Starting phenix.real_space_refine on Sat Jul 4 21:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zp7_11337/07_2026/6zp7_11337.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp7_11337/07_2026/6zp7_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_11337/07_2026/6zp7_11337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp7_11337/07_2026/6zp7_11337.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zp7_11337/07_2026/6zp7_11337.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zp7_11337/07_2026/6zp7_11337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zp7_11337/07_2026/6zp7_11337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp7_11337/07_2026/6zp7_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.34, per 1000 atoms: 0.23 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: 1.90 Conformation dependent library (CDL) restraints added in 854.9 milliseconds 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: 0.99 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: 5.11 Time building geometry restraints manager: 2.59 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 - 17.92: 12338 17.92 - 35.84: 1055 35.84 - 53.76: 180 53.76 - 71.69: 32 71.69 - 89.61: 21 Dihedral angle restraints: 13626 sinusoidal: 5296 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 13623 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: 4122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O DMS A1307 " -0.204 2.00e-02 2.50e+03 2.78e-01 7.71e+02 pdb=" C1 DMS A1307 " -0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1307 " -0.137 2.00e-02 2.50e+03 pdb=" S DMS A1307 " 0.479 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1308 " 0.201 2.00e-02 2.50e+03 2.76e-01 7.60e+02 pdb=" C1 DMS A1308 " 0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1308 " 0.137 2.00e-02 2.50e+03 pdb=" S DMS A1308 " -0.475 2.00e-02 2.50e+03 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 ... (remaining 4119 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 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 : 0.009 0.278 4078 Dihedral : 13.619 89.607 8137 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 are 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/Z covalent geometry : bond 0.01289 / 0.76 (24088) covalent geometry : angle 0.91889 / 0.47 (32818) SS BOND : bond 0.01418 / 0.95 ( 35) SS BOND : angle 2.14573 / 1.52 ( 70) hydrogen bonds : bond 0.12621 / 8.17 ( 909) hydrogen bonds : angle 7.31486 / 4.99 ( 2571) link_BETA1-4 : bond 0.01095 / 0.58 ( 1) link_BETA1-4 : angle 21.97651 / 12.86 ( 3) link_NAG-ASN : bond 0.40730 / 27.01 ( 44) link_NAG-ASN : angle 14.79956 / 9.58 ( 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 : 0.893 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: 0.1697 time to fit residues: 117.4467 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 : 0.859 ------------------------------------------------------------------------------- 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... A 52 GLN ** 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 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 B1101 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.103961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.075169 restraints weight = 81164.610| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.30 r_work: 0.3271 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24168 Z= 0.175 Angle : 1.147 46.035 33023 Z= 0.462 Chirality : 0.086 0.761 4070 Planarity : 0.004 0.043 4078 Dihedral : 4.953 53.937 3047 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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 are not related in a simple way. whole: -0.45 (0.15), residues: 2795 helix: 1.40 (0.19), residues: 648 sheet: 0.01 (0.20), residues: 614 loop : -1.21 (0.14), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 214 TYR 0.027 0.002 TYR B1067 PHE 0.030 0.002 PHE C 238 TRP 0.025 0.002 TRP A 104 HIS 0.006 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (24088) covalent geometry : angle 1.06458 / 0.44 (32818) SS BOND : bond 0.00408 / 0.29 ( 35) SS BOND : angle 2.10320 / 1.27 ( 70) hydrogen bonds : bond 0.04638 / 2.98 ( 909) hydrogen bonds : angle 5.98243 / 4.10 ( 2571) link_BETA1-4 : bond 0.03092 / 1.63 ( 1) link_BETA1-4 : angle 27.23319 / 15.42 ( 3) link_NAG-ASN : bond 0.01741 / 1.17 ( 44) link_NAG-ASN : angle 5.31454 / 3.45 ( 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 283 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.892 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 53 ASP cc_start: 0.8032 (t0) cc_final: 0.7831 (t70) REVERT: A 203 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8969 (mp) REVERT: A 725 GLU cc_start: 0.8883 (tp30) cc_final: 0.8583 (tp30) REVERT: A 1005 GLN cc_start: 0.8615 (mt0) cc_final: 0.8382 (mt0) REVERT: C 298 GLU cc_start: 0.8897 (tp30) cc_final: 0.8649 (mt-10) REVERT: C 661 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7873 (tm-30) REVERT: C 805 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 869 MET cc_start: 0.9127 (mtt) cc_final: 0.8905 (mtm) REVERT: C 950 ASP cc_start: 0.9222 (OUTLIER) cc_final: 0.8823 (t0) REVERT: B 54 LEU cc_start: 0.8635 (mm) cc_final: 0.8411 (mm) REVERT: B 392 PHE cc_start: 0.7921 (m-10) cc_final: 0.7716 (m-10) REVERT: B 780 GLU cc_start: 0.9019 (tp30) cc_final: 0.8746 (tt0) REVERT: B 996 LEU cc_start: 0.9194 (tp) cc_final: 0.8986 (tt) outliers start: 51 outliers final: 23 residues processed: 268 average time/residue: 0.1461 time to fit residues: 64.8314 Evaluate side-chains 218 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 421 TYR 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 385 THR Chi-restraints excluded: chain B residue 517 LEU 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: 3.9990 chunk 211 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS C 49 HIS C 99 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 703 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 125 ASN B 536 ASN 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** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.092658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061764 restraints weight = 80393.627| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.16 r_work: 0.2954 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 24168 Z= 0.305 Angle : 1.048 17.054 33023 Z= 0.452 Chirality : 0.083 0.765 4070 Planarity : 0.005 0.055 4078 Dihedral : 4.947 44.994 3045 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 3.71 % Allowed : 14.42 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2795 helix: 1.26 (0.20), residues: 654 sheet: -0.21 (0.20), residues: 611 loop : -1.12 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 408 TYR 0.035 0.002 TYR C 365 PHE 0.020 0.002 PHE C 92 TRP 0.017 0.002 TRP C 353 HIS 0.007 0.002 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (24088) covalent geometry : angle 1.00093 / 0.44 (32818) SS BOND : bond 0.01025 / 0.82 ( 35) SS BOND : angle 1.78933 / 1.17 ( 70) hydrogen bonds : bond 0.04749 / 3.06 ( 909) hydrogen bonds : angle 5.84883 / 4.00 ( 2571) link_BETA1-4 : bond 0.05978 / 3.15 ( 1) link_BETA1-4 : angle 9.27507 / 5.13 ( 3) link_NAG-ASN : bond 0.01391 / 0.91 ( 44) link_NAG-ASN : angle 4.66957 / 3.04 ( 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 272 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 179 time to evaluate : 0.883 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: 0.6847 (m-80) cc_final: 0.5723 (m-10) REVERT: A 787 GLN cc_start: 0.9122 (mt0) cc_final: 0.8840 (mt0) REVERT: A 873 TYR cc_start: 0.9619 (OUTLIER) cc_final: 0.9078 (m-80) REVERT: A 988 GLU cc_start: 0.9025 (mp0) cc_final: 0.8809 (mp0) REVERT: C 53 ASP cc_start: 0.8772 (p0) cc_final: 0.8331 (p0) REVERT: C 118 LEU cc_start: 0.9181 (tt) cc_final: 0.8959 (mp) REVERT: C 275 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.7931 (t80) REVERT: C 298 GLU cc_start: 0.9235 (tp30) cc_final: 0.8880 (mt-10) REVERT: C 461 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.4891 (mt) REVERT: C 661 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 869 MET cc_start: 0.9340 (mtt) cc_final: 0.9104 (mtm) REVERT: C 950 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.8808 (t0) REVERT: B 216 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8370 (pp) REVERT: B 979 ASP cc_start: 0.9003 (t0) cc_final: 0.8743 (t0) outliers start: 93 outliers final: 45 residues processed: 262 average time/residue: 0.1443 time to fit residues: 63.0450 Evaluate side-chains 196 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 493 GLN 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 938 LEU 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 275 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE 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 911 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE 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 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS 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 1132 ILE 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: 0.5980 chunk 240 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 40.0000 chunk 83 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 409 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** 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 = 0.3840 r_free = 0.3840 target = 0.094310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063935 restraints weight = 78914.982| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.12 r_work: 0.3005 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4465 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= 0.158 Angle : 0.917 16.621 33023 Z= 0.385 Chirality : 0.081 0.713 4070 Planarity : 0.004 0.060 4078 Dihedral : 4.553 44.865 3042 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.63 % Allowed : 16.61 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 2795 helix: 1.83 (0.20), residues: 640 sheet: -0.18 (0.20), residues: 616 loop : -1.07 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 273 TYR 0.021 0.001 TYR B1067 PHE 0.034 0.001 PHE C 238 TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24088) covalent geometry : angle 0.86783 / 0.37 (32818) SS BOND : bond 0.00312 / 0.22 ( 35) SS BOND : angle 1.50550 / 0.94 ( 70) hydrogen bonds : bond 0.04091 / 2.61 ( 909) hydrogen bonds : angle 5.44756 / 3.72 ( 2571) link_BETA1-4 : bond 0.01134 / 0.60 ( 1) link_BETA1-4 : angle 8.18370 / 4.55 ( 3) link_NAG-ASN : bond 0.01529 / 0.99 ( 44) link_NAG-ASN : angle 4.50036 / 2.96 ( 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 241 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 175 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8467 (mt) cc_final: 0.8152 (mp) REVERT: A 338 PHE cc_start: 0.6999 (m-80) cc_final: 0.5951 (m-10) REVERT: A 762 GLN cc_start: 0.8853 (mt0) cc_final: 0.8647 (mt0) REVERT: A 773 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8640 (tt0) REVERT: A 873 TYR cc_start: 0.9606 (OUTLIER) cc_final: 0.9232 (m-80) REVERT: C 53 ASP cc_start: 0.8657 (p0) cc_final: 0.8148 (p0) REVERT: C 118 LEU cc_start: 0.9239 (tt) cc_final: 0.9030 (mp) REVERT: C 298 GLU cc_start: 0.9148 (tp30) cc_final: 0.8842 (mt-10) REVERT: C 417 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6380 (ptmt) REVERT: C 461 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.4687 (tp) REVERT: C 528 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7410 (mttt) REVERT: C 661 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 773 GLU cc_start: 0.8949 (tp30) cc_final: 0.8622 (tp30) REVERT: C 779 GLN cc_start: 0.9396 (tt0) cc_final: 0.8871 (tm-30) REVERT: C 780 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8626 (mm-30) REVERT: C 805 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9229 (tt) REVERT: C 902 MET cc_start: 0.9421 (tpp) cc_final: 0.9145 (tpt) REVERT: C 950 ASP cc_start: 0.9306 (OUTLIER) cc_final: 0.8749 (t0) REVERT: B 216 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8403 (pp) REVERT: B 239 GLN cc_start: 0.7110 (mp10) cc_final: 0.6289 (mp10) REVERT: B 267 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8046 (m) REVERT: B 564 GLN cc_start: 0.8020 (tp-100) cc_final: 0.7199 (tp-100) REVERT: B 1005 GLN cc_start: 0.9294 (tp40) cc_final: 0.8978 (tp-100) outliers start: 66 outliers final: 34 residues processed: 231 average time/residue: 0.1350 time to fit residues: 52.3245 Evaluate side-chains 193 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 916 LEU Chi-restraints excluded: chain A residue 968 SER 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 220 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 417 LYS 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 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 C residue 1074 ASN 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 595 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 754 LEU Chi-restraints excluded: chain B residue 1012 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: 1.9990 chunk 8 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 394 ASN A 690 GLN A 907 ASN C 564 GLN ** 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.092291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061698 restraints weight = 79551.284| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.10 r_work: 0.2952 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24168 Z= 0.214 Angle : 0.915 16.824 33023 Z= 0.390 Chirality : 0.081 0.702 4070 Planarity : 0.004 0.062 4078 Dihedral : 4.503 45.864 3042 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.90 % Allowed : 16.97 % 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 are not related in a simple way. whole: -0.22 (0.15), residues: 2795 helix: 1.79 (0.20), residues: 650 sheet: -0.18 (0.20), residues: 616 loop : -1.01 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.024 0.002 TYR B1067 PHE 0.029 0.001 PHE B 392 TRP 0.023 0.001 TRP C 353 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (24088) covalent geometry : angle 0.87019 / 0.38 (32818) SS BOND : bond 0.00398 / 0.25 ( 35) SS BOND : angle 1.80162 / 1.11 ( 70) hydrogen bonds : bond 0.04047 / 2.62 ( 909) hydrogen bonds : angle 5.34743 / 3.65 ( 2571) link_BETA1-4 : bond 0.01626 / 0.86 ( 1) link_BETA1-4 : angle 7.88342 / 4.38 ( 3) link_NAG-ASN : bond 0.01389 / 0.91 ( 44) link_NAG-ASN : angle 4.22463 / 2.80 ( 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 256 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 158 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8713 (tt0) REVERT: A 873 TYR cc_start: 0.9588 (OUTLIER) cc_final: 0.9279 (m-80) REVERT: A 988 GLU cc_start: 0.9101 (mp0) cc_final: 0.8841 (pm20) REVERT: C 53 ASP cc_start: 0.8833 (p0) cc_final: 0.8421 (p0) REVERT: C 298 GLU cc_start: 0.9261 (tp30) cc_final: 0.8912 (mt-10) REVERT: C 417 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6541 (ptmt) REVERT: C 461 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.4708 (tp) REVERT: C 528 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7596 (mtpt) REVERT: C 661 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8241 (tm-30) REVERT: C 773 GLU cc_start: 0.9059 (tp30) cc_final: 0.8654 (tp30) REVERT: C 779 GLN cc_start: 0.9394 (tt0) cc_final: 0.8863 (tm-30) REVERT: C 887 THR cc_start: 0.9646 (OUTLIER) cc_final: 0.9397 (p) REVERT: C 950 ASP cc_start: 0.9274 (m-30) cc_final: 0.8756 (t0) REVERT: B 216 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8451 (pp) REVERT: B 239 GLN cc_start: 0.7123 (mp10) cc_final: 0.6792 (mm-40) REVERT: B 267 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8099 (m) REVERT: B 378 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8466 (ttpp) REVERT: B 387 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9141 (mm) REVERT: B 756 TYR cc_start: 0.8448 (m-10) cc_final: 0.8236 (m-80) REVERT: B 960 ASN cc_start: 0.9302 (m-40) cc_final: 0.8966 (t0) REVERT: B 1005 GLN cc_start: 0.9286 (tp40) cc_final: 0.9000 (tp-100) outliers start: 98 outliers final: 56 residues processed: 242 average time/residue: 0.1292 time to fit residues: 53.6662 Evaluate side-chains 208 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 742 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 938 LEU 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 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 392 PHE 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 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 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 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 226 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 595 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 754 LEU Chi-restraints excluded: chain B residue 981 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 26 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 164 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.093508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.062425 restraints weight = 80097.739| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.25 r_work: 0.2989 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24168 Z= 0.136 Angle : 0.868 16.597 33023 Z= 0.363 Chirality : 0.081 0.701 4070 Planarity : 0.004 0.054 4078 Dihedral : 4.332 45.909 3042 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.23 % Allowed : 19.04 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2795 helix: 2.13 (0.20), residues: 648 sheet: -0.08 (0.20), residues: 619 loop : -0.98 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.021 0.001 TYR B1067 PHE 0.037 0.001 PHE C 238 TRP 0.018 0.001 TRP C 104 HIS 0.003 0.000 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (24088) covalent geometry : angle 0.82152 / 0.35 (32818) SS BOND : bond 0.00203 / 0.12 ( 35) SS BOND : angle 1.09935 / 0.71 ( 70) hydrogen bonds : bond 0.03698 / 2.37 ( 909) hydrogen bonds : angle 5.13847 / 3.50 ( 2571) link_BETA1-4 : bond 0.01252 / 0.66 ( 1) link_BETA1-4 : angle 7.89567 / 4.38 ( 3) link_NAG-ASN : bond 0.01585 / 1.02 ( 44) link_NAG-ASN : angle 4.34140 / 2.88 ( 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 220 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8549 (mt) cc_final: 0.8176 (mp) REVERT: A 338 PHE cc_start: 0.7238 (m-80) cc_final: 0.6719 (t80) REVERT: A 773 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8714 (tt0) REVERT: A 988 GLU cc_start: 0.8958 (mp0) cc_final: 0.8619 (pm20) REVERT: A 990 GLU cc_start: 0.8986 (tp30) cc_final: 0.8658 (mt-10) REVERT: C 53 ASP cc_start: 0.8684 (p0) cc_final: 0.8281 (p0) REVERT: C 298 GLU cc_start: 0.9201 (tp30) cc_final: 0.8934 (mt-10) REVERT: C 417 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6583 (ptmt) REVERT: C 461 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.4671 (tp) REVERT: C 528 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7623 (mtpt) REVERT: C 661 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 779 GLN cc_start: 0.9404 (tt0) cc_final: 0.9154 (tp40) REVERT: C 902 MET cc_start: 0.9464 (tpp) cc_final: 0.9133 (tpt) REVERT: C 950 ASP cc_start: 0.9284 (m-30) cc_final: 0.8763 (t0) REVERT: B 33 THR cc_start: 0.8753 (p) cc_final: 0.8544 (t) REVERT: B 216 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8499 (pp) REVERT: B 239 GLN cc_start: 0.7130 (mp10) cc_final: 0.6552 (tp40) REVERT: B 267 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8206 (m) REVERT: B 387 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.8851 (mp) REVERT: B 756 TYR cc_start: 0.8443 (m-10) cc_final: 0.8098 (m-80) REVERT: B 960 ASN cc_start: 0.9260 (m-40) cc_final: 0.8977 (t0) REVERT: B 983 ARG cc_start: 0.8360 (ptt90) cc_final: 0.7982 (ppt170) REVERT: B 1005 GLN cc_start: 0.9204 (tp40) cc_final: 0.8884 (tp-100) REVERT: B 1010 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8787 (tm-30) outliers start: 56 outliers final: 38 residues processed: 212 average time/residue: 0.1290 time to fit residues: 46.2587 Evaluate side-chains 197 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 916 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 A residue 1120 THR Chi-restraints excluded: chain C residue 47 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 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 974 SER 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 595 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 754 LEU Chi-restraints excluded: chain B residue 934 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 184 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 394 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.090183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059344 restraints weight = 79704.222| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.10 r_work: 0.2914 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 24168 Z= 0.269 Angle : 0.928 17.040 33023 Z= 0.401 Chirality : 0.080 0.705 4070 Planarity : 0.004 0.052 4078 Dihedral : 4.619 48.951 3042 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.23 % Allowed : 19.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2795 helix: 1.65 (0.20), residues: 664 sheet: -0.22 (0.20), residues: 631 loop : -0.94 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 355 TYR 0.024 0.002 TYR B1067 PHE 0.035 0.002 PHE B 392 TRP 0.019 0.002 TRP C 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 (24088) covalent geometry : angle 0.88723 / 0.39 (32818) SS BOND : bond 0.00525 / 0.31 ( 35) SS BOND : angle 1.72288 / 1.08 ( 70) hydrogen bonds : bond 0.04192 / 2.70 ( 909) hydrogen bonds : angle 5.42338 / 3.69 ( 2571) link_BETA1-4 : bond 0.01031 / 0.54 ( 1) link_BETA1-4 : angle 7.95317 / 4.42 ( 3) link_NAG-ASN : bond 0.01291 / 0.86 ( 44) link_NAG-ASN : angle 4.08403 / 2.73 ( 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 225 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 144 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7274 (m-80) cc_final: 0.6760 (t80) REVERT: A 464 PHE cc_start: 0.7540 (m-80) cc_final: 0.7115 (m-80) REVERT: A 773 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8815 (tt0) REVERT: A 947 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8781 (mmmm) REVERT: A 988 GLU cc_start: 0.8967 (mp0) cc_final: 0.8669 (pm20) REVERT: A 990 GLU cc_start: 0.9131 (tp30) cc_final: 0.8686 (mt-10) REVERT: A 991 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9212 (p) REVERT: C 53 ASP cc_start: 0.8995 (p0) cc_final: 0.8582 (p0) REVERT: C 298 GLU cc_start: 0.9346 (tp30) cc_final: 0.8940 (mt-10) REVERT: C 417 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6742 (ptmt) REVERT: C 461 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5049 (tp) REVERT: C 528 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7596 (mtpt) REVERT: C 779 GLN cc_start: 0.9384 (tt0) cc_final: 0.9134 (tp40) REVERT: C 887 THR cc_start: 0.9664 (OUTLIER) cc_final: 0.9357 (p) REVERT: C 950 ASP cc_start: 0.9301 (m-30) cc_final: 0.8773 (t0) REVERT: B 216 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8536 (pp) REVERT: B 239 GLN cc_start: 0.7336 (mp-120) cc_final: 0.6935 (mm-40) REVERT: B 387 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.8901 (mp) REVERT: B 394 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7966 (p0) REVERT: B 960 ASN cc_start: 0.9323 (m-40) cc_final: 0.8989 (t0) REVERT: B 1005 GLN cc_start: 0.9294 (tp40) cc_final: 0.8983 (tp-100) outliers start: 81 outliers final: 52 residues processed: 214 average time/residue: 0.1410 time to fit residues: 50.9176 Evaluate side-chains 198 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS 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 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 402 ILE 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 540 ASN 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 923 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 ASP 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 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR 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 595 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 192 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 206 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.091710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060812 restraints weight = 79892.429| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.18 r_work: 0.2941 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.5652 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= 0.149 Angle : 0.862 16.681 33023 Z= 0.365 Chirality : 0.081 0.704 4070 Planarity : 0.004 0.058 4078 Dihedral : 4.419 50.198 3042 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.39 % Allowed : 20.20 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2795 helix: 1.94 (0.20), residues: 658 sheet: -0.15 (0.21), residues: 605 loop : -0.92 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1019 TYR 0.021 0.001 TYR B1067 PHE 0.041 0.001 PHE C 238 TRP 0.019 0.001 TRP C 104 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (24088) covalent geometry : angle 0.81734 / 0.35 (32818) SS BOND : bond 0.00241 / 0.14 ( 35) SS BOND : angle 1.13486 / 0.74 ( 70) hydrogen bonds : bond 0.03748 / 2.40 ( 909) hydrogen bonds : angle 5.17775 / 3.54 ( 2571) link_BETA1-4 : bond 0.01326 / 0.70 ( 1) link_BETA1-4 : angle 7.81545 / 4.34 ( 3) link_NAG-ASN : bond 0.01518 / 0.98 ( 44) link_NAG-ASN : angle 4.21415 / 2.80 ( 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 211 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7200 (m-80) cc_final: 0.6621 (t80) REVERT: A 464 PHE cc_start: 0.7744 (m-80) cc_final: 0.7427 (m-80) REVERT: A 773 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8766 (tt0) REVERT: A 947 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8712 (mmmm) REVERT: A 988 GLU cc_start: 0.8957 (mp0) cc_final: 0.8620 (pm20) REVERT: A 991 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9112 (p) REVERT: C 53 ASP cc_start: 0.8858 (p0) cc_final: 0.8464 (p0) REVERT: C 298 GLU cc_start: 0.9282 (tp30) cc_final: 0.8986 (mt-10) REVERT: C 461 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.4962 (tp) REVERT: C 528 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7596 (mtpt) REVERT: C 661 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 779 GLN cc_start: 0.9419 (tt0) cc_final: 0.9159 (tp40) REVERT: C 950 ASP cc_start: 0.9288 (m-30) cc_final: 0.8745 (t0) REVERT: B 216 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8570 (pp) REVERT: B 239 GLN cc_start: 0.7277 (mp-120) cc_final: 0.6648 (tp40) REVERT: B 387 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.8892 (mp) REVERT: B 960 ASN cc_start: 0.9297 (m-40) cc_final: 0.9014 (t0) REVERT: B 1010 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8833 (tm-30) outliers start: 60 outliers final: 42 residues processed: 205 average time/residue: 0.1310 time to fit residues: 45.6547 Evaluate side-chains 190 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 597 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 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 991 VAL Chi-restraints excluded: chain A residue 1114 ILE 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 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 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 974 SER 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 229 LEU Chi-restraints excluded: chain B residue 376 THR 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 595 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 934 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 273 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 203 optimal weight: 0.4980 chunk 256 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 762 GLN B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.091035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060859 restraints weight = 79099.802| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.01 r_work: 0.2925 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24168 Z= 0.197 Angle : 0.878 16.746 33023 Z= 0.376 Chirality : 0.080 0.706 4070 Planarity : 0.004 0.058 4078 Dihedral : 4.444 50.926 3042 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.43 % Allowed : 20.40 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2795 helix: 1.83 (0.20), residues: 665 sheet: -0.20 (0.21), residues: 615 loop : -0.89 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.022 0.001 TYR B1067 PHE 0.034 0.001 PHE B 392 TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (24088) covalent geometry : angle 0.83521 / 0.36 (32818) SS BOND : bond 0.00358 / 0.22 ( 35) SS BOND : angle 1.47392 / 0.92 ( 70) hydrogen bonds : bond 0.03847 / 2.48 ( 909) hydrogen bonds : angle 5.18052 / 3.54 ( 2571) link_BETA1-4 : bond 0.00857 / 0.45 ( 1) link_BETA1-4 : angle 7.79994 / 4.33 ( 3) link_NAG-ASN : bond 0.01396 / 0.90 ( 44) link_NAG-ASN : angle 4.09360 / 2.72 ( 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 201 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 140 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7156 (m-80) cc_final: 0.6623 (t80) REVERT: A 773 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8797 (tt0) REVERT: A 947 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8718 (mmmm) REVERT: A 950 ASP cc_start: 0.9282 (t0) cc_final: 0.8745 (t0) REVERT: A 954 GLN cc_start: 0.9261 (mt0) cc_final: 0.8951 (mt0) REVERT: A 985 ASP cc_start: 0.8823 (t70) cc_final: 0.8405 (t0) REVERT: A 988 GLU cc_start: 0.9014 (mp0) cc_final: 0.8621 (pm20) REVERT: A 990 GLU cc_start: 0.9132 (tp30) cc_final: 0.8660 (mt-10) REVERT: A 991 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9181 (p) REVERT: C 53 ASP cc_start: 0.8946 (p0) cc_final: 0.8564 (p0) REVERT: C 298 GLU cc_start: 0.9321 (tp30) cc_final: 0.9012 (mt-10) REVERT: C 461 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.4813 (tp) REVERT: C 528 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7695 (mtpt) REVERT: C 564 GLN cc_start: 0.8252 (mt0) cc_final: 0.7988 (tp40) REVERT: C 661 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 779 GLN cc_start: 0.9410 (tt0) cc_final: 0.9182 (tp40) REVERT: C 950 ASP cc_start: 0.9307 (m-30) cc_final: 0.8778 (t0) REVERT: B 216 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8532 (pp) REVERT: B 387 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8905 (mp) REVERT: B 571 ASP cc_start: 0.8362 (m-30) cc_final: 0.7957 (p0) REVERT: B 960 ASN cc_start: 0.9317 (m-40) cc_final: 0.9035 (t0) outliers start: 61 outliers final: 48 residues processed: 195 average time/residue: 0.1240 time to fit residues: 41.1564 Evaluate side-chains 185 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 597 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 931 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 984 LEU 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 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 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 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 974 SER 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 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 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 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 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: 2.9990 chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 762 GLN B1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.091092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060524 restraints weight = 80671.898| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.13 r_work: 0.2935 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.5921 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= 0.186 Angle : 0.867 16.710 33023 Z= 0.371 Chirality : 0.080 0.706 4070 Planarity : 0.004 0.059 4078 Dihedral : 4.448 52.516 3042 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.43 % Allowed : 20.44 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2795 helix: 1.85 (0.20), residues: 665 sheet: -0.24 (0.21), residues: 613 loop : -0.87 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.022 0.001 TYR B1067 PHE 0.041 0.001 PHE C 238 TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (24088) covalent geometry : angle 0.82461 / 0.36 (32818) SS BOND : bond 0.00308 / 0.18 ( 35) SS BOND : angle 1.12702 / 0.73 ( 70) hydrogen bonds : bond 0.03806 / 2.44 ( 909) hydrogen bonds : angle 5.14524 / 3.53 ( 2571) link_BETA1-4 : bond 0.00969 / 0.51 ( 1) link_BETA1-4 : angle 7.73053 / 4.29 ( 3) link_NAG-ASN : bond 0.01428 / 0.92 ( 44) link_NAG-ASN : angle 4.10785 / 2.73 ( 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 204 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.9039 (m-30) cc_final: 0.8769 (t0) REVERT: A 338 PHE cc_start: 0.7132 (m-80) cc_final: 0.6620 (t80) REVERT: A 773 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8792 (tt0) REVERT: A 947 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8728 (mmmm) REVERT: A 985 ASP cc_start: 0.8842 (t70) cc_final: 0.8385 (t0) REVERT: A 988 GLU cc_start: 0.9014 (mp0) cc_final: 0.8572 (pm20) REVERT: A 991 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9139 (p) REVERT: C 53 ASP cc_start: 0.8917 (p0) cc_final: 0.8548 (p0) REVERT: C 461 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.4789 (tp) REVERT: C 528 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7686 (mtpt) REVERT: C 661 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8312 (tm-30) REVERT: C 887 THR cc_start: 0.9629 (OUTLIER) cc_final: 0.9356 (p) REVERT: C 950 ASP cc_start: 0.9312 (m-30) cc_final: 0.8777 (t0) REVERT: B 216 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8560 (pp) REVERT: B 239 GLN cc_start: 0.7463 (mp-120) cc_final: 0.6831 (tp40) REVERT: B 378 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8423 (ttpp) REVERT: B 387 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8922 (mp) REVERT: B 571 ASP cc_start: 0.8325 (m-30) cc_final: 0.7981 (p0) REVERT: B 811 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8253 (tttp) REVERT: B 960 ASN cc_start: 0.9313 (m-40) cc_final: 0.9034 (t0) REVERT: B 1010 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8821 (tm-30) outliers start: 61 outliers final: 48 residues processed: 198 average time/residue: 0.1371 time to fit residues: 46.2883 Evaluate side-chains 195 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 597 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 931 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 984 LEU 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 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 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 974 SER 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 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 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 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 811 LYS Chi-restraints excluded: chain B residue 934 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5148 > 50: distance: 24 - 76: 29.251 distance: 27 - 73: 22.677 distance: 33 - 37: 16.282 distance: 37 - 38: 10.675 distance: 38 - 39: 18.207 distance: 38 - 41: 22.632 distance: 39 - 40: 24.041 distance: 39 - 47: 23.078 distance: 41 - 42: 18.631 distance: 42 - 43: 8.689 distance: 42 - 44: 16.143 distance: 43 - 45: 12.334 distance: 44 - 46: 7.731 distance: 45 - 46: 17.764 distance: 47 - 48: 13.603 distance: 48 - 49: 12.826 distance: 48 - 51: 34.780 distance: 49 - 50: 20.753 distance: 49 - 55: 19.354 distance: 51 - 52: 47.129 distance: 52 - 53: 24.990 distance: 52 - 54: 23.741 distance: 55 - 56: 13.216 distance: 56 - 57: 22.529 distance: 57 - 58: 18.210 distance: 57 - 59: 11.919 distance: 59 - 60: 21.505 distance: 60 - 61: 29.662 distance: 60 - 63: 29.682 distance: 61 - 62: 27.927 distance: 61 - 68: 31.084 distance: 63 - 64: 35.356 distance: 64 - 65: 40.358 distance: 65 - 66: 31.303 distance: 66 - 67: 28.690 distance: 68 - 69: 16.585 distance: 69 - 70: 18.938 distance: 69 - 72: 25.295 distance: 70 - 71: 19.069 distance: 70 - 73: 37.097 distance: 73 - 74: 20.793 distance: 74 - 75: 30.256 distance: 74 - 77: 21.072 distance: 75 - 76: 13.112 distance: 75 - 83: 4.958 distance: 77 - 78: 15.845 distance: 78 - 79: 15.860 distance: 78 - 80: 7.558 distance: 79 - 81: 13.399 distance: 80 - 82: 19.134 distance: 81 - 82: 10.417 distance: 83 - 84: 5.820 distance: 83 - 161: 17.443 distance: 84 - 85: 12.006 distance: 84 - 87: 29.292 distance: 85 - 86: 22.275 distance: 85 - 94: 16.650 distance: 86 - 158: 27.159 distance: 87 - 88: 24.415 distance: 88 - 89: 7.495 distance: 88 - 90: 8.219 distance: 89 - 91: 16.140 distance: 90 - 92: 13.150 distance: 91 - 93: 8.545 distance: 92 - 93: 8.519 distance: 94 - 95: 9.815 distance: 94 - 100: 13.589 distance: 95 - 96: 19.079 distance: 95 - 98: 3.922 distance: 96 - 97: 29.882 distance: 96 - 101: 27.578 distance: 98 - 99: 15.809 distance: 99 - 100: 20.588 distance: 101 - 102: 10.881 distance: 102 - 103: 17.703 distance: 102 - 105: 24.148 distance: 103 - 104: 23.575 distance: 103 - 112: 18.282 distance: 105 - 106: 8.927 distance: 106 - 107: 7.305 distance: 107 - 108: 7.854 distance: 108 - 109: 10.517 distance: 109 - 110: 8.399 distance: 109 - 111: 13.126 distance: 112 - 113: 6.700 distance: 113 - 114: 15.713 distance: 113 - 116: 11.887 distance: 114 - 115: 21.297 distance: 114 - 121: 3.576 distance: 116 - 117: 20.480 distance: 117 - 118: 22.886 distance: 118 - 119: 19.271 distance: 118 - 120: 6.759