Starting phenix.real_space_refine on Fri Jun 20 09:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zp7_11337/06_2025/6zp7_11337.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp7_11337/06_2025/6zp7_11337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zp7_11337/06_2025/6zp7_11337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp7_11337/06_2025/6zp7_11337.map" model { file = "/net/cci-nas-00/data/ceres_data/6zp7_11337/06_2025/6zp7_11337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp7_11337/06_2025/6zp7_11337.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.19, per 1000 atoms: 0.64 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: 6.18 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.24 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: 10.99 Time building geometry restraints manager: 7.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 23707 1.54 - 1.86: 379 1.86 - 2.18: 1 2.18 - 2.50: 0 2.50 - 2.83: 1 Bond restraints: 24088 Sorted by residual: bond pdb=" C CYS A 525 " pdb=" N GLY A 526 " ideal model delta sigma weight residual 1.330 2.827 -1.497 1.49e-02 4.50e+03 1.01e+04 bond pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 1.331 1.992 -0.661 2.07e-02 2.33e+03 1.02e+03 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 1.528 1.589 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 24083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.75: 32784 6.75 - 13.49: 23 13.49 - 20.24: 7 20.24 - 26.99: 2 26.99 - 33.73: 2 Bond angle restraints: 32818 Sorted by residual: angle pdb=" O LEU A 335 " pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 122.81 90.95 31.86 1.42e+00 4.96e-01 5.03e+02 angle pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta sigma weight residual 121.87 88.14 33.73 1.57e+00 4.06e-01 4.62e+02 angle pdb=" CA LEU A 335 " pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 115.54 140.08 -24.54 1.52e+00 4.33e-01 2.61e+02 angle pdb=" O CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " ideal model delta sigma weight residual 123.24 108.40 14.84 1.23e+00 6.61e-01 1.46e+02 angle pdb=" O1 NAG W 2 " pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 108.68 134.98 -26.30 3.00e+00 1.11e-01 7.68e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 14605 23.06 - 46.12: 824 46.12 - 69.17: 155 69.17 - 92.23: 94 92.23 - 115.29: 50 Dihedral angle restraints: 15728 sinusoidal: 7398 harmonic: 8330 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -11.43 -74.57 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -13.39 -72.61 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -154.61 68.61 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 15725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.031: 4054 1.031 - 2.061: 12 2.061 - 3.092: 1 3.092 - 4.123: 1 4.123 - 5.154: 2 Chirality restraints: 4070 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 2.75 -5.15 2.00e-02 2.50e+03 6.64e+04 chirality pdb=" C1 NAG B1302 " pdb=" C2 NAG B1302 " pdb=" O1 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False 2.31 -2.42 4.73 2.00e-01 2.50e+01 5.60e+02 chirality pdb=" C1 NAG W 2 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False 2.31 -1.09 3.40 2.00e-01 2.50e+01 2.90e+02 ... (remaining 4067 not shown) Planarity restraints: 4119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " 0.287 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" CG ASN B 165 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.233 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " -0.231 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " 0.248 2.00e-02 2.50e+03 2.13e-01 5.66e+02 pdb=" CG ASN B 122 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.348 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.182 2.00e-02 2.50e+03 1.99e-01 4.97e+02 pdb=" CG ASN B 343 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.276 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.270 2.00e-02 2.50e+03 ... (remaining 4116 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 44 0.99 - 1.96: 140 1.96 - 2.94: 11785 2.94 - 3.92: 61290 3.92 - 4.90: 114014 Warning: very small nonbonded interaction distances. Nonbonded interactions: 187273 Sorted by model distance: nonbonded pdb=" O4 NAG I 1 " pdb=" O1 NAG I 2 " model vdw 0.008 3.040 nonbonded pdb=" O4 NAG c 1 " pdb=" O1 NAG c 2 " model vdw 0.020 3.040 nonbonded pdb=" O4 NAG Z 1 " pdb=" O1 NAG Z 2 " model vdw 0.024 3.040 nonbonded pdb=" O4 NAG D 1 " pdb=" O1 NAG D 2 " model vdw 0.031 3.040 nonbonded pdb=" O4 NAG Y 1 " pdb=" O1 NAG Y 2 " model vdw 0.037 3.040 ... (remaining 187268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 66 or resid 82 through 131 or resid 165 through \ 172 or resid 189 through 241 or resid 265 through 442 or resid 460 through 470 \ or resid 510 through 620 or resid 641 through 828 or resid 854 through 1146)) selection = (chain 'B' and (resid 28 through 131 or resid 165 through 172 or resid 189 throu \ gh 241 or resid 265 through 442 or resid 460 through 1146)) selection = (chain 'C' and (resid 28 through 131 or resid 165 through 172 or resid 189 throu \ gh 241 or resid 265 through 442 or resid 460 through 470 or resid 510 through 62 \ 0 or resid 641 through 828 or resid 854 through 1146)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 57.770 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.180 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.497 24168 Z= 1.153 Angle : 1.330 49.724 33023 Z= 0.566 Chirality : 0.165 5.154 4070 Planarity : 0.005 0.104 4075 Dihedral : 16.891 115.289 10239 Min Nonbonded Distance : 0.008 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.52 % Allowed : 5.38 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP B 886 HIS 0.005 0.001 HIS C 655 PHE 0.037 0.002 PHE C 559 TYR 0.026 0.002 TYR B1067 ARG 0.014 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.40730 ( 44) link_NAG-ASN : angle 14.79956 ( 132) link_BETA1-4 : bond 0.01095 ( 1) link_BETA1-4 : angle 21.97651 ( 3) hydrogen bonds : bond 0.12621 ( 909) hydrogen bonds : angle 7.31486 ( 2571) SS BOND : bond 0.01418 ( 35) SS BOND : angle 2.14573 ( 70) covalent geometry : bond 0.01289 (24088) covalent geometry : angle 0.91889 (32818) *********************** 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 : 2.833 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 568 ASP cc_start: 0.5116 (p0) cc_final: 0.4849 (p0) outliers start: 13 outliers final: 5 residues processed: 442 average time/residue: 0.3552 time to fit residues: 245.2196 Evaluate side-chains 203 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 240 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 258 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 564 GLN A 644 GLN A 690 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 Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.103350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.074072 restraints weight = 81175.002| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.28 r_work: 0.3248 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24168 Z= 0.180 Angle : 1.073 36.194 33023 Z= 0.442 Chirality : 0.086 0.837 4070 Planarity : 0.004 0.042 4075 Dihedral : 13.173 115.280 5149 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.07 % Allowed : 12.83 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2795 helix: 1.46 (0.20), residues: 648 sheet: 0.02 (0.20), residues: 601 loop : -1.21 (0.14), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 104 HIS 0.006 0.001 HIS B1101 PHE 0.033 0.002 PHE C 238 TYR 0.028 0.001 TYR B1067 ARG 0.005 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01694 ( 44) link_NAG-ASN : angle 5.69581 ( 132) link_BETA1-4 : bond 0.04832 ( 1) link_BETA1-4 : angle 31.90435 ( 3) hydrogen bonds : bond 0.04528 ( 909) hydrogen bonds : angle 5.93459 ( 2571) SS BOND : bond 0.00410 ( 35) SS BOND : angle 2.04366 ( 70) covalent geometry : bond 0.00380 (24088) covalent geometry : angle 0.96281 (32818) *********************** 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 278 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 2.685 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: A 53 ASP cc_start: 0.8087 (t0) cc_final: 0.7885 (t70) REVERT: A 203 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9003 (mp) REVERT: A 403 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6803 (mtp180) REVERT: A 725 GLU cc_start: 0.8883 (tp30) cc_final: 0.8594 (tp30) REVERT: A 784 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8438 (mt0) REVERT: A 904 TYR cc_start: 0.8260 (m-10) cc_final: 0.7993 (m-10) REVERT: A 1005 GLN cc_start: 0.8650 (mt0) cc_final: 0.8406 (mt0) REVERT: C 53 ASP cc_start: 0.8239 (p0) cc_final: 0.7933 (p0) REVERT: C 298 GLU cc_start: 0.8951 (tp30) cc_final: 0.8723 (tp30) REVERT: C 661 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 740 MET cc_start: 0.8836 (tpt) cc_final: 0.8599 (tpt) REVERT: C 869 MET cc_start: 0.9151 (mtt) cc_final: 0.8917 (mtm) REVERT: C 950 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.8795 (t0) REVERT: B 386 LYS cc_start: 0.9205 (mttm) cc_final: 0.8860 (mtmt) REVERT: B 387 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8933 (mm) REVERT: B 780 GLU cc_start: 0.9035 (tp30) cc_final: 0.8768 (tt0) REVERT: B 1029 MET cc_start: 0.9314 (tpp) cc_final: 0.9019 (tpp) outliers start: 52 outliers final: 27 residues processed: 265 average time/residue: 0.3166 time to fit residues: 139.1549 Evaluate side-chains 214 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 90 VAL 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 403 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 805 ILE 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 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 127 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU 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 Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 135 optimal weight: 50.0000 chunk 258 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 161 optimal weight: 0.6980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS C 99 ASN C 564 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 787 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.094162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063800 restraints weight = 78776.944| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.14 r_work: 0.2988 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 24168 Z= 0.258 Angle : 0.943 18.262 33023 Z= 0.411 Chirality : 0.082 0.958 4070 Planarity : 0.005 0.052 4075 Dihedral : 9.938 92.346 5145 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.47 % Allowed : 14.70 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 2795 helix: 1.49 (0.20), residues: 650 sheet: -0.19 (0.20), residues: 627 loop : -1.10 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.006 0.001 HIS A 655 PHE 0.025 0.002 PHE B 392 TYR 0.024 0.002 TYR B1067 ARG 0.009 0.001 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.01423 ( 44) link_NAG-ASN : angle 5.14548 ( 132) link_BETA1-4 : bond 0.01890 ( 1) link_BETA1-4 : angle 11.30652 ( 3) hydrogen bonds : bond 0.04477 ( 909) hydrogen bonds : angle 5.75891 ( 2571) SS BOND : bond 0.00748 ( 35) SS BOND : angle 1.66073 ( 70) covalent geometry : bond 0.00581 (24088) covalent geometry : angle 0.87764 (32818) *********************** 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 267 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 180 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7240 (m-80) cc_final: 0.6052 (m-10) REVERT: A 403 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7054 (mtp180) REVERT: A 873 TYR cc_start: 0.9612 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: C 53 ASP cc_start: 0.8682 (p0) cc_final: 0.8232 (p0) REVERT: C 298 GLU cc_start: 0.9173 (tp30) cc_final: 0.8844 (mt-10) REVERT: C 461 LEU cc_start: 0.5854 (OUTLIER) cc_final: 0.4806 (tp) REVERT: C 661 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 950 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.8806 (t0) REVERT: B 216 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8287 (pp) REVERT: B 386 LYS cc_start: 0.9181 (mttm) cc_final: 0.8918 (mtmm) outliers start: 87 outliers final: 44 residues processed: 258 average time/residue: 0.3207 time to fit residues: 139.0977 Evaluate side-chains 201 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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 403 ARG 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 341 VAL Chi-restraints excluded: chain C residue 392 PHE 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 C residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER 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 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 158 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 284 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 138 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 784 GLN A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 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 = 0.3864 r_free = 0.3864 target = 0.095602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064911 restraints weight = 80246.069| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.20 r_work: 0.3023 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4176 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= 0.139 Angle : 0.840 17.340 33023 Z= 0.360 Chirality : 0.082 0.949 4070 Planarity : 0.004 0.060 4075 Dihedral : 9.170 84.440 5144 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.71 % Allowed : 16.33 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2795 helix: 1.96 (0.20), residues: 641 sheet: -0.15 (0.20), residues: 608 loop : -1.03 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 PHE 0.035 0.001 PHE C 238 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01601 ( 44) link_NAG-ASN : angle 5.11252 ( 132) link_BETA1-4 : bond 0.01982 ( 1) link_BETA1-4 : angle 10.02278 ( 3) hydrogen bonds : bond 0.03925 ( 909) hydrogen bonds : angle 5.36267 ( 2571) SS BOND : bond 0.00232 ( 35) SS BOND : angle 1.16394 ( 70) covalent geometry : bond 0.00300 (24088) covalent geometry : angle 0.77019 (32818) *********************** 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 249 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8541 (mt) cc_final: 0.8185 (mp) REVERT: A 403 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7110 (mtp180) REVERT: A 762 GLN cc_start: 0.8844 (mt0) cc_final: 0.8590 (mt0) REVERT: A 787 GLN cc_start: 0.9009 (mt0) cc_final: 0.8664 (mt0) REVERT: A 873 TYR cc_start: 0.9597 (OUTLIER) cc_final: 0.8999 (m-80) REVERT: C 53 ASP cc_start: 0.8543 (p0) cc_final: 0.8069 (p0) REVERT: C 298 GLU cc_start: 0.9074 (tp30) cc_final: 0.8796 (mt-10) REVERT: C 461 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.4768 (tp) REVERT: C 661 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8206 (tm-30) REVERT: C 773 GLU cc_start: 0.8885 (tp30) cc_final: 0.8532 (tp30) REVERT: C 779 GLN cc_start: 0.9406 (tt0) cc_final: 0.8865 (tm-30) REVERT: C 950 ASP cc_start: 0.9320 (OUTLIER) cc_final: 0.8780 (t0) REVERT: B 216 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8297 (pp) REVERT: B 239 GLN cc_start: 0.6775 (mp10) cc_final: 0.5795 (mp10) REVERT: B 267 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8082 (m) REVERT: B 386 LYS cc_start: 0.9197 (mttm) cc_final: 0.8761 (mtmt) REVERT: B 1005 GLN cc_start: 0.9291 (tp40) cc_final: 0.8971 (tp-100) REVERT: B 1010 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8719 (tm-30) outliers start: 68 outliers final: 37 residues processed: 242 average time/residue: 0.3483 time to fit residues: 140.3002 Evaluate side-chains 206 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 3.002 ------------------------------------------------------------------------------- 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 403 ARG 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 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain 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 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 50 SER 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 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 23 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 chunk 202 optimal weight: 8.9990 chunk 205 optimal weight: 0.2980 chunk 133 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 268 optimal weight: 0.9990 chunk 259 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN B 394 ASN B1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.095563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064975 restraints weight = 79454.349| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.18 r_work: 0.3045 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24168 Z= 0.129 Angle : 0.811 16.392 33023 Z= 0.346 Chirality : 0.081 0.985 4070 Planarity : 0.004 0.068 4075 Dihedral : 8.422 79.413 5144 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.67 % Allowed : 17.37 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2795 helix: 2.14 (0.20), residues: 645 sheet: -0.08 (0.20), residues: 636 loop : -0.96 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 353 HIS 0.003 0.000 HIS B 49 PHE 0.028 0.001 PHE B 392 TYR 0.020 0.001 TYR B1067 ARG 0.026 0.001 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.01624 ( 44) link_NAG-ASN : angle 5.04460 ( 132) link_BETA1-4 : bond 0.02827 ( 1) link_BETA1-4 : angle 9.88977 ( 3) hydrogen bonds : bond 0.03660 ( 909) hydrogen bonds : angle 5.13394 ( 2571) SS BOND : bond 0.00206 ( 35) SS BOND : angle 1.15015 ( 70) covalent geometry : bond 0.00271 (24088) covalent geometry : angle 0.73992 (32818) *********************** 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 248 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8543 (mt) cc_final: 0.8209 (mp) REVERT: A 403 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7154 (mtp180) REVERT: A 762 GLN cc_start: 0.8812 (mt0) cc_final: 0.8550 (mt0) REVERT: A 787 GLN cc_start: 0.9013 (mt0) cc_final: 0.8651 (mt0) REVERT: A 873 TYR cc_start: 0.9595 (OUTLIER) cc_final: 0.9093 (m-80) REVERT: C 53 ASP cc_start: 0.8538 (p0) cc_final: 0.8062 (p0) REVERT: C 298 GLU cc_start: 0.9173 (tp30) cc_final: 0.8928 (mt-10) REVERT: C 417 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6399 (ptmt) REVERT: C 461 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.4542 (tp) REVERT: C 661 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 773 GLU cc_start: 0.8843 (tp30) cc_final: 0.8377 (tp30) REVERT: C 779 GLN cc_start: 0.9399 (tt0) cc_final: 0.9133 (tp40) REVERT: C 950 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.8760 (t0) REVERT: C 955 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8353 (t0) REVERT: B 216 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8224 (pp) REVERT: B 239 GLN cc_start: 0.6833 (mp10) cc_final: 0.6076 (tp40) REVERT: B 267 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8177 (m) REVERT: B 386 LYS cc_start: 0.9190 (mttm) cc_final: 0.8770 (mtmt) REVERT: B 564 GLN cc_start: 0.8063 (tp40) cc_final: 0.7157 (tp-100) REVERT: B 1005 GLN cc_start: 0.9241 (tp40) cc_final: 0.8896 (tp-100) REVERT: B 1010 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8768 (tm-30) outliers start: 67 outliers final: 39 residues processed: 237 average time/residue: 0.3223 time to fit residues: 128.3270 Evaluate side-chains 209 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 403 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 873 TYR 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 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 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 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 955 ASN 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 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 385 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 106 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 175 optimal weight: 0.0980 chunk 126 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 227 optimal weight: 0.0770 chunk 64 optimal weight: 4.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.095876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065439 restraints weight = 79145.549| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.21 r_work: 0.3047 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24168 Z= 0.122 Angle : 0.791 16.040 33023 Z= 0.338 Chirality : 0.081 1.000 4070 Planarity : 0.004 0.068 4075 Dihedral : 8.036 76.097 5144 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.63 % Allowed : 17.69 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 2795 helix: 2.22 (0.20), residues: 646 sheet: 0.03 (0.20), residues: 634 loop : -0.94 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.003 0.000 HIS B 49 PHE 0.039 0.001 PHE C 238 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01636 ( 44) link_NAG-ASN : angle 4.96856 ( 132) link_BETA1-4 : bond 0.03117 ( 1) link_BETA1-4 : angle 9.92874 ( 3) hydrogen bonds : bond 0.03526 ( 909) hydrogen bonds : angle 5.00156 ( 2571) SS BOND : bond 0.00200 ( 35) SS BOND : angle 1.13293 ( 70) covalent geometry : bond 0.00253 (24088) covalent geometry : angle 0.72048 (32818) *********************** 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 246 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8520 (mt) cc_final: 0.8218 (mp) REVERT: A 403 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7323 (mtp180) REVERT: A 725 GLU cc_start: 0.8848 (tp30) cc_final: 0.8622 (tp30) REVERT: A 762 GLN cc_start: 0.8805 (mt0) cc_final: 0.8539 (mt0) REVERT: A 787 GLN cc_start: 0.9000 (mt0) cc_final: 0.8635 (mt0) REVERT: A 873 TYR cc_start: 0.9597 (OUTLIER) cc_final: 0.9155 (m-80) REVERT: C 53 ASP cc_start: 0.8496 (p0) cc_final: 0.8029 (p0) REVERT: C 298 GLU cc_start: 0.9146 (tp30) cc_final: 0.8883 (mt-10) REVERT: C 417 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6395 (ptmt) REVERT: C 461 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.4441 (tp) REVERT: C 528 LYS cc_start: 0.8277 (mttt) cc_final: 0.8069 (mttt) REVERT: C 661 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 773 GLU cc_start: 0.8825 (tp30) cc_final: 0.8610 (tp30) REVERT: C 779 GLN cc_start: 0.9402 (tt0) cc_final: 0.9127 (tp40) REVERT: C 950 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8727 (t0) REVERT: B 216 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 239 GLN cc_start: 0.6890 (mp10) cc_final: 0.6212 (tp40) REVERT: B 267 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (m) REVERT: B 386 LYS cc_start: 0.9176 (mttm) cc_final: 0.8796 (mtmt) REVERT: B 564 GLN cc_start: 0.7970 (tp40) cc_final: 0.6962 (tp-100) REVERT: B 1005 GLN cc_start: 0.9192 (tp40) cc_final: 0.8843 (tp-100) REVERT: B 1010 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8781 (tm-30) outliers start: 66 outliers final: 44 residues processed: 235 average time/residue: 0.3146 time to fit residues: 126.4677 Evaluate side-chains 215 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 3.638 ------------------------------------------------------------------------------- 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 403 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 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 552 LEU Chi-restraints excluded: chain C residue 553 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 950 ASP 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 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 277 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 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 784 GLN 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 95 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 274 optimal weight: 0.0570 chunk 11 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 266 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 755 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.093307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062872 restraints weight = 79360.748| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.14 r_work: 0.2982 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24168 Z= 0.217 Angle : 0.823 15.889 33023 Z= 0.358 Chirality : 0.080 0.965 4070 Planarity : 0.004 0.070 4075 Dihedral : 7.949 72.746 5144 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.75 % Allowed : 18.25 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 2795 helix: 2.04 (0.20), residues: 647 sheet: 0.00 (0.21), residues: 606 loop : -0.90 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.004 0.001 HIS B 49 PHE 0.014 0.001 PHE C 92 TYR 0.023 0.001 TYR B1067 ARG 0.006 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.01457 ( 44) link_NAG-ASN : angle 4.78178 ( 132) link_BETA1-4 : bond 0.03444 ( 1) link_BETA1-4 : angle 9.85039 ( 3) hydrogen bonds : bond 0.03815 ( 909) hydrogen bonds : angle 5.14281 ( 2571) SS BOND : bond 0.00336 ( 35) SS BOND : angle 1.28567 ( 70) covalent geometry : bond 0.00484 (24088) covalent geometry : angle 0.75972 (32818) *********************** 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 224 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 155 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7416 (mtp180) REVERT: A 762 GLN cc_start: 0.8842 (mt0) cc_final: 0.8584 (mt0) REVERT: A 873 TYR cc_start: 0.9611 (OUTLIER) cc_final: 0.9245 (m-80) REVERT: C 53 ASP cc_start: 0.8693 (p0) cc_final: 0.8287 (p0) REVERT: C 298 GLU cc_start: 0.9249 (tp30) cc_final: 0.8941 (mt-10) REVERT: C 417 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6529 (ptmt) REVERT: C 461 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.4555 (tp) REVERT: C 528 LYS cc_start: 0.8374 (mttt) cc_final: 0.8077 (mttt) REVERT: C 779 GLN cc_start: 0.9408 (tt0) cc_final: 0.9136 (tp40) REVERT: C 950 ASP cc_start: 0.9285 (m-30) cc_final: 0.8783 (t0) REVERT: B 216 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8227 (pp) REVERT: B 239 GLN cc_start: 0.7027 (mp10) cc_final: 0.6225 (tp40) REVERT: B 267 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8150 (m) REVERT: B 386 LYS cc_start: 0.9116 (mttm) cc_final: 0.8709 (mtmm) REVERT: B 564 GLN cc_start: 0.8148 (tp40) cc_final: 0.7277 (tp-100) REVERT: B 1005 GLN cc_start: 0.9282 (tp40) cc_final: 0.8951 (tp-100) outliers start: 69 outliers final: 48 residues processed: 215 average time/residue: 0.2931 time to fit residues: 106.3324 Evaluate side-chains 203 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 403 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 806 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 985 ASP 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 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 553 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 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 33 THR 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 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 267 VAL Chi-restraints excluded: chain B residue 277 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 981 LEU 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 195 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 197 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 249 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 256 optimal weight: 0.0050 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.094374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063449 restraints weight = 80086.242| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.22 r_work: 0.3013 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24168 Z= 0.132 Angle : 0.793 15.849 33023 Z= 0.340 Chirality : 0.080 0.992 4070 Planarity : 0.004 0.071 4075 Dihedral : 7.673 68.883 5144 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.43 % Allowed : 18.92 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2795 helix: 2.17 (0.20), residues: 647 sheet: 0.02 (0.20), residues: 619 loop : -0.87 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.003 0.000 HIS B 49 PHE 0.039 0.001 PHE C 238 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.01607 ( 44) link_NAG-ASN : angle 4.86298 ( 132) link_BETA1-4 : bond 0.03092 ( 1) link_BETA1-4 : angle 10.04735 ( 3) hydrogen bonds : bond 0.03559 ( 909) hydrogen bonds : angle 4.95684 ( 2571) SS BOND : bond 0.00212 ( 35) SS BOND : angle 1.09672 ( 70) covalent geometry : bond 0.00281 (24088) covalent geometry : angle 0.72515 (32818) *********************** 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 230 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8510 (mt) cc_final: 0.8192 (mp) REVERT: A 725 GLU cc_start: 0.8853 (tp30) cc_final: 0.8651 (tp30) REVERT: A 873 TYR cc_start: 0.9570 (OUTLIER) cc_final: 0.9131 (m-10) REVERT: A 988 GLU cc_start: 0.8812 (mp0) cc_final: 0.8432 (pm20) REVERT: C 53 ASP cc_start: 0.8614 (p0) cc_final: 0.8201 (p0) REVERT: C 298 GLU cc_start: 0.9185 (tp30) cc_final: 0.8935 (mt-10) REVERT: C 417 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6551 (ptmt) REVERT: C 461 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.4688 (tp) REVERT: C 528 LYS cc_start: 0.8393 (mttt) cc_final: 0.8092 (mttt) REVERT: C 661 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 779 GLN cc_start: 0.9418 (tt0) cc_final: 0.9153 (tp40) REVERT: C 950 ASP cc_start: 0.9284 (m-30) cc_final: 0.8798 (t0) REVERT: B 216 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8261 (pp) REVERT: B 239 GLN cc_start: 0.7022 (mp10) cc_final: 0.6312 (tp40) REVERT: B 267 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8267 (m) REVERT: B 386 LYS cc_start: 0.9074 (mttm) cc_final: 0.8690 (mtmm) REVERT: B 387 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8897 (mp) REVERT: B 740 MET cc_start: 0.9020 (tpp) cc_final: 0.8818 (mtp) REVERT: B 960 ASN cc_start: 0.9260 (m-40) cc_final: 0.8962 (t0) REVERT: B 1005 GLN cc_start: 0.9216 (tp40) cc_final: 0.8867 (tp-100) REVERT: B 1010 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8779 (tm-30) outliers start: 61 outliers final: 48 residues processed: 221 average time/residue: 0.3013 time to fit residues: 112.2103 Evaluate side-chains 213 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP 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 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 553 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 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 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 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE 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 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 237 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 278 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 234 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.094769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.063994 restraints weight = 79801.169| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.21 r_work: 0.3028 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24168 Z= 0.126 Angle : 0.786 16.100 33023 Z= 0.337 Chirality : 0.080 0.987 4070 Planarity : 0.004 0.070 4075 Dihedral : 7.338 63.418 5144 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.07 % Allowed : 19.48 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2795 helix: 2.22 (0.20), residues: 650 sheet: 0.04 (0.20), residues: 614 loop : -0.83 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.003 0.000 HIS B 49 PHE 0.024 0.001 PHE B 392 TYR 0.022 0.001 TYR A 904 ARG 0.005 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.01610 ( 44) link_NAG-ASN : angle 4.79840 ( 132) link_BETA1-4 : bond 0.03301 ( 1) link_BETA1-4 : angle 10.05199 ( 3) hydrogen bonds : bond 0.03447 ( 909) hydrogen bonds : angle 4.83748 ( 2571) SS BOND : bond 0.00195 ( 35) SS BOND : angle 1.05260 ( 70) covalent geometry : bond 0.00269 (24088) covalent geometry : angle 0.71928 (32818) *********************** 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 223 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8493 (mt) cc_final: 0.8193 (mp) REVERT: A 338 PHE cc_start: 0.7273 (m-80) cc_final: 0.6919 (t80) REVERT: A 725 GLU cc_start: 0.8862 (tp30) cc_final: 0.8649 (tp30) REVERT: A 873 TYR cc_start: 0.9556 (OUTLIER) cc_final: 0.9123 (m-10) REVERT: C 53 ASP cc_start: 0.8632 (p0) cc_final: 0.8203 (p0) REVERT: C 298 GLU cc_start: 0.9186 (tp30) cc_final: 0.8945 (mt-10) REVERT: C 461 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.4556 (tp) REVERT: C 528 LYS cc_start: 0.8515 (mttt) cc_final: 0.8220 (mttt) REVERT: C 779 GLN cc_start: 0.9383 (tt0) cc_final: 0.9165 (tp40) REVERT: C 950 ASP cc_start: 0.9268 (m-30) cc_final: 0.8772 (t0) REVERT: B 40 ASP cc_start: 0.8468 (p0) cc_final: 0.8260 (p0) REVERT: B 216 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8239 (pp) REVERT: B 267 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (m) REVERT: B 386 LYS cc_start: 0.9050 (mttm) cc_final: 0.8765 (mtmm) REVERT: B 387 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8829 (mp) REVERT: B 740 MET cc_start: 0.8951 (tpp) cc_final: 0.8698 (mtp) REVERT: B 759 PHE cc_start: 0.8805 (m-10) cc_final: 0.8500 (m-10) REVERT: B 960 ASN cc_start: 0.9260 (m-40) cc_final: 0.8961 (t0) REVERT: B 1005 GLN cc_start: 0.9173 (tp40) cc_final: 0.8803 (tp-100) REVERT: B 1010 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8773 (tm-30) outliers start: 52 outliers final: 40 residues processed: 214 average time/residue: 0.3194 time to fit residues: 116.0937 Evaluate side-chains 209 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 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 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE 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 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 16 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 180 optimal weight: 0.5980 chunk 262 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.092858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061763 restraints weight = 80382.802| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.21 r_work: 0.2980 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24168 Z= 0.180 Angle : 0.806 16.349 33023 Z= 0.351 Chirality : 0.080 0.958 4070 Planarity : 0.004 0.071 4075 Dihedral : 7.322 57.354 5144 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.91 % Allowed : 19.84 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2795 helix: 2.07 (0.20), residues: 650 sheet: 0.13 (0.21), residues: 592 loop : -0.78 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.004 0.001 HIS B 49 PHE 0.030 0.001 PHE B 392 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.01510 ( 44) link_NAG-ASN : angle 4.69124 ( 132) link_BETA1-4 : bond 0.03526 ( 1) link_BETA1-4 : angle 10.11303 ( 3) hydrogen bonds : bond 0.03690 ( 909) hydrogen bonds : angle 4.97598 ( 2571) SS BOND : bond 0.00282 ( 35) SS BOND : angle 1.38555 ( 70) covalent geometry : bond 0.00405 (24088) covalent geometry : angle 0.74277 (32818) ********************** 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 205 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7113 (m-80) cc_final: 0.6717 (t80) REVERT: A 725 GLU cc_start: 0.8851 (tp30) cc_final: 0.8632 (tp30) REVERT: A 869 MET cc_start: 0.9579 (mtm) cc_final: 0.9341 (mtm) REVERT: A 873 TYR cc_start: 0.9576 (OUTLIER) cc_final: 0.9281 (m-80) REVERT: A 988 GLU cc_start: 0.8962 (mp0) cc_final: 0.8675 (pm20) REVERT: C 53 ASP cc_start: 0.8834 (p0) cc_final: 0.8435 (p0) REVERT: C 298 GLU cc_start: 0.9235 (tp30) cc_final: 0.8961 (mt-10) REVERT: C 461 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.4729 (tp) REVERT: C 528 LYS cc_start: 0.8468 (mttt) cc_final: 0.8140 (mttt) REVERT: C 950 ASP cc_start: 0.9301 (m-30) cc_final: 0.8771 (t0) REVERT: B 102 ARG cc_start: 0.6343 (mtt180) cc_final: 0.6005 (tpp-160) REVERT: B 216 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8224 (pp) REVERT: B 223 LEU cc_start: 0.8976 (mt) cc_final: 0.8668 (mt) REVERT: B 267 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8124 (m) REVERT: B 378 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8486 (ttpp) REVERT: B 386 LYS cc_start: 0.9031 (mttm) cc_final: 0.8751 (mtmm) REVERT: B 387 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8878 (mp) REVERT: B 960 ASN cc_start: 0.9282 (m-40) cc_final: 0.8989 (t0) REVERT: B 1005 GLN cc_start: 0.9226 (tp40) cc_final: 0.8869 (tp-100) REVERT: B 1010 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8699 (tm-30) outliers start: 48 outliers final: 39 residues processed: 198 average time/residue: 0.3170 time to fit residues: 104.9259 Evaluate side-chains 190 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 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 985 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 911 VAL 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 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE 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 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 228 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 232 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 188 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.094015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063190 restraints weight = 79921.328| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.21 r_work: 0.3002 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5506 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= 0.138 Angle : 0.790 16.368 33023 Z= 0.342 Chirality : 0.080 0.958 4070 Planarity : 0.004 0.067 4075 Dihedral : 7.197 57.694 5144 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.87 % Allowed : 20.00 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2795 helix: 2.14 (0.20), residues: 651 sheet: 0.12 (0.21), residues: 598 loop : -0.77 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 PHE 0.039 0.001 PHE C 238 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.01587 ( 44) link_NAG-ASN : angle 4.75015 ( 132) link_BETA1-4 : bond 0.03628 ( 1) link_BETA1-4 : angle 10.16727 ( 3) hydrogen bonds : bond 0.03551 ( 909) hydrogen bonds : angle 4.87978 ( 2571) SS BOND : bond 0.00227 ( 35) SS BOND : angle 0.99778 ( 70) covalent geometry : bond 0.00303 (24088) covalent geometry : angle 0.72556 (32818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13742.53 seconds wall clock time: 241 minutes 42.07 seconds (14502.07 seconds total)