Starting phenix.real_space_refine on Sun Aug 24 23:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zp7_11337/08_2025/6zp7_11337.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp7_11337/08_2025/6zp7_11337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zp7_11337/08_2025/6zp7_11337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp7_11337/08_2025/6zp7_11337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zp7_11337/08_2025/6zp7_11337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp7_11337/08_2025/6zp7_11337.map" } resolution = 3.3 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= 0.036 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 14927 2.51 5 N 3780 2.21 5 O 4807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23615 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7709 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 48, 'TRANS': 939} Chain breaks: 8 Chain: "C" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7367 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 12 Chain: "B" Number of atoms: 7243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7243 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 44, 'TRANS': 885} Chain breaks: 10 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 114 Unusual residues: {'DMS': 3, 'MAN': 1, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.27, per 1000 atoms: 0.27 Number of scatterers: 23615 At special positions: 0 Unit cell: (128.781, 131.922, 196.836, 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 4807 8.00 N 3780 7.00 C 14927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.00 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.00 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.06 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 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 Atom "HETATM23586 O5 NAG B1303 .*. O " rejected from bonding due to valence issues. Atom "HETATM23178 O5 NAG a 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM23148 O5 NAG Z 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM23556 O5 NAG B1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM22620 O5 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM22920 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 331 " " NAG B1305 " - " ASN B 165 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 122 " " NAG D 1 " - " ASN A 657 " " 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 A 282 " " NAG K 1 " - " ASN A 331 " " NAG L 1 " - " ASN A 709 " " NAG M 1 " - " ASN C 709 " " NAG N 1 " - " ASN C1134 " " NAG O 1 " - " ASN C1074 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 282 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 282 " " NAG b 1 " - " ASN B 343 " " NAG c 1 " - " ASN B 122 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 968.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 43 sheets defined 27.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.971A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.386A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.683A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.711A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.144A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.639A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) 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 983 removed outlier: 3.748A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.109A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.172A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.907A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.150A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.223A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.920A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.502A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.607A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.037A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 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 983 removed outlier: 3.558A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.947A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.687A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.571A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.126A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.372A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.585A pdb=" N ASP B 571 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 568 through 572' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.547A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.569A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.627A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.534A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.597A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) 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 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.256A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.172A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.759A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.765A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.872A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.040A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.692A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.561A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.442A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.137A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.769A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 171 removed outlier: 4.021A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.990A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.309A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.326A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.447A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.907A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.907A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AD4, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.682A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD6, first strand: chain 'B' and resid 200 through 207 removed outlier: 3.558A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AD8, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.760A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.822A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.800A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.188A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.560A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.560A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1122 938 hydrogen bonds defined for protein. 2571 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: 5.99 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 23707 1.54 - 1.86: 379 1.86 - 2.18: 1 2.18 - 2.50: 0 2.50 - 2.83: 1 Bond restraints: 24088 Sorted by residual: bond pdb=" C CYS A 525 " pdb=" N GLY A 526 " ideal model delta sigma weight residual 1.330 2.827 -1.497 1.49e-02 4.50e+03 1.01e+04 bond pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 1.331 1.992 -0.661 2.07e-02 2.33e+03 1.02e+03 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 1.528 1.589 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 24083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.75: 32784 6.75 - 13.49: 23 13.49 - 20.24: 7 20.24 - 26.99: 2 26.99 - 33.73: 2 Bond angle restraints: 32818 Sorted by residual: angle pdb=" O LEU A 335 " pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 122.81 90.95 31.86 1.42e+00 4.96e-01 5.03e+02 angle pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta sigma weight residual 121.87 88.14 33.73 1.57e+00 4.06e-01 4.62e+02 angle pdb=" CA LEU A 335 " pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 115.54 140.08 -24.54 1.52e+00 4.33e-01 2.61e+02 angle pdb=" O CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " ideal model delta sigma weight residual 123.24 108.40 14.84 1.23e+00 6.61e-01 1.46e+02 angle pdb=" O1 NAG W 2 " pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 108.68 134.98 -26.30 3.00e+00 1.11e-01 7.68e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 14605 23.06 - 46.12: 824 46.12 - 69.17: 155 69.17 - 92.23: 94 92.23 - 115.29: 50 Dihedral angle restraints: 15728 sinusoidal: 7398 harmonic: 8330 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -11.43 -74.57 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -13.39 -72.61 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -154.61 68.61 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 15725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.031: 4054 1.031 - 2.061: 12 2.061 - 3.092: 1 3.092 - 4.123: 1 4.123 - 5.154: 2 Chirality restraints: 4070 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 2.75 -5.15 2.00e-02 2.50e+03 6.64e+04 chirality pdb=" C1 NAG B1302 " pdb=" C2 NAG B1302 " pdb=" O1 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False 2.31 -2.42 4.73 2.00e-01 2.50e+01 5.60e+02 chirality pdb=" C1 NAG W 2 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False 2.31 -1.09 3.40 2.00e-01 2.50e+01 2.90e+02 ... (remaining 4067 not shown) Planarity restraints: 4119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " 0.287 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" CG ASN B 165 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.233 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " -0.231 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " 0.248 2.00e-02 2.50e+03 2.13e-01 5.66e+02 pdb=" CG ASN B 122 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.348 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.182 2.00e-02 2.50e+03 1.99e-01 4.97e+02 pdb=" CG ASN B 343 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.276 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.270 2.00e-02 2.50e+03 ... (remaining 4116 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 44 0.99 - 1.96: 140 1.96 - 2.94: 11785 2.94 - 3.92: 61290 3.92 - 4.90: 114014 Warning: very small nonbonded interaction distances. Nonbonded interactions: 187273 Sorted by model distance: nonbonded pdb=" O4 NAG I 1 " pdb=" O1 NAG I 2 " model vdw 0.008 3.040 nonbonded pdb=" O4 NAG c 1 " pdb=" O1 NAG c 2 " model vdw 0.020 3.040 nonbonded pdb=" O4 NAG Z 1 " pdb=" O1 NAG Z 2 " model vdw 0.024 3.040 nonbonded pdb=" O4 NAG D 1 " pdb=" O1 NAG D 2 " model vdw 0.031 3.040 nonbonded pdb=" O4 NAG Y 1 " pdb=" O1 NAG Y 2 " model vdw 0.037 3.040 ... (remaining 187268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 66 or resid 82 through 131 or resid 165 through \ 172 or resid 189 through 241 or resid 265 through 442 or resid 460 through 470 \ or resid 510 through 620 or resid 641 through 828 or resid 854 through 1146)) selection = (chain 'B' and (resid 28 through 131 or resid 165 through 172 or resid 189 throu \ gh 241 or resid 265 through 442 or resid 460 through 1146)) selection = (chain 'C' and (resid 28 through 131 or resid 165 through 172 or resid 189 throu \ gh 241 or resid 265 through 442 or resid 460 through 470 or resid 510 through 62 \ 0 or resid 641 through 828 or resid 854 through 1146)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } 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: 7.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.040 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 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 : 0.022 1.497 24168 Z= 1.153 Angle : 1.330 49.724 33023 Z= 0.566 Chirality : 0.165 5.154 4070 Planarity : 0.005 0.104 4075 Dihedral : 16.891 115.289 10239 Min Nonbonded Distance : 0.008 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.52 % Allowed : 5.38 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.14), residues: 2793 helix: 0.56 (0.19), residues: 660 sheet: -0.20 (0.19), residues: 629 loop : -1.35 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 214 TYR 0.026 0.002 TYR B1067 PHE 0.037 0.002 PHE C 559 TRP 0.023 0.002 TRP B 886 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.01289 (24088) covalent geometry : angle 0.91889 (32818) SS BOND : bond 0.01418 ( 35) SS BOND : angle 2.14573 ( 70) hydrogen bonds : bond 0.12621 ( 909) hydrogen bonds : angle 7.31486 ( 2571) link_BETA1-4 : bond 0.01095 ( 1) link_BETA1-4 : angle 21.97651 ( 3) link_NAG-ASN : bond 0.40730 ( 44) link_NAG-ASN : angle 14.79956 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 431 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.5116 (p0) cc_final: 0.4899 (p0) outliers start: 13 outliers final: 5 residues processed: 442 average time/residue: 0.1770 time to fit residues: 121.9707 Evaluate side-chains 204 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 199 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 617 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 564 GLN A 644 GLN A 804 GLN A 901 GLN A 914 ASN A 965 GLN A1036 GLN A1088 HIS A1106 GLN A1135 ASN C 99 ASN C 211 ASN C 437 ASN C 540 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C 955 ASN C1010 GLN C1101 HIS B 314 GLN B 563 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1011 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.103808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.075052 restraints weight = 81243.587| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.31 r_work: 0.3271 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24168 Z= 0.178 Angle : 1.058 34.055 33023 Z= 0.438 Chirality : 0.084 0.914 4070 Planarity : 0.004 0.042 4075 Dihedral : 13.620 128.360 5149 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 12.55 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 2795 helix: 1.40 (0.20), residues: 648 sheet: 0.04 (0.20), residues: 604 loop : -1.22 (0.14), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 273 TYR 0.027 0.001 TYR B1067 PHE 0.030 0.002 PHE C 238 TRP 0.024 0.002 TRP A 104 HIS 0.006 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00381 (24088) covalent geometry : angle 0.95749 (32818) SS BOND : bond 0.00747 ( 35) SS BOND : angle 2.14583 ( 70) hydrogen bonds : bond 0.04698 ( 909) hydrogen bonds : angle 5.99201 ( 2571) link_BETA1-4 : bond 0.02837 ( 1) link_BETA1-4 : angle 28.10599 ( 3) link_NAG-ASN : bond 0.01588 ( 44) link_NAG-ASN : angle 5.61321 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.856 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 203 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8971 (mp) REVERT: A 725 GLU cc_start: 0.8890 (tp30) cc_final: 0.8593 (tp30) REVERT: A 1005 GLN cc_start: 0.8606 (mt0) cc_final: 0.8370 (mt0) REVERT: C 298 GLU cc_start: 0.8895 (tp30) cc_final: 0.8650 (mt-10) REVERT: C 661 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7873 (tm-30) REVERT: C 805 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8988 (tt) REVERT: C 869 MET cc_start: 0.9119 (mtt) cc_final: 0.8895 (mtm) REVERT: C 950 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8819 (t0) REVERT: B 780 GLU cc_start: 0.9004 (tp30) cc_final: 0.8728 (tt0) REVERT: B 996 LEU cc_start: 0.9197 (tp) cc_final: 0.8994 (tt) REVERT: B 1029 MET cc_start: 0.9254 (tpp) cc_final: 0.9022 (tpp) outliers start: 51 outliers final: 24 residues processed: 269 average time/residue: 0.1509 time to fit residues: 67.1678 Evaluate side-chains 213 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 1108 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 250 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 211 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 655 HIS A 751 ASN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN C 99 ASN C 564 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 125 ASN B 762 GLN B 787 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.095046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064766 restraints weight = 79148.043| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.14 r_work: 0.3019 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 24168 Z= 0.230 Angle : 0.923 17.819 33023 Z= 0.402 Chirality : 0.083 0.948 4070 Planarity : 0.005 0.047 4075 Dihedral : 9.982 114.118 5147 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 3.59 % Allowed : 14.50 % Favored : 81.91 % 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 aren not related in a simple way. whole: -0.36 (0.15), residues: 2795 helix: 1.56 (0.20), residues: 649 sheet: -0.17 (0.20), residues: 623 loop : -1.08 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 765 TYR 0.028 0.002 TYR C 365 PHE 0.029 0.002 PHE B 392 TRP 0.019 0.002 TRP C 353 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00516 (24088) covalent geometry : angle 0.85660 (32818) SS BOND : bond 0.00478 ( 35) SS BOND : angle 1.60606 ( 70) hydrogen bonds : bond 0.04375 ( 909) hydrogen bonds : angle 5.68049 ( 2571) link_BETA1-4 : bond 0.01693 ( 1) link_BETA1-4 : angle 10.25500 ( 3) link_NAG-ASN : bond 0.01473 ( 44) link_NAG-ASN : angle 5.18546 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 186 time to evaluate : 0.931 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 338 PHE cc_start: 0.6896 (m-80) cc_final: 0.5747 (m-10) REVERT: A 787 GLN cc_start: 0.9042 (mt0) cc_final: 0.8713 (mt0) REVERT: A 873 TYR cc_start: 0.9598 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: A 988 GLU cc_start: 0.8986 (mp0) cc_final: 0.8774 (mp0) REVERT: C 53 ASP cc_start: 0.8600 (p0) cc_final: 0.8135 (p0) REVERT: C 118 LEU cc_start: 0.9160 (tt) cc_final: 0.8941 (mp) REVERT: C 298 GLU cc_start: 0.9144 (tp30) cc_final: 0.8807 (mt-10) REVERT: C 461 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.4550 (tp) REVERT: C 661 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 805 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9119 (tt) REVERT: C 869 MET cc_start: 0.9245 (mtt) cc_final: 0.9026 (mtm) REVERT: C 950 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.8799 (t0) REVERT: B 216 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8206 (pp) REVERT: B 979 ASP cc_start: 0.8933 (t0) cc_final: 0.8704 (t0) outliers start: 90 outliers final: 40 residues processed: 267 average time/residue: 0.1506 time to fit residues: 66.8635 Evaluate side-chains 206 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 45 optimal weight: 0.0470 chunk 240 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 25 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 493 GLN A 762 GLN A 784 GLN A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 409 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 992 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.096319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066019 restraints weight = 78831.957| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.15 r_work: 0.3025 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24168 Z= 0.135 Angle : 0.831 16.829 33023 Z= 0.356 Chirality : 0.082 0.958 4070 Planarity : 0.004 0.055 4075 Dihedral : 9.113 99.334 5144 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.55 % Allowed : 16.53 % Favored : 80.92 % 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 aren not related in a simple way. whole: -0.13 (0.15), residues: 2795 helix: 1.97 (0.20), residues: 647 sheet: -0.13 (0.20), residues: 614 loop : -1.00 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.020 0.001 TYR B1067 PHE 0.034 0.001 PHE C 238 TRP 0.021 0.001 TRP C 104 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00287 (24088) covalent geometry : angle 0.75964 (32818) SS BOND : bond 0.00217 ( 35) SS BOND : angle 1.19003 ( 70) hydrogen bonds : bond 0.03863 ( 909) hydrogen bonds : angle 5.29962 ( 2571) link_BETA1-4 : bond 0.01739 ( 1) link_BETA1-4 : angle 9.89192 ( 3) link_NAG-ASN : bond 0.01606 ( 44) link_NAG-ASN : angle 5.15025 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8536 (mt) cc_final: 0.8198 (mp) REVERT: A 338 PHE cc_start: 0.7093 (m-80) cc_final: 0.6015 (m-10) REVERT: A 464 PHE cc_start: 0.7983 (m-10) cc_final: 0.7561 (m-80) REVERT: A 571 ASP cc_start: 0.7133 (p0) cc_final: 0.6931 (p0) REVERT: A 873 TYR cc_start: 0.9600 (OUTLIER) cc_final: 0.8924 (m-80) REVERT: A 902 MET cc_start: 0.9383 (tpp) cc_final: 0.9118 (tpp) REVERT: C 53 ASP cc_start: 0.8549 (p0) cc_final: 0.8067 (p0) REVERT: C 118 LEU cc_start: 0.9223 (tt) cc_final: 0.9008 (mp) REVERT: C 298 GLU cc_start: 0.9054 (tp30) cc_final: 0.8797 (mt-10) REVERT: C 461 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.4579 (tp) REVERT: C 613 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: C 661 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 773 GLU cc_start: 0.8747 (tp30) cc_final: 0.8387 (tp30) REVERT: C 779 GLN cc_start: 0.9410 (tt0) cc_final: 0.8854 (tm-30) REVERT: C 780 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8533 (mm-30) REVERT: C 805 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9170 (tt) REVERT: C 950 ASP cc_start: 0.9297 (OUTLIER) cc_final: 0.8748 (t0) REVERT: B 216 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8219 (pp) REVERT: B 239 GLN cc_start: 0.6624 (mp10) cc_final: 0.5881 (tp40) REVERT: B 267 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8095 (m) REVERT: B 1005 GLN cc_start: 0.9278 (tp40) cc_final: 0.8953 (tp-100) REVERT: B 1010 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8722 (tm-30) outliers start: 64 outliers final: 28 residues processed: 241 average time/residue: 0.1476 time to fit residues: 59.7636 Evaluate side-chains 196 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 176 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.095039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.064651 restraints weight = 79171.670| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.14 r_work: 0.3016 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24168 Z= 0.169 Angle : 0.824 16.646 33023 Z= 0.356 Chirality : 0.081 0.963 4070 Planarity : 0.004 0.058 4075 Dihedral : 8.532 88.663 5144 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.87 % Allowed : 17.25 % Favored : 79.88 % 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 aren not related in a simple way. whole: -0.06 (0.15), residues: 2795 helix: 2.07 (0.20), residues: 642 sheet: -0.10 (0.20), residues: 639 loop : -0.96 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 765 TYR 0.025 0.001 TYR A 453 PHE 0.016 0.001 PHE B 392 TRP 0.023 0.001 TRP C 353 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00376 (24088) covalent geometry : angle 0.75686 (32818) SS BOND : bond 0.00264 ( 35) SS BOND : angle 1.21506 ( 70) hydrogen bonds : bond 0.03802 ( 909) hydrogen bonds : angle 5.23430 ( 2571) link_BETA1-4 : bond 0.02778 ( 1) link_BETA1-4 : angle 9.43599 ( 3) link_NAG-ASN : bond 0.01503 ( 44) link_NAG-ASN : angle 4.98261 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8547 (mt) cc_final: 0.8195 (mp) REVERT: A 873 TYR cc_start: 0.9599 (OUTLIER) cc_final: 0.9110 (m-80) REVERT: A 902 MET cc_start: 0.9403 (tpp) cc_final: 0.9171 (tpp) REVERT: C 53 ASP cc_start: 0.8595 (p0) cc_final: 0.8097 (p0) REVERT: C 298 GLU cc_start: 0.9156 (tp30) cc_final: 0.8833 (mt-10) REVERT: C 417 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6418 (ptmt) REVERT: C 461 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.4532 (tp) REVERT: C 661 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8211 (tm-30) REVERT: C 773 GLU cc_start: 0.8889 (tp30) cc_final: 0.8475 (tp30) REVERT: C 779 GLN cc_start: 0.9401 (tt0) cc_final: 0.8862 (tm-30) REVERT: C 950 ASP cc_start: 0.9308 (m-30) cc_final: 0.8793 (t0) REVERT: B 216 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8259 (pp) REVERT: B 239 GLN cc_start: 0.6707 (mp10) cc_final: 0.6270 (mm-40) REVERT: B 267 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8079 (m) REVERT: B 428 ASP cc_start: 0.8796 (p0) cc_final: 0.8557 (p0) REVERT: B 1005 GLN cc_start: 0.9289 (tp40) cc_final: 0.8973 (tp-100) REVERT: B 1010 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8694 (tm-30) outliers start: 72 outliers final: 44 residues processed: 232 average time/residue: 0.1426 time to fit residues: 55.7957 Evaluate side-chains 210 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 26 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A1058 HIS C 52 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 536 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059780 restraints weight = 80111.134| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.07 r_work: 0.2906 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 24168 Z= 0.294 Angle : 0.901 17.585 33023 Z= 0.402 Chirality : 0.080 0.900 4070 Planarity : 0.005 0.055 4075 Dihedral : 8.650 80.480 5144 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.19 % Allowed : 17.69 % Favored : 79.12 % 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 aren not related in a simple way. whole: -0.31 (0.15), residues: 2795 helix: 1.62 (0.20), residues: 642 sheet: -0.25 (0.20), residues: 641 loop : -0.99 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 273 TYR 0.025 0.002 TYR B1067 PHE 0.039 0.002 PHE C 238 TRP 0.021 0.002 TRP C 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00657 (24088) covalent geometry : angle 0.84214 (32818) SS BOND : bond 0.00471 ( 35) SS BOND : angle 1.59751 ( 70) hydrogen bonds : bond 0.04410 ( 909) hydrogen bonds : angle 5.61078 ( 2571) link_BETA1-4 : bond 0.02727 ( 1) link_BETA1-4 : angle 9.38405 ( 3) link_NAG-ASN : bond 0.01358 ( 44) link_NAG-ASN : angle 4.85097 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 149 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7409 (m-80) cc_final: 0.7079 (t80) REVERT: A 464 PHE cc_start: 0.7789 (m-80) cc_final: 0.7024 (m-80) REVERT: A 873 TYR cc_start: 0.9618 (OUTLIER) cc_final: 0.9318 (m-80) REVERT: A 988 GLU cc_start: 0.8948 (mp0) cc_final: 0.8640 (pm20) REVERT: A 991 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9223 (p) REVERT: C 53 ASP cc_start: 0.8908 (p0) cc_final: 0.8453 (p0) REVERT: C 298 GLU cc_start: 0.9319 (tp30) cc_final: 0.8956 (mt-10) REVERT: C 417 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6593 (ptmt) REVERT: C 461 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.4843 (tp) REVERT: C 887 THR cc_start: 0.9689 (OUTLIER) cc_final: 0.9396 (p) REVERT: C 950 ASP cc_start: 0.9309 (m-30) cc_final: 0.8805 (t0) REVERT: B 216 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8492 (pp) REVERT: B 239 GLN cc_start: 0.7139 (mp10) cc_final: 0.6645 (mm-40) REVERT: B 756 TYR cc_start: 0.8553 (m-10) cc_final: 0.8326 (m-80) REVERT: B 960 ASN cc_start: 0.9316 (m-40) cc_final: 0.8975 (t0) REVERT: B 1005 GLN cc_start: 0.9331 (tp40) cc_final: 0.9042 (tp-100) outliers start: 80 outliers final: 49 residues processed: 220 average time/residue: 0.1303 time to fit residues: 47.9806 Evaluate side-chains 188 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 184 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1011 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.092362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061833 restraints weight = 78948.642| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.09 r_work: 0.2962 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24168 Z= 0.157 Angle : 0.821 16.575 33023 Z= 0.356 Chirality : 0.080 0.959 4070 Planarity : 0.004 0.059 4075 Dihedral : 8.229 77.593 5144 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.63 % Allowed : 19.00 % Favored : 78.37 % 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 aren not related in a simple way. whole: -0.14 (0.16), residues: 2795 helix: 1.97 (0.20), residues: 634 sheet: -0.10 (0.20), residues: 617 loop : -0.99 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1019 TYR 0.023 0.001 TYR B1067 PHE 0.024 0.001 PHE B 392 TRP 0.019 0.001 TRP C 104 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00345 (24088) covalent geometry : angle 0.75375 (32818) SS BOND : bond 0.00290 ( 35) SS BOND : angle 1.17407 ( 70) hydrogen bonds : bond 0.03869 ( 909) hydrogen bonds : angle 5.29447 ( 2571) link_BETA1-4 : bond 0.02886 ( 1) link_BETA1-4 : angle 9.54874 ( 3) link_NAG-ASN : bond 0.01540 ( 44) link_NAG-ASN : angle 4.94465 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 150 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8499 (mt) cc_final: 0.8128 (mp) REVERT: A 338 PHE cc_start: 0.7410 (m-80) cc_final: 0.7077 (t80) REVERT: A 873 TYR cc_start: 0.9577 (OUTLIER) cc_final: 0.9339 (m-80) REVERT: A 988 GLU cc_start: 0.8930 (mp0) cc_final: 0.8623 (pm20) REVERT: A 991 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9155 (p) REVERT: C 53 ASP cc_start: 0.8858 (p0) cc_final: 0.8402 (p0) REVERT: C 298 GLU cc_start: 0.9237 (tp30) cc_final: 0.8942 (mt-10) REVERT: C 417 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6531 (ptmt) REVERT: C 461 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.4834 (tp) REVERT: C 661 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8272 (tm-30) REVERT: C 779 GLN cc_start: 0.9426 (tt0) cc_final: 0.9152 (tp40) REVERT: C 950 ASP cc_start: 0.9288 (m-30) cc_final: 0.8781 (t0) REVERT: B 216 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8528 (pp) REVERT: B 239 GLN cc_start: 0.7047 (mp10) cc_final: 0.6165 (mp10) REVERT: B 267 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8240 (m) REVERT: B 378 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8450 (ttpp) REVERT: B 387 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8887 (mp) REVERT: B 756 TYR cc_start: 0.8512 (m-10) cc_final: 0.8247 (m-80) REVERT: B 960 ASN cc_start: 0.9277 (m-40) cc_final: 0.9002 (t0) REVERT: B 1005 GLN cc_start: 0.9260 (tp40) cc_final: 0.8944 (tp-100) REVERT: B 1010 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8834 (tm-30) outliers start: 66 outliers final: 48 residues processed: 206 average time/residue: 0.1294 time to fit residues: 45.0504 Evaluate side-chains 197 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 192 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 206 optimal weight: 0.4980 chunk 143 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.092638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062221 restraints weight = 78809.470| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.06 r_work: 0.2964 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24168 Z= 0.148 Angle : 0.806 15.894 33023 Z= 0.349 Chirality : 0.080 0.962 4070 Planarity : 0.004 0.058 4075 Dihedral : 7.942 74.862 5144 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.79 % Allowed : 18.76 % Favored : 78.45 % 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 aren not related in a simple way. whole: -0.06 (0.16), residues: 2795 helix: 1.99 (0.20), residues: 646 sheet: -0.07 (0.21), residues: 611 loop : -0.93 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.021 0.001 TYR B1067 PHE 0.040 0.001 PHE C 238 TRP 0.017 0.001 TRP C 104 HIS 0.036 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00325 (24088) covalent geometry : angle 0.73887 (32818) SS BOND : bond 0.00255 ( 35) SS BOND : angle 1.29478 ( 70) hydrogen bonds : bond 0.03707 ( 909) hydrogen bonds : angle 5.14015 ( 2571) link_BETA1-4 : bond 0.03127 ( 1) link_BETA1-4 : angle 9.55461 ( 3) link_NAG-ASN : bond 0.01551 ( 44) link_NAG-ASN : angle 4.88835 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 151 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8482 (mt) cc_final: 0.8124 (mp) REVERT: A 338 PHE cc_start: 0.7267 (m-80) cc_final: 0.6874 (t80) REVERT: A 773 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8978 (tt0) REVERT: A 988 GLU cc_start: 0.8985 (mp0) cc_final: 0.8687 (pm20) REVERT: A 990 GLU cc_start: 0.9042 (tp30) cc_final: 0.8664 (mt-10) REVERT: A 991 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9152 (p) REVERT: C 53 ASP cc_start: 0.8825 (p0) cc_final: 0.8428 (p0) REVERT: C 298 GLU cc_start: 0.9247 (tp30) cc_final: 0.8953 (mt-10) REVERT: C 417 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6560 (ptmt) REVERT: C 461 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.4825 (tp) REVERT: C 661 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 779 GLN cc_start: 0.9423 (tt0) cc_final: 0.9158 (tp40) REVERT: C 950 ASP cc_start: 0.9283 (m-30) cc_final: 0.8759 (t0) REVERT: B 216 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8521 (pp) REVERT: B 239 GLN cc_start: 0.7059 (mp10) cc_final: 0.6356 (tp40) REVERT: B 267 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8249 (m) REVERT: B 378 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8473 (ttpp) REVERT: B 387 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8849 (mp) REVERT: B 394 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7762 (p0) REVERT: B 756 TYR cc_start: 0.8534 (m-10) cc_final: 0.8194 (m-80) REVERT: B 960 ASN cc_start: 0.9269 (m-40) cc_final: 0.9000 (t0) REVERT: B 1005 GLN cc_start: 0.9224 (tp40) cc_final: 0.8901 (tp-100) REVERT: B 1010 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8841 (tm-30) outliers start: 70 outliers final: 52 residues processed: 212 average time/residue: 0.1179 time to fit residues: 42.4462 Evaluate side-chains 203 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 273 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 256 optimal weight: 0.0170 chunk 159 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.092886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062509 restraints weight = 78878.262| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.11 r_work: 0.2967 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24168 Z= 0.146 Angle : 0.801 15.840 33023 Z= 0.347 Chirality : 0.080 0.962 4070 Planarity : 0.004 0.058 4075 Dihedral : 7.766 72.083 5144 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.99 % Allowed : 18.92 % Favored : 78.09 % 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 aren not related in a simple way. whole: -0.02 (0.16), residues: 2795 helix: 2.02 (0.20), residues: 655 sheet: -0.08 (0.21), residues: 603 loop : -0.89 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.021 0.001 TYR B1067 PHE 0.027 0.001 PHE B 392 TRP 0.025 0.001 TRP C 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00320 (24088) covalent geometry : angle 0.73447 (32818) SS BOND : bond 0.00250 ( 35) SS BOND : angle 1.14604 ( 70) hydrogen bonds : bond 0.03649 ( 909) hydrogen bonds : angle 5.06879 ( 2571) link_BETA1-4 : bond 0.03185 ( 1) link_BETA1-4 : angle 9.67331 ( 3) link_NAG-ASN : bond 0.01557 ( 44) link_NAG-ASN : angle 4.86517 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 147 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8478 (mt) cc_final: 0.8128 (mp) REVERT: A 338 PHE cc_start: 0.7137 (m-80) cc_final: 0.6731 (t80) REVERT: A 773 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8983 (tt0) REVERT: A 869 MET cc_start: 0.9594 (mtm) cc_final: 0.9355 (mtm) REVERT: A 947 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8693 (mmmm) REVERT: A 988 GLU cc_start: 0.8994 (mp0) cc_final: 0.8698 (pm20) REVERT: C 53 ASP cc_start: 0.8752 (p0) cc_final: 0.8334 (p0) REVERT: C 298 GLU cc_start: 0.9270 (tp30) cc_final: 0.8983 (mt-10) REVERT: C 387 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8636 (mm) REVERT: C 461 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.4663 (tp) REVERT: C 661 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8281 (tm-30) REVERT: C 740 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8365 (tmm) REVERT: C 779 GLN cc_start: 0.9406 (tt0) cc_final: 0.9143 (tp40) REVERT: C 950 ASP cc_start: 0.9291 (m-30) cc_final: 0.8772 (t0) REVERT: B 216 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8486 (pp) REVERT: B 378 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8543 (ttpp) REVERT: B 387 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8894 (mp) REVERT: B 756 TYR cc_start: 0.8558 (m-10) cc_final: 0.8224 (m-80) REVERT: B 960 ASN cc_start: 0.9271 (m-40) cc_final: 0.9000 (t0) REVERT: B 1010 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8837 (tm-30) outliers start: 75 outliers final: 58 residues processed: 209 average time/residue: 0.1398 time to fit residues: 49.9983 Evaluate side-chains 207 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 237 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 250 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.092977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062653 restraints weight = 79033.202| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.12 r_work: 0.2978 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24168 Z= 0.137 Angle : 0.797 15.964 33023 Z= 0.345 Chirality : 0.080 0.962 4070 Planarity : 0.004 0.058 4075 Dihedral : 7.616 69.447 5144 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.63 % Allowed : 19.52 % Favored : 77.85 % 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 aren not related in a simple way. whole: 0.01 (0.16), residues: 2795 helix: 2.04 (0.20), residues: 654 sheet: -0.09 (0.20), residues: 610 loop : -0.86 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.021 0.001 TYR B1067 PHE 0.040 0.001 PHE C 238 TRP 0.023 0.001 TRP C 104 HIS 0.003 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00299 (24088) covalent geometry : angle 0.73089 (32818) SS BOND : bond 0.00220 ( 35) SS BOND : angle 1.08393 ( 70) hydrogen bonds : bond 0.03610 ( 909) hydrogen bonds : angle 4.98952 ( 2571) link_BETA1-4 : bond 0.03258 ( 1) link_BETA1-4 : angle 9.69166 ( 3) link_NAG-ASN : bond 0.01582 ( 44) link_NAG-ASN : angle 4.84686 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8471 (mt) cc_final: 0.8127 (mp) REVERT: A 338 PHE cc_start: 0.7148 (m-80) cc_final: 0.6732 (t80) REVERT: A 773 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8975 (tt0) REVERT: A 947 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8665 (mmmm) REVERT: A 954 GLN cc_start: 0.9310 (mt0) cc_final: 0.9088 (mt0) REVERT: A 988 GLU cc_start: 0.8999 (mp0) cc_final: 0.8699 (pm20) REVERT: C 53 ASP cc_start: 0.8752 (p0) cc_final: 0.8331 (p0) REVERT: C 298 GLU cc_start: 0.9254 (tp30) cc_final: 0.8978 (mt-10) REVERT: C 387 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8606 (mm) REVERT: C 461 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.4609 (tp) REVERT: C 564 GLN cc_start: 0.8203 (mt0) cc_final: 0.7921 (tp40) REVERT: C 661 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8295 (tm-30) REVERT: C 779 GLN cc_start: 0.9395 (tt0) cc_final: 0.9144 (tp40) REVERT: C 887 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9373 (p) REVERT: C 950 ASP cc_start: 0.9285 (m-30) cc_final: 0.8775 (t0) REVERT: B 216 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8476 (pp) REVERT: B 378 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8539 (ttpp) REVERT: B 387 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8915 (mp) REVERT: B 756 TYR cc_start: 0.8570 (m-10) cc_final: 0.8213 (m-80) REVERT: B 779 GLN cc_start: 0.9449 (tm-30) cc_final: 0.9238 (tm-30) REVERT: B 960 ASN cc_start: 0.9254 (m-40) cc_final: 0.8988 (t0) REVERT: B 1002 GLN cc_start: 0.9253 (tp40) cc_final: 0.9049 (tm-30) REVERT: B 1010 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8771 (tm-30) outliers start: 66 outliers final: 53 residues processed: 208 average time/residue: 0.1371 time to fit residues: 48.8674 Evaluate side-chains 203 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 190 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 145 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.092394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061696 restraints weight = 80396.253| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.12 r_work: 0.2951 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24168 Z= 0.177 Angle : 0.807 16.184 33023 Z= 0.352 Chirality : 0.080 0.942 4070 Planarity : 0.004 0.057 4075 Dihedral : 7.532 65.948 5144 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.67 % Allowed : 19.72 % Favored : 77.61 % 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 aren not related in a simple way. whole: 0.00 (0.16), residues: 2795 helix: 2.01 (0.20), residues: 654 sheet: -0.10 (0.21), residues: 604 loop : -0.85 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.029 0.001 TYR A 904 PHE 0.032 0.001 PHE B 392 TRP 0.021 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00398 (24088) covalent geometry : angle 0.74243 (32818) SS BOND : bond 0.00283 ( 35) SS BOND : angle 1.28665 ( 70) hydrogen bonds : bond 0.03693 ( 909) hydrogen bonds : angle 5.02652 ( 2571) link_BETA1-4 : bond 0.03239 ( 1) link_BETA1-4 : angle 9.67946 ( 3) link_NAG-ASN : bond 0.01503 ( 44) link_NAG-ASN : angle 4.77034 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6358.94 seconds wall clock time: 110 minutes 19.89 seconds (6619.89 seconds total)