Starting phenix.real_space_refine on Fri Sep 19 11:59:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ell_48153/09_2025/9ell_48153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ell_48153/09_2025/9ell_48153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ell_48153/09_2025/9ell_48153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ell_48153/09_2025/9ell_48153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ell_48153/09_2025/9ell_48153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ell_48153/09_2025/9ell_48153.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 111 5.16 5 C 16318 2.51 5 N 4158 2.21 5 O 4980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25567 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8284 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 56, 'TRANS': 999} Chain breaks: 6 Chain: "B" Number of atoms: 8214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8214 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 9 Chain: "C" Number of atoms: 8264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8264 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 56, 'TRANS': 996} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.28, per 1000 atoms: 0.25 Number of scatterers: 25567 At special positions: 0 Unit cell: (126.368, 142.164, 198.168, 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 111 16.00 O 4980 8.00 N 4158 7.00 C 16318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.25 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.89 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.55 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM25299 O5 NAG A1303 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 354 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 61 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 61 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 354 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 234 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 709 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C 717 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5910 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 40 sheets defined 26.4% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.160A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.635A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.604A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.009A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.282A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.573A pdb=" N SER A1147 " --> pdb=" O LEU A1143 " (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 372 removed outlier: 3.648A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.606A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 835 through 840 removed outlier: 3.678A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 888 No H-bonds generated for 'chain 'B' and resid 886 through 888' Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.101A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.631A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 removed outlier: 3.923A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1147 " --> pdb=" O LEU B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.557A pdb=" N SER C 71 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.511A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.669A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.180A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.677A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 627 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.599A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.869A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.774A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.751A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1139 through 1149 removed outlier: 3.556A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.418A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.353A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.886A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.001A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.256A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.283A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.931A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.154A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.302A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.631A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.631A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.512A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 4.052A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.797A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.064A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 191 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.783A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.330A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.310A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.459A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.607A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.773A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.721A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.160A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.449A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.111A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.599A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.078A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.820A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.820A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.697A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 2946 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: 7.55 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 8078 1.36 - 1.50: 7657 1.50 - 1.64: 10289 1.64 - 1.79: 37 1.79 - 1.93: 102 Bond restraints: 26163 Sorted by residual: bond pdb=" N PRO A 139 " pdb=" CD PRO A 139 " ideal model delta sigma weight residual 1.473 1.750 -0.277 1.40e-02 5.10e+03 3.90e+02 bond pdb=" N ASN B 81 " pdb=" CA ASN B 81 " ideal model delta sigma weight residual 1.453 1.504 -0.050 9.20e-03 1.18e+04 3.00e+01 bond pdb=" CG LEU B1049 " pdb=" CD1 LEU B1049 " ideal model delta sigma weight residual 1.521 1.357 0.164 3.30e-02 9.18e+02 2.48e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 1.808 1.935 -0.127 3.30e-02 9.18e+02 1.47e+01 ... (remaining 26158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 35047 3.97 - 7.94: 513 7.94 - 11.91: 16 11.91 - 15.88: 2 15.88 - 19.86: 1 Bond angle restraints: 35579 Sorted by residual: angle pdb=" CA CYS B 131 " pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " ideal model delta sigma weight residual 114.40 134.26 -19.86 2.30e+00 1.89e-01 7.45e+01 angle pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" CD PRO A 561 " ideal model delta sigma weight residual 112.00 101.59 10.41 1.40e+00 5.10e-01 5.52e+01 angle pdb=" N ARG B 214 " pdb=" CA ARG B 214 " pdb=" C ARG B 214 " ideal model delta sigma weight residual 111.28 119.03 -7.75 1.09e+00 8.42e-01 5.05e+01 angle pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 114.40 127.40 -13.00 2.30e+00 1.89e-01 3.19e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.42 -6.72 1.22e+00 6.72e-01 3.04e+01 ... (remaining 35574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 15305 22.52 - 45.03: 752 45.03 - 67.55: 163 67.55 - 90.06: 75 90.06 - 112.58: 30 Dihedral angle restraints: 16325 sinusoidal: 7138 harmonic: 9187 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -166.64 80.64 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CD ARG B 454 " pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " pdb=" NH1 ARG B 454 " ideal model delta sinusoidal sigma weight residual 0.00 66.85 -66.85 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 39.94 53.06 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 16322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4138 0.188 - 0.375: 33 0.375 - 0.563: 2 0.563 - 0.750: 1 0.750 - 0.938: 2 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.65e+00 ... (remaining 4173 not shown) Planarity restraints: 4546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 454 " -0.844 9.50e-02 1.11e+02 3.79e-01 9.91e+01 pdb=" NE ARG B 454 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG B 454 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG B 454 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 454 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 847 " 0.680 9.50e-02 1.11e+02 3.06e-01 6.33e+01 pdb=" NE ARG B 847 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG B 847 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG B 847 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 847 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.066 2.00e-02 2.50e+03 6.76e-02 5.71e+01 pdb=" CG ASN A1074 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.092 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.074 2.00e-02 2.50e+03 ... (remaining 4543 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 54 2.42 - 3.04: 15808 3.04 - 3.66: 36781 3.66 - 4.28: 57175 4.28 - 4.90: 95968 Nonbonded interactions: 205786 Sorted by model distance: nonbonded pdb=" OE1 GLU A1017 " pdb=" NH1 ARG B1019 " model vdw 1.798 3.120 nonbonded pdb=" OD1 ASN A 99 " pdb=" NH2 ARG A 190 " model vdw 1.961 3.120 nonbonded pdb=" CB LEU C 189 " pdb=" CD1 ILE C 210 " model vdw 1.980 3.860 nonbonded pdb=" NZ LYS B 458 " pdb=" NZ LYS B 481 " model vdw 1.985 3.200 nonbonded pdb=" OH TYR B 37 " pdb=" OD1 ASP B 53 " model vdw 2.011 3.040 ... (remaining 205781 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 26 through 65 or resid 75 through 138 or resid 154 through \ 172 or resid 188 through 210 or resid 213 through 356 or resid 360 through 387 \ or resid 391 through 676 or resid 689 through 837 or resid 852 through 1304)) selection = (chain 'B' and (resid 26 through 138 or resid 154 through 210 or resid 213 throu \ gh 676 or resid 689 through 837 or resid 852 through 1304)) selection = (chain 'C' and (resid 26 through 65 or resid 75 through 138 or resid 154 through \ 172 or resid 188 through 356 or resid 360 through 387 or resid 391 through 1304 \ )) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } 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: 12.970 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: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.010 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.008 0.480 26260 Z= 0.378 Angle : 1.210 46.954 35832 Z= 0.649 Chirality : 0.066 0.938 4176 Planarity : 0.012 0.379 4509 Dihedral : 15.404 112.578 10301 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.14 % Allowed : 11.86 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.14), residues: 3109 helix: 1.53 (0.18), residues: 711 sheet: 0.82 (0.20), residues: 606 loop : -0.37 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.003 ARG B 454 TYR 0.036 0.003 TYR A 204 PHE 0.068 0.003 PHE A 400 TRP 0.039 0.004 TRP B 353 HIS 0.023 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00724 (26163) covalent geometry : angle 1.12466 (35579) SS BOND : bond 0.08878 ( 38) SS BOND : angle 7.47176 ( 76) hydrogen bonds : bond 0.13126 ( 1013) hydrogen bonds : angle 7.68434 ( 2946) link_BETA1-4 : bond 0.00527 ( 22) link_BETA1-4 : angle 1.91192 ( 66) link_NAG-ASN : bond 0.00742 ( 37) link_NAG-ASN : angle 5.18535 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 335 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7866 (mp0) cc_final: 0.7431 (tt0) REVERT: A 464 PHE cc_start: 0.7802 (m-10) cc_final: 0.7550 (m-10) REVERT: A 466 ARG cc_start: 0.6028 (mtm-85) cc_final: 0.4899 (mmt-90) REVERT: A 493 GLN cc_start: 0.7334 (tp40) cc_final: 0.6442 (pm20) REVERT: A 554 LYS cc_start: 0.7835 (tptp) cc_final: 0.7104 (ptpp) REVERT: A 646 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.8234 (mmm160) REVERT: B 317 ASN cc_start: 0.8771 (m-40) cc_final: 0.8536 (m-40) REVERT: B 886 TRP cc_start: 0.6456 (p90) cc_final: 0.5671 (p90) REVERT: B 1101 HIS cc_start: 0.8140 (m90) cc_final: 0.7934 (m-70) REVERT: C 239 GLN cc_start: 0.8152 (tt0) cc_final: 0.7824 (mm110) REVERT: C 456 PHE cc_start: 0.6865 (t80) cc_final: 0.6505 (m-10) REVERT: C 509 ARG cc_start: 0.6545 (mtt180) cc_final: 0.5293 (ptm160) outliers start: 4 outliers final: 3 residues processed: 337 average time/residue: 0.5586 time to fit residues: 223.4742 Evaluate side-chains 281 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain C residue 453 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 188 ASN A 321 GLN A 360 ASN A 564 GLN A 606 ASN A 641 ASN A 935 GLN A1048 HIS B 115 GLN B 165 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS B 913 GLN B 955 ASN B1002 GLN B1119 ASN C 321 GLN C 506 GLN C 658 ASN C1005 GLN C1048 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.173179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127226 restraints weight = 33276.067| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.34 r_work: 0.3334 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26260 Z= 0.165 Angle : 0.703 12.643 35832 Z= 0.359 Chirality : 0.049 0.525 4176 Planarity : 0.005 0.081 4509 Dihedral : 8.531 87.865 4607 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.82 % Allowed : 11.21 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.14), residues: 3109 helix: 2.42 (0.19), residues: 715 sheet: 0.56 (0.19), residues: 640 loop : -0.54 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 577 TYR 0.021 0.002 TYR A1067 PHE 0.024 0.002 PHE C 168 TRP 0.016 0.002 TRP B 353 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00378 (26163) covalent geometry : angle 0.67520 (35579) SS BOND : bond 0.00459 ( 38) SS BOND : angle 1.85227 ( 76) hydrogen bonds : bond 0.04850 ( 1013) hydrogen bonds : angle 6.08215 ( 2946) link_BETA1-4 : bond 0.00752 ( 22) link_BETA1-4 : angle 2.37480 ( 66) link_NAG-ASN : bond 0.00654 ( 37) link_NAG-ASN : angle 2.75203 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.5704 (t-90) REVERT: A 351 TYR cc_start: 0.7536 (p90) cc_final: 0.7081 (p90) REVERT: A 439 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7340 (t160) REVERT: A 506 GLN cc_start: 0.8839 (mt0) cc_final: 0.8353 (mt0) REVERT: A 1045 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8172 (mppt) REVERT: A 1113 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8084 (mm110) REVERT: B 32 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: B 314 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7995 (mm-40) REVERT: B 529 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8043 (mptt) REVERT: B 1101 HIS cc_start: 0.8191 (m90) cc_final: 0.7932 (m-70) REVERT: C 160 TYR cc_start: 0.4832 (t80) cc_final: 0.4622 (t80) REVERT: C 168 PHE cc_start: 0.6139 (m-80) cc_final: 0.5736 (m-80) REVERT: C 239 GLN cc_start: 0.8179 (tt0) cc_final: 0.7585 (mm110) REVERT: C 326 ILE cc_start: 0.8027 (mm) cc_final: 0.7345 (tt) REVERT: C 456 PHE cc_start: 0.6839 (t80) cc_final: 0.6462 (m-10) REVERT: C 509 ARG cc_start: 0.6358 (mtt180) cc_final: 0.4931 (ptt90) REVERT: C 571 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8418 (t70) REVERT: C 582 LEU cc_start: 0.7902 (mm) cc_final: 0.7628 (tp) REVERT: C 646 ARG cc_start: 0.8497 (mmt180) cc_final: 0.8213 (mmp80) REVERT: C 787 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8190 (mt0) outliers start: 78 outliers final: 28 residues processed: 366 average time/residue: 0.5203 time to fit residues: 228.4214 Evaluate side-chains 305 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 132 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 271 GLN A 360 ASN A 409 GLN A 658 ASN A 935 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 935 GLN B1002 GLN C 658 ASN C1005 GLN C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.169524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123174 restraints weight = 33289.362| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.36 r_work: 0.3279 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26260 Z= 0.192 Angle : 0.670 13.569 35832 Z= 0.343 Chirality : 0.049 0.468 4176 Planarity : 0.005 0.060 4509 Dihedral : 6.796 82.733 4605 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.33 % Allowed : 12.55 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 3109 helix: 2.37 (0.19), residues: 723 sheet: 0.32 (0.19), residues: 676 loop : -0.74 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.020 0.002 TYR C 351 PHE 0.027 0.002 PHE A 400 TRP 0.013 0.002 TRP C 886 HIS 0.008 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00457 (26163) covalent geometry : angle 0.64290 (35579) SS BOND : bond 0.00422 ( 38) SS BOND : angle 1.66954 ( 76) hydrogen bonds : bond 0.04867 ( 1013) hydrogen bonds : angle 5.91241 ( 2946) link_BETA1-4 : bond 0.00687 ( 22) link_BETA1-4 : angle 2.02723 ( 66) link_NAG-ASN : bond 0.00576 ( 37) link_NAG-ASN : angle 2.83013 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 278 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7671 (m-80) cc_final: 0.7362 (m-80) REVERT: A 205 SER cc_start: 0.9016 (p) cc_final: 0.8767 (t) REVERT: A 309 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: A 339 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5809 (t-90) REVERT: A 351 TYR cc_start: 0.7837 (p90) cc_final: 0.7630 (p90) REVERT: A 464 PHE cc_start: 0.7936 (m-10) cc_final: 0.7725 (m-10) REVERT: A 493 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6974 (tp40) REVERT: A 554 LYS cc_start: 0.8185 (tptp) cc_final: 0.7368 (ptpp) REVERT: A 560 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6242 (tp) REVERT: A 918 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: A 1113 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8105 (mm110) REVERT: B 32 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: B 216 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6294 (t80) REVERT: B 314 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8170 (mm-40) REVERT: B 436 TRP cc_start: 0.6423 (p-90) cc_final: 0.5814 (p-90) REVERT: B 529 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8003 (mppt) REVERT: B 675 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: B 1101 HIS cc_start: 0.8268 (m90) cc_final: 0.7946 (m-70) REVERT: C 168 PHE cc_start: 0.6259 (m-80) cc_final: 0.5809 (m-80) REVERT: C 189 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7785 (tt) REVERT: C 239 GLN cc_start: 0.8266 (tt0) cc_final: 0.7822 (tp40) REVERT: C 351 TYR cc_start: 0.7949 (p90) cc_final: 0.7269 (p90) REVERT: C 456 PHE cc_start: 0.7100 (t80) cc_final: 0.6449 (m-10) REVERT: C 509 ARG cc_start: 0.6520 (mtt180) cc_final: 0.4956 (ptt90) REVERT: C 571 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8523 (t70) REVERT: C 582 LEU cc_start: 0.7938 (mm) cc_final: 0.7718 (tp) REVERT: C 646 ARG cc_start: 0.8506 (mmt180) cc_final: 0.8240 (mmp80) REVERT: C 787 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8207 (mt0) outliers start: 92 outliers final: 38 residues processed: 330 average time/residue: 0.4931 time to fit residues: 197.3420 Evaluate side-chains 308 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 39 optimal weight: 0.4980 chunk 313 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 360 ASN A 439 ASN A 935 GLN A1119 ASN B 165 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN C 164 ASN C 658 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125481 restraints weight = 33278.366| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.26 r_work: 0.3307 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26260 Z= 0.142 Angle : 0.622 13.037 35832 Z= 0.316 Chirality : 0.048 0.672 4176 Planarity : 0.004 0.058 4509 Dihedral : 6.045 83.853 4605 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.33 % Allowed : 12.91 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.15), residues: 3109 helix: 2.48 (0.19), residues: 724 sheet: 0.18 (0.19), residues: 681 loop : -0.74 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 237 TYR 0.040 0.001 TYR A 396 PHE 0.026 0.001 PHE A 392 TRP 0.010 0.001 TRP C 886 HIS 0.008 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00325 (26163) covalent geometry : angle 0.59203 (35579) SS BOND : bond 0.00334 ( 38) SS BOND : angle 1.62824 ( 76) hydrogen bonds : bond 0.04304 ( 1013) hydrogen bonds : angle 5.71713 ( 2946) link_BETA1-4 : bond 0.00629 ( 22) link_BETA1-4 : angle 1.88904 ( 66) link_NAG-ASN : bond 0.00841 ( 37) link_NAG-ASN : angle 2.94969 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 286 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7726 (m-80) cc_final: 0.7390 (m-80) REVERT: A 205 SER cc_start: 0.9049 (p) cc_final: 0.8833 (t) REVERT: A 529 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8160 (mptt) REVERT: A 560 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6218 (tp) REVERT: A 1113 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8094 (mm110) REVERT: B 216 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6234 (t80) REVERT: B 237 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6630 (mtp-110) REVERT: B 529 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7974 (mppt) REVERT: B 675 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: B 1101 HIS cc_start: 0.8280 (m90) cc_final: 0.8077 (m-70) REVERT: C 129 LYS cc_start: 0.7615 (mttm) cc_final: 0.7174 (mtmm) REVERT: C 168 PHE cc_start: 0.6242 (m-80) cc_final: 0.5831 (m-80) REVERT: C 189 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7712 (tt) REVERT: C 237 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.8008 (ttm110) REVERT: C 239 GLN cc_start: 0.8284 (tt0) cc_final: 0.7960 (tp40) REVERT: C 351 TYR cc_start: 0.7988 (p90) cc_final: 0.7388 (p90) REVERT: C 456 PHE cc_start: 0.7202 (t80) cc_final: 0.6461 (m-10) REVERT: C 498 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7408 (mpt-90) REVERT: C 509 ARG cc_start: 0.6590 (mtt180) cc_final: 0.4949 (ptt90) REVERT: C 529 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7517 (mmmm) REVERT: C 571 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8586 (t70) REVERT: C 646 ARG cc_start: 0.8432 (mmt180) cc_final: 0.8193 (mmp80) REVERT: C 787 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8209 (mt0) outliers start: 92 outliers final: 33 residues processed: 341 average time/residue: 0.5121 time to fit residues: 211.9123 Evaluate side-chains 291 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 110 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 274 optimal weight: 1.9990 chunk 144 optimal weight: 0.0870 chunk 167 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 360 ASN A 409 GLN A 804 GLN A 935 GLN A1119 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS C 321 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.178012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130577 restraints weight = 32663.341| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.48 r_work: 0.3359 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26260 Z= 0.118 Angle : 0.585 11.830 35832 Z= 0.299 Chirality : 0.046 0.433 4176 Planarity : 0.004 0.057 4509 Dihedral : 5.448 80.176 4603 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.04 % Allowed : 13.71 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 3109 helix: 2.57 (0.19), residues: 726 sheet: 0.20 (0.19), residues: 699 loop : -0.79 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.027 0.001 TYR C 265 PHE 0.034 0.001 PHE A 168 TRP 0.011 0.001 TRP A 452 HIS 0.009 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00264 (26163) covalent geometry : angle 0.55549 (35579) SS BOND : bond 0.00347 ( 38) SS BOND : angle 1.64903 ( 76) hydrogen bonds : bond 0.03964 ( 1013) hydrogen bonds : angle 5.56989 ( 2946) link_BETA1-4 : bond 0.00606 ( 22) link_BETA1-4 : angle 1.60445 ( 66) link_NAG-ASN : bond 0.00706 ( 37) link_NAG-ASN : angle 2.87913 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8086 (mt0) cc_final: 0.7093 (mm-40) REVERT: A 200 TYR cc_start: 0.7619 (m-80) cc_final: 0.7263 (m-80) REVERT: A 205 SER cc_start: 0.8958 (p) cc_final: 0.8726 (t) REVERT: A 339 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7315 (m-70) REVERT: A 493 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6900 (tp40) REVERT: A 529 LYS cc_start: 0.8578 (mmtp) cc_final: 0.8097 (mptt) REVERT: A 554 LYS cc_start: 0.8028 (tptp) cc_final: 0.7179 (ptpp) REVERT: A 560 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6210 (tp) REVERT: B 216 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6451 (t80) REVERT: B 529 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7937 (mppt) REVERT: B 675 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: B 828 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7133 (pt) REVERT: B 1045 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8202 (mptm) REVERT: B 1101 HIS cc_start: 0.8259 (m90) cc_final: 0.7935 (m-70) REVERT: C 129 LYS cc_start: 0.7464 (mttm) cc_final: 0.7008 (mtmm) REVERT: C 168 PHE cc_start: 0.6153 (m-80) cc_final: 0.5742 (m-80) REVERT: C 189 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7438 (tt) REVERT: C 239 GLN cc_start: 0.8195 (tt0) cc_final: 0.7751 (tp40) REVERT: C 271 GLN cc_start: 0.8674 (mt0) cc_final: 0.8384 (pt0) REVERT: C 281 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: C 351 TYR cc_start: 0.7979 (p90) cc_final: 0.7352 (p90) REVERT: C 456 PHE cc_start: 0.7230 (t80) cc_final: 0.6467 (m-10) REVERT: C 498 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7382 (mpt-90) REVERT: C 509 ARG cc_start: 0.6567 (mtt180) cc_final: 0.4854 (ptt90) REVERT: C 571 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8506 (t70) REVERT: C 646 ARG cc_start: 0.8340 (mmt180) cc_final: 0.8024 (mmp80) REVERT: C 787 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: C 1073 LYS cc_start: 0.8160 (mttp) cc_final: 0.7781 (mttm) REVERT: C 1101 HIS cc_start: 0.8347 (m90) cc_final: 0.8107 (m90) outliers start: 84 outliers final: 30 residues processed: 314 average time/residue: 0.4761 time to fit residues: 182.6278 Evaluate side-chains 278 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 145 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 174 optimal weight: 0.0970 chunk 26 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 519 HIS A 935 GLN A1119 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129064 restraints weight = 32883.590| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.42 r_work: 0.3331 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26260 Z= 0.140 Angle : 0.607 13.034 35832 Z= 0.306 Chirality : 0.047 0.410 4176 Planarity : 0.004 0.059 4509 Dihedral : 5.387 74.489 4603 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.11 % Allowed : 14.07 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3109 helix: 2.62 (0.19), residues: 720 sheet: 0.10 (0.19), residues: 709 loop : -0.83 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 237 TYR 0.026 0.001 TYR C 265 PHE 0.029 0.002 PHE A 168 TRP 0.010 0.001 TRP B 436 HIS 0.009 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00328 (26163) covalent geometry : angle 0.57697 (35579) SS BOND : bond 0.00324 ( 38) SS BOND : angle 1.85616 ( 76) hydrogen bonds : bond 0.04115 ( 1013) hydrogen bonds : angle 5.52588 ( 2946) link_BETA1-4 : bond 0.00604 ( 22) link_BETA1-4 : angle 1.50726 ( 66) link_NAG-ASN : bond 0.00627 ( 37) link_NAG-ASN : angle 2.90958 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 261 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8121 (mt0) cc_final: 0.7109 (mm-40) REVERT: A 200 TYR cc_start: 0.7709 (m-80) cc_final: 0.7291 (m-80) REVERT: A 205 SER cc_start: 0.8964 (p) cc_final: 0.8740 (t) REVERT: A 339 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7296 (m-70) REVERT: A 440 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7072 (tmmm) REVERT: A 493 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6933 (tp40) REVERT: A 506 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: A 529 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8158 (mptt) REVERT: A 1113 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8081 (mm110) REVERT: B 216 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6442 (t80) REVERT: B 237 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6453 (mtp-110) REVERT: B 529 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7980 (mppt) REVERT: B 675 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: B 1101 HIS cc_start: 0.8295 (m90) cc_final: 0.7967 (m-70) REVERT: C 168 PHE cc_start: 0.6352 (m-80) cc_final: 0.5924 (m-80) REVERT: C 239 GLN cc_start: 0.8279 (tt0) cc_final: 0.7890 (tp40) REVERT: C 281 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: C 351 TYR cc_start: 0.7990 (p90) cc_final: 0.7361 (p90) REVERT: C 456 PHE cc_start: 0.7335 (t80) cc_final: 0.6421 (m-10) REVERT: C 498 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7372 (mpt-90) REVERT: C 509 ARG cc_start: 0.6613 (mtt180) cc_final: 0.4699 (ptm160) REVERT: C 571 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8537 (t70) REVERT: C 646 ARG cc_start: 0.8370 (mmt180) cc_final: 0.8061 (mmp80) REVERT: C 787 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: C 1073 LYS cc_start: 0.8212 (mttp) cc_final: 0.7902 (mttm) outliers start: 86 outliers final: 35 residues processed: 311 average time/residue: 0.4596 time to fit residues: 172.9989 Evaluate side-chains 290 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 277 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 300 optimal weight: 0.5980 chunk 144 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 297 optimal weight: 0.0050 chunk 298 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.177558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130178 restraints weight = 32766.806| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.50 r_work: 0.3362 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26260 Z= 0.117 Angle : 0.592 14.658 35832 Z= 0.299 Chirality : 0.046 0.404 4176 Planarity : 0.004 0.060 4509 Dihedral : 5.155 70.821 4603 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.42 % Allowed : 14.79 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 3109 helix: 2.67 (0.19), residues: 720 sheet: 0.14 (0.19), residues: 722 loop : -0.85 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 237 TYR 0.018 0.001 TYR A1067 PHE 0.034 0.001 PHE A 168 TRP 0.011 0.001 TRP B 436 HIS 0.009 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00263 (26163) covalent geometry : angle 0.55935 (35579) SS BOND : bond 0.00315 ( 38) SS BOND : angle 1.82823 ( 76) hydrogen bonds : bond 0.03831 ( 1013) hydrogen bonds : angle 5.43452 ( 2946) link_BETA1-4 : bond 0.00587 ( 22) link_BETA1-4 : angle 1.46498 ( 66) link_NAG-ASN : bond 0.00620 ( 37) link_NAG-ASN : angle 3.03715 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 267 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8128 (mt0) cc_final: 0.7199 (mm-40) REVERT: A 200 TYR cc_start: 0.7604 (m-80) cc_final: 0.7216 (m-80) REVERT: A 205 SER cc_start: 0.8924 (p) cc_final: 0.8695 (t) REVERT: A 339 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7213 (m-70) REVERT: A 340 GLU cc_start: 0.7994 (mp0) cc_final: 0.7589 (tt0) REVERT: A 440 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7031 (tmmm) REVERT: A 493 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6952 (tp40) REVERT: A 506 GLN cc_start: 0.8428 (mt0) cc_final: 0.7675 (mp10) REVERT: A 529 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8162 (mptt) REVERT: A 554 LYS cc_start: 0.7997 (tptp) cc_final: 0.7196 (ptpp) REVERT: B 237 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6454 (mtp-110) REVERT: B 529 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8030 (mptt) REVERT: B 675 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: B 828 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7009 (pt) REVERT: B 1045 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8162 (mptm) REVERT: B 1101 HIS cc_start: 0.8286 (m90) cc_final: 0.7968 (m-70) REVERT: C 168 PHE cc_start: 0.6074 (m-80) cc_final: 0.5783 (m-80) REVERT: C 189 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7532 (tt) REVERT: C 239 GLN cc_start: 0.8335 (tt0) cc_final: 0.7906 (tp40) REVERT: C 351 TYR cc_start: 0.7952 (p90) cc_final: 0.7393 (p90) REVERT: C 452 TRP cc_start: 0.7460 (m-10) cc_final: 0.6655 (m100) REVERT: C 456 PHE cc_start: 0.7373 (t80) cc_final: 0.6444 (m-10) REVERT: C 498 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7405 (mpt-90) REVERT: C 509 ARG cc_start: 0.6656 (mtt180) cc_final: 0.4949 (ptt180) REVERT: C 571 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8484 (t70) REVERT: C 646 ARG cc_start: 0.8348 (mmt180) cc_final: 0.8020 (mmp80) REVERT: C 787 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: C 1073 LYS cc_start: 0.8179 (mttp) cc_final: 0.7848 (mttm) outliers start: 67 outliers final: 34 residues processed: 311 average time/residue: 0.4904 time to fit residues: 185.6609 Evaluate side-chains 290 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 207 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 266 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 242 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 280 ASN ** 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 = 0.4120 r_free = 0.4120 target = 0.176967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129675 restraints weight = 32812.341| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.44 r_work: 0.3337 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26260 Z= 0.130 Angle : 0.603 17.300 35832 Z= 0.303 Chirality : 0.046 0.394 4176 Planarity : 0.004 0.063 4509 Dihedral : 5.067 62.830 4603 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.31 % Allowed : 15.01 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 3109 helix: 2.65 (0.19), residues: 719 sheet: 0.20 (0.19), residues: 720 loop : -0.88 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 237 TYR 0.027 0.001 TYR A 489 PHE 0.034 0.001 PHE A 168 TRP 0.011 0.001 TRP A 353 HIS 0.010 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00303 (26163) covalent geometry : angle 0.56978 (35579) SS BOND : bond 0.00444 ( 38) SS BOND : angle 2.26304 ( 76) hydrogen bonds : bond 0.03930 ( 1013) hydrogen bonds : angle 5.40961 ( 2946) link_BETA1-4 : bond 0.00580 ( 22) link_BETA1-4 : angle 1.41971 ( 66) link_NAG-ASN : bond 0.00727 ( 37) link_NAG-ASN : angle 2.96559 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7869 (p0) cc_final: 0.7594 (p0) REVERT: A 115 GLN cc_start: 0.8137 (mt0) cc_final: 0.7179 (mm-40) REVERT: A 205 SER cc_start: 0.8936 (p) cc_final: 0.8733 (t) REVERT: A 339 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7231 (m-70) REVERT: A 403 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7931 (mtpm) REVERT: A 493 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6992 (tp40) REVERT: A 506 GLN cc_start: 0.8419 (mt0) cc_final: 0.7707 (mp10) REVERT: A 529 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8196 (mptt) REVERT: A 1113 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8085 (mm110) REVERT: B 237 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6482 (mtp-110) REVERT: B 529 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8025 (mptt) REVERT: B 675 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: B 1045 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8205 (mptm) REVERT: B 1101 HIS cc_start: 0.8328 (m90) cc_final: 0.8000 (m-70) REVERT: C 168 PHE cc_start: 0.6096 (m-80) cc_final: 0.5815 (m-80) REVERT: C 189 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7594 (tt) REVERT: C 239 GLN cc_start: 0.8362 (tt0) cc_final: 0.7919 (tp40) REVERT: C 452 TRP cc_start: 0.7469 (m-10) cc_final: 0.6701 (m100) REVERT: C 456 PHE cc_start: 0.7442 (t80) cc_final: 0.6430 (m-10) REVERT: C 498 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7409 (mpt-90) REVERT: C 509 ARG cc_start: 0.6697 (mtt180) cc_final: 0.4713 (ptm160) REVERT: C 571 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8492 (t70) REVERT: C 582 LEU cc_start: 0.7954 (mm) cc_final: 0.7702 (tp) REVERT: C 646 ARG cc_start: 0.8395 (mmt180) cc_final: 0.8181 (mmp80) REVERT: C 787 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: C 1073 LYS cc_start: 0.8192 (mttp) cc_final: 0.7868 (mttm) outliers start: 64 outliers final: 36 residues processed: 297 average time/residue: 0.4919 time to fit residues: 176.1688 Evaluate side-chains 290 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 259 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 72 optimal weight: 0.0050 chunk 160 optimal weight: 1.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129033 restraints weight = 32857.224| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.47 r_work: 0.3330 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26260 Z= 0.129 Angle : 0.596 18.230 35832 Z= 0.299 Chirality : 0.046 0.431 4176 Planarity : 0.004 0.063 4509 Dihedral : 4.955 53.183 4603 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.03 % Allowed : 15.66 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3109 helix: 2.63 (0.19), residues: 717 sheet: 0.11 (0.19), residues: 714 loop : -0.86 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.031 0.001 TYR C 351 PHE 0.035 0.001 PHE A 168 TRP 0.014 0.001 TRP B 436 HIS 0.011 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00300 (26163) covalent geometry : angle 0.56519 (35579) SS BOND : bond 0.00354 ( 38) SS BOND : angle 1.87843 ( 76) hydrogen bonds : bond 0.03872 ( 1013) hydrogen bonds : angle 5.37907 ( 2946) link_BETA1-4 : bond 0.00585 ( 22) link_BETA1-4 : angle 1.39224 ( 66) link_NAG-ASN : bond 0.00691 ( 37) link_NAG-ASN : angle 2.94395 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7919 (p0) cc_final: 0.7671 (p0) REVERT: A 200 TYR cc_start: 0.7636 (m-80) cc_final: 0.7289 (m-80) REVERT: A 339 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7265 (m-70) REVERT: A 340 GLU cc_start: 0.8104 (mp0) cc_final: 0.7725 (tt0) REVERT: A 403 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7969 (ttpp) REVERT: A 506 GLN cc_start: 0.8350 (mt0) cc_final: 0.7655 (mp10) REVERT: A 529 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8205 (mptt) REVERT: A 554 LYS cc_start: 0.8043 (tptp) cc_final: 0.7201 (pmtt) REVERT: B 127 PHE cc_start: 0.6653 (m-80) cc_final: 0.6307 (m-10) REVERT: B 237 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6514 (mtp-110) REVERT: B 529 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8009 (mptt) REVERT: B 675 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6945 (mp10) REVERT: B 828 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6869 (pt) REVERT: B 1045 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8210 (mptm) REVERT: B 1101 HIS cc_start: 0.8346 (m90) cc_final: 0.7994 (m-70) REVERT: C 239 GLN cc_start: 0.8395 (tt0) cc_final: 0.7945 (tp40) REVERT: C 452 TRP cc_start: 0.7487 (m-10) cc_final: 0.6687 (m100) REVERT: C 456 PHE cc_start: 0.7486 (t80) cc_final: 0.6406 (m-10) REVERT: C 498 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7403 (mpt-90) REVERT: C 509 ARG cc_start: 0.6709 (mtt180) cc_final: 0.4923 (ptt180) REVERT: C 571 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8475 (t70) REVERT: C 582 LEU cc_start: 0.7905 (mm) cc_final: 0.7645 (tp) REVERT: C 646 ARG cc_start: 0.8402 (mmt180) cc_final: 0.8124 (mmp80) REVERT: C 654 GLU cc_start: 0.7640 (tp30) cc_final: 0.7398 (tp30) REVERT: C 787 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: C 1073 LYS cc_start: 0.8220 (mttp) cc_final: 0.7902 (mttm) outliers start: 56 outliers final: 37 residues processed: 286 average time/residue: 0.4607 time to fit residues: 160.9256 Evaluate side-chains 287 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 27 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 252 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 167 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 360 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 804 GLN B 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129182 restraints weight = 32720.050| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.49 r_work: 0.3338 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26260 Z= 0.130 Angle : 0.595 12.023 35832 Z= 0.302 Chirality : 0.047 0.441 4176 Planarity : 0.004 0.065 4509 Dihedral : 4.921 54.147 4603 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.88 % Allowed : 16.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3109 helix: 2.57 (0.19), residues: 724 sheet: 0.12 (0.19), residues: 711 loop : -0.85 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.031 0.001 TYR B1067 PHE 0.061 0.002 PHE A 400 TRP 0.013 0.001 TRP B 436 HIS 0.012 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00301 (26163) covalent geometry : angle 0.56517 (35579) SS BOND : bond 0.00340 ( 38) SS BOND : angle 1.75723 ( 76) hydrogen bonds : bond 0.03921 ( 1013) hydrogen bonds : angle 5.36923 ( 2946) link_BETA1-4 : bond 0.00620 ( 22) link_BETA1-4 : angle 1.38100 ( 66) link_NAG-ASN : bond 0.00703 ( 37) link_NAG-ASN : angle 2.92266 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7878 (p0) cc_final: 0.7613 (p0) REVERT: A 200 TYR cc_start: 0.7625 (m-80) cc_final: 0.7383 (m-80) REVERT: A 339 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7245 (m-70) REVERT: A 340 GLU cc_start: 0.8066 (mp0) cc_final: 0.7681 (tt0) REVERT: A 403 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7963 (ttpp) REVERT: A 464 PHE cc_start: 0.8108 (m-10) cc_final: 0.7717 (m-10) REVERT: A 481 LYS cc_start: 0.7439 (mmtt) cc_final: 0.6726 (ptpp) REVERT: A 506 GLN cc_start: 0.8320 (mt0) cc_final: 0.7655 (mp10) REVERT: A 529 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8190 (mptt) REVERT: A 554 LYS cc_start: 0.8009 (tptp) cc_final: 0.7164 (pmtt) REVERT: B 127 PHE cc_start: 0.6652 (m-80) cc_final: 0.6333 (m-10) REVERT: B 194 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.5927 (p90) REVERT: B 237 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6669 (mtp85) REVERT: B 529 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8006 (mptt) REVERT: B 619 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: B 675 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: B 828 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6832 (pt) REVERT: B 906 PHE cc_start: 0.7807 (m-80) cc_final: 0.7392 (m-80) REVERT: B 1045 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8203 (mptm) REVERT: B 1101 HIS cc_start: 0.8329 (m90) cc_final: 0.7951 (m-70) REVERT: C 239 GLN cc_start: 0.8387 (tt0) cc_final: 0.7909 (tp40) REVERT: C 241 LEU cc_start: 0.7292 (mt) cc_final: 0.6998 (pp) REVERT: C 452 TRP cc_start: 0.7495 (m-10) cc_final: 0.6715 (m100) REVERT: C 456 PHE cc_start: 0.7522 (t80) cc_final: 0.6390 (m-10) REVERT: C 498 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7374 (mpt-90) REVERT: C 509 ARG cc_start: 0.6744 (mtt180) cc_final: 0.4739 (ptm160) REVERT: C 571 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8480 (t70) REVERT: C 582 LEU cc_start: 0.7914 (mm) cc_final: 0.7671 (tp) REVERT: C 646 ARG cc_start: 0.8361 (mmt180) cc_final: 0.8057 (mmp80) REVERT: C 654 GLU cc_start: 0.7605 (tp30) cc_final: 0.7388 (tp30) REVERT: C 787 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: C 1073 LYS cc_start: 0.8199 (mttp) cc_final: 0.7808 (tttt) outliers start: 52 outliers final: 36 residues processed: 285 average time/residue: 0.4929 time to fit residues: 170.4913 Evaluate side-chains 288 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 192 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 157 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A1088 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS B 954 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127868 restraints weight = 32708.835| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.54 r_work: 0.3323 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26260 Z= 0.144 Angle : 0.603 12.168 35832 Z= 0.306 Chirality : 0.047 0.442 4176 Planarity : 0.004 0.064 4509 Dihedral : 4.901 54.169 4603 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.99 % Allowed : 16.27 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3109 helix: 2.61 (0.19), residues: 718 sheet: 0.13 (0.19), residues: 710 loop : -0.87 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.034 0.001 TYR A 423 PHE 0.046 0.002 PHE A 400 TRP 0.016 0.002 TRP C 886 HIS 0.013 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00340 (26163) covalent geometry : angle 0.57380 (35579) SS BOND : bond 0.00362 ( 38) SS BOND : angle 1.78927 ( 76) hydrogen bonds : bond 0.04052 ( 1013) hydrogen bonds : angle 5.40842 ( 2946) link_BETA1-4 : bond 0.00562 ( 22) link_BETA1-4 : angle 1.36392 ( 66) link_NAG-ASN : bond 0.00688 ( 37) link_NAG-ASN : angle 2.94452 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9398.58 seconds wall clock time: 160 minutes 52.86 seconds (9652.86 seconds total)