0.8826 (m-30) cc_final: 0.8363 (m-30) REVERT: C 984 LEU cc_start: 0.8357 (tt) cc_final: 0.8109 (tt) REVERT: C 988 GLU cc_start: 0.8839 (mp0) cc_final: 0.8509 (tp30) REVERT: C 994 ASP cc_start: 0.8595 (m-30) cc_final: 0.8384 (t70) REVERT: C 1017 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8965 (tt0) outliers start: 56 outliers final: 41 residues processed: 249 average time/residue: 0.1408 time to fit residues: 57.0282 Evaluate side-chains 230 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 57 optimal weight: 0.3980 chunk 230 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 960 ASN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.105590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.068686 restraints weight = 53200.690| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.24 r_work: 0.2979 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22844 Z= 0.136 Angle : 0.568 9.636 31183 Z= 0.288 Chirality : 0.044 0.184 3703 Planarity : 0.004 0.053 3920 Dihedral : 3.931 17.518 2930 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.94 % Allowed : 16.05 % Favored : 82.00 % Cbeta Deviations : 0.00 % 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: 0.81 (0.16), residues: 2699 helix: 2.36 (0.19), residues: 667 sheet: 0.18 (0.18), residues: 647 loop : -0.13 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.021 0.001 TYR B 170 PHE 0.024 0.001 PHE B 823 TRP 0.027 0.002 TRP A 104 HIS 0.006 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (22755) covalent geometry : angle 0.55746 / 0.29 (30950) SS BOND : bond 0.00174 / 0.10 ( 34) SS BOND : angle 1.37447 / 0.95 ( 68) hydrogen bonds : bond 0.03611 / 2.38 ( 985) hydrogen bonds : angle 5.08905 / 3.51 ( 2868) link_BETA1-4 : bond 0.00282 / 0.18 ( 18) link_BETA1-4 : angle 0.87640 / 0.60 ( 54) link_NAG-ASN : bond 0.00230 / 0.15 ( 37) link_NAG-ASN : angle 1.59750 / 1.11 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.593 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: A 99 ASN cc_start: 0.8301 (m-40) cc_final: 0.7648 (p0) REVERT: A 137 ASN cc_start: 0.7339 (m-40) cc_final: 0.6607 (p0) REVERT: A 173 GLN cc_start: 0.8614 (pm20) cc_final: 0.8341 (tp40) REVERT: A 200 TYR cc_start: 0.8003 (m-80) cc_final: 0.7648 (m-80) REVERT: A 269 TYR cc_start: 0.8828 (m-80) cc_final: 0.7906 (m-80) REVERT: A 314 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 955 ASN cc_start: 0.8591 (m110) cc_final: 0.8384 (t0) REVERT: A 988 GLU cc_start: 0.9026 (mp0) cc_final: 0.8696 (pm20) REVERT: A 995 ARG cc_start: 0.9155 (mtp-110) cc_final: 0.8629 (mtp85) REVERT: B 55 PHE cc_start: 0.8170 (m-80) cc_final: 0.7630 (m-80) REVERT: B 66 HIS cc_start: 0.5641 (OUTLIER) cc_final: 0.5157 (t-90) REVERT: B 170 TYR cc_start: 0.8201 (t80) cc_final: 0.7750 (t80) REVERT: B 177 MET cc_start: 0.7171 (pmm) cc_final: 0.6956 (pmm) REVERT: B 242 LEU cc_start: 0.8131 (mm) cc_final: 0.7552 (mp) REVERT: B 269 TYR cc_start: 0.7749 (m-10) cc_final: 0.7373 (m-10) REVERT: B 755 GLN cc_start: 0.9078 (mt0) cc_final: 0.8778 (tt0) REVERT: B 955 ASN cc_start: 0.8559 (m110) cc_final: 0.8320 (t0) REVERT: B 988 GLU cc_start: 0.9165 (tp30) cc_final: 0.8799 (tp30) REVERT: B 995 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8561 (ptm160) REVERT: C 52 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8378 (tm-30) REVERT: C 324 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: C 351 TYR cc_start: 0.8860 (p90) cc_final: 0.8556 (p90) REVERT: C 512 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7893 (p) REVERT: C 572 THR cc_start: 0.7804 (m) cc_final: 0.7553 (p) REVERT: C 773 GLU cc_start: 0.8713 (tt0) cc_final: 0.8407 (tt0) REVERT: C 855 PHE cc_start: 0.8475 (m-10) cc_final: 0.8161 (m-80) REVERT: C 856 ASN cc_start: 0.9193 (m110) cc_final: 0.8837 (m-40) REVERT: C 923 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9414 (mp) REVERT: C 950 ASP cc_start: 0.8781 (m-30) cc_final: 0.8333 (m-30) REVERT: C 988 GLU cc_start: 0.8698 (mp0) cc_final: 0.8420 (tp30) outliers start: 47 outliers final: 38 residues processed: 228 average time/residue: 0.1405 time to fit residues: 52.6375 Evaluate side-chains 225 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 241 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 246 optimal weight: 0.2980 chunk 234 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.067500 restraints weight = 53377.434| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.22 r_work: 0.2952 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22844 Z= 0.183 Angle : 0.591 9.270 31183 Z= 0.299 Chirality : 0.044 0.186 3703 Planarity : 0.004 0.058 3920 Dihedral : 3.986 18.286 2930 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.99 % Allowed : 15.97 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.16), residues: 2699 helix: 2.38 (0.19), residues: 666 sheet: 0.18 (0.19), residues: 638 loop : -0.15 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.020 0.001 TYR A1067 PHE 0.024 0.001 PHE B 823 TRP 0.031 0.002 TRP A 104 HIS 0.006 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (22755) covalent geometry : angle 0.58024 / 0.30 (30950) SS BOND : bond 0.00380 / 0.29 ( 34) SS BOND : angle 1.35134 / 0.94 ( 68) hydrogen bonds : bond 0.03802 / 2.51 ( 985) hydrogen bonds : angle 5.15491 / 3.56 ( 2868) link_BETA1-4 : bond 0.00232 / 0.15 ( 18) link_BETA1-4 : angle 0.92375 / 0.63 ( 54) link_NAG-ASN : bond 0.00293 / 0.19 ( 37) link_NAG-ASN : angle 1.66741 / 1.17 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8334 (m-40) cc_final: 0.7660 (p0) REVERT: A 137 ASN cc_start: 0.7467 (m-40) cc_final: 0.6691 (p0) REVERT: A 173 GLN cc_start: 0.8668 (pm20) cc_final: 0.8392 (tp40) REVERT: A 200 TYR cc_start: 0.8038 (m-80) cc_final: 0.7681 (m-80) REVERT: A 314 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 988 GLU cc_start: 0.9096 (mp0) cc_final: 0.8751 (pm20) REVERT: A 995 ARG cc_start: 0.9189 (mtp-110) cc_final: 0.8563 (mtp85) REVERT: B 55 PHE cc_start: 0.8185 (m-80) cc_final: 0.7686 (m-80) REVERT: B 66 HIS cc_start: 0.5646 (OUTLIER) cc_final: 0.5337 (t70) REVERT: B 170 TYR cc_start: 0.8238 (t80) cc_final: 0.7781 (t80) REVERT: B 177 MET cc_start: 0.7316 (pmm) cc_final: 0.7096 (pmm) REVERT: B 242 LEU cc_start: 0.8103 (mm) cc_final: 0.7524 (mp) REVERT: B 269 TYR cc_start: 0.7762 (m-10) cc_final: 0.7258 (m-10) REVERT: B 740 MET cc_start: 0.9220 (tpp) cc_final: 0.8346 (tmm) REVERT: B 755 GLN cc_start: 0.9095 (mt0) cc_final: 0.8777 (tt0) REVERT: B 955 ASN cc_start: 0.8540 (m110) cc_final: 0.8333 (t0) REVERT: B 988 GLU cc_start: 0.9204 (tp30) cc_final: 0.8823 (tp30) REVERT: C 52 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8505 (tm-30) REVERT: C 324 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: C 351 TYR cc_start: 0.8844 (p90) cc_final: 0.8611 (p90) REVERT: C 512 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 572 THR cc_start: 0.7846 (m) cc_final: 0.7584 (p) REVERT: C 773 GLU cc_start: 0.8698 (tt0) cc_final: 0.8395 (tt0) REVERT: C 855 PHE cc_start: 0.8471 (m-10) cc_final: 0.8135 (m-80) REVERT: C 856 ASN cc_start: 0.9192 (m110) cc_final: 0.8821 (m-40) REVERT: C 923 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9438 (mp) REVERT: C 988 GLU cc_start: 0.8766 (mp0) cc_final: 0.8418 (tp30) REVERT: C 990 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8219 (tm-30) outliers start: 48 outliers final: 40 residues processed: 222 average time/residue: 0.1327 time to fit residues: 48.1739 Evaluate side-chains 221 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 150 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 262 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.105587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.068785 restraints weight = 53275.546| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.27 r_work: 0.2981 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.7459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22844 Z= 0.123 Angle : 0.566 9.573 31183 Z= 0.287 Chirality : 0.044 0.190 3703 Planarity : 0.004 0.055 3920 Dihedral : 3.919 19.379 2930 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.86 % Allowed : 16.18 % Favored : 81.96 % Cbeta Deviations : 0.00 % 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: 0.88 (0.16), residues: 2699 helix: 2.45 (0.19), residues: 661 sheet: 0.27 (0.19), residues: 628 loop : -0.12 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 995 TYR 0.021 0.001 TYR B 170 PHE 0.024 0.001 PHE B 823 TRP 0.037 0.002 TRP A 104 HIS 0.005 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (22755) covalent geometry : angle 0.55655 / 0.28 (30950) SS BOND : bond 0.00171 / 0.10 ( 34) SS BOND : angle 1.25341 / 0.88 ( 68) hydrogen bonds : bond 0.03551 / 2.33 ( 985) hydrogen bonds : angle 5.03970 / 3.48 ( 2868) link_BETA1-4 : bond 0.00315 / 0.20 ( 18) link_BETA1-4 : angle 0.84510 / 0.58 ( 54) link_NAG-ASN : bond 0.00217 / 0.14 ( 37) link_NAG-ASN : angle 1.54302 / 1.07 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5627.50 seconds wall clock time: 97 minutes 14.29 seconds (5834.29 seconds total)