Starting phenix.real_space_refine on Fri Mar 6 05:09:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru3_24695/03_2026/7ru3_24695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru3_24695/03_2026/7ru3_24695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru3_24695/03_2026/7ru3_24695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru3_24695/03_2026/7ru3_24695.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru3_24695/03_2026/7ru3_24695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru3_24695/03_2026/7ru3_24695.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 130 5.16 5 C 17906 2.51 5 N 4644 2.21 5 O 5477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28157 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 8304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8304 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 56, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 7737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7737 Classifications: {'peptide': 989} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 16 Chain: "B" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.17, per 1000 atoms: 0.22 Number of scatterers: 28157 At special positions: 0 Unit cell: (150.38, 141.11, 194.67, 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 130 16.00 O 5477 8.00 N 4644 7.00 C 17906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.10 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.09 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.10 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 705 " distance=2.73 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 C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.12 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.07 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=2.05 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.78 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.20 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.75 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1074 " " NAG A1313 " - " ASN A1098 " " NAG A1314 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG D 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1098 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 60 sheets defined 24.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.925A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.453A pdb=" N ARG A 408 " --> pdb=" O ASP 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 502 through 505 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.516A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.535A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 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 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.265A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.108A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.169A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.510A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.505A 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 1140 through 1147 removed outlier: 3.926A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.649A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.679A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 806 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.526A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 856' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.115A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.338A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.338A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 54 removed outlier: 4.641A pdb=" N ARG L 54 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU L 47 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.884A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA9, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.095A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.413A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.138A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.637A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.752A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB9, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.681A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.363A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.589A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.827A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.419A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AC7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.842A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.110A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.405A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.691A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.471A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.656A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.564A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.133A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.284A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.399A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.595A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 719 through 728 removed outlier: 6.302A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.777A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.186A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.368A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.908A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 112 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N PHE B 135 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 141 through 143 removed outlier: 5.775A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 112 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N PHE B 135 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AF1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.135A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.135A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.450A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF7, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.011A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.821A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AG2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.227A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.227A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.437A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N GLN F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N SER F 67 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 11.403A pdb=" N VAL F 28 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N SER F 65 " --> pdb=" O VAL F 28 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.602A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 12 1238 hydrogen bonds defined for protein. 3303 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: 7.13 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 6867 1.32 - 1.47: 10119 1.47 - 1.62: 11617 1.62 - 1.78: 53 1.78 - 1.93: 122 Bond restraints: 28778 Sorted by residual: bond pdb=" CB LEU B 828 " pdb=" CG LEU B 828 " ideal model delta sigma weight residual 1.530 1.680 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" NE ARG C 466 " pdb=" CZ ARG C 466 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.69e+01 bond pdb=" CZ2 TRP A 152 " pdb=" CH2 TRP A 152 " ideal model delta sigma weight residual 1.368 1.495 -0.127 1.90e-02 2.77e+03 4.46e+01 bond pdb=" CB TYR C1067 " pdb=" CG TYR C1067 " ideal model delta sigma weight residual 1.512 1.365 0.147 2.20e-02 2.07e+03 4.45e+01 bond pdb=" CB TYR F 49 " pdb=" CG TYR F 49 " ideal model delta sigma weight residual 1.512 1.371 0.141 2.20e-02 2.07e+03 4.12e+01 ... (remaining 28773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.86: 39124 9.86 - 19.73: 13 19.73 - 29.59: 1 29.59 - 39.46: 5 39.46 - 49.32: 1 Bond angle restraints: 39144 Sorted by residual: angle pdb=" N SER F 52 " pdb=" CA SER F 52 " pdb=" C SER F 52 " ideal model delta sigma weight residual 112.72 146.50 -33.78 1.28e+00 6.10e-01 6.96e+02 angle pdb=" N2 NAG A1304 " pdb=" C7 NAG A1304 " pdb=" O7 NAG A1304 " ideal model delta sigma weight residual 123.46 172.78 -49.32 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C8 NAG A1304 " pdb=" C7 NAG A1304 " pdb=" O7 NAG A1304 " ideal model delta sigma weight residual 121.48 85.60 35.88 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C2 NAG A1304 " pdb=" N2 NAG A1304 " pdb=" C7 NAG A1304 " ideal model delta sigma weight residual 124.56 159.58 -35.02 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C2 NAG A1308 " pdb=" N2 NAG A1308 " pdb=" C7 NAG A1308 " ideal model delta sigma weight residual 124.56 159.41 -34.85 3.00e+00 1.11e-01 1.35e+02 ... (remaining 39139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17050 17.95 - 35.90: 434 35.90 - 53.85: 145 53.85 - 71.81: 67 71.81 - 89.76: 23 Dihedral angle restraints: 17719 sinusoidal: 7453 harmonic: 10266 Sorted by residual: dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS B 705 " pdb=" CB CYS B 705 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -162.18 76.18 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -141.84 55.84 1 1.00e+01 1.00e-02 4.21e+01 ... (remaining 17716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 4314 0.222 - 0.444: 240 0.444 - 0.666: 14 0.666 - 0.887: 0 0.887 - 1.109: 1 Chirality restraints: 4569 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.44e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.94e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.92e+01 ... (remaining 4566 not shown) Planarity restraints: 5032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.101 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN C1074 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.161 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " 0.073 2.00e-02 2.50e+03 7.75e-02 7.51e+01 pdb=" CG ASN C 616 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " -0.122 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.094 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 6.99e-02 6.10e+01 pdb=" CG ASN A1074 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG A1312 " 0.084 2.00e-02 2.50e+03 ... (remaining 5029 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 351 2.62 - 3.19: 25255 3.19 - 3.76: 44048 3.76 - 4.33: 62512 4.33 - 4.90: 100128 Nonbonded interactions: 232294 Sorted by model distance: nonbonded pdb=" NZ LYS B 529 " pdb=" O ILE E 53 " model vdw 2.056 3.120 nonbonded pdb=" O ILE A 235 " pdb=" CG2 ILE A 235 " model vdw 2.263 3.460 nonbonded pdb=" N HIS A 519 " pdb=" O HIS A 519 " model vdw 2.330 2.496 nonbonded pdb=" C SER F 52 " pdb=" OG SER F 52 " model vdw 2.350 2.616 nonbonded pdb=" NZ LYS A 557 " pdb=" OD2 ASP A 574 " model vdw 2.380 3.120 ... (remaining 232289 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 17 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 185 through 255 or resid 257 through 260 or resid 263 through 337 \ or resid 341 through 396 or resid 400 through 415 or resid 418 through 426 or re \ sid 429 through 441 or resid 450 through 454 or resid 462 through 466 or resid 4 \ 92 through 515 or resid 522 through 618 or resid 641 through 827 or resid 851 th \ rough 1305)) selection = (chain 'B' and (resid 17 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 185 through 260 or resid 263 through 337 or resid 341 through 396 \ or resid 400 through 415 or resid 418 through 426 or resid 429 through 441 or re \ sid 450 through 454 or resid 462 through 466 or resid 492 through 515 or resid 5 \ 22 through 827 or resid 851 through 1305)) selection = (chain 'C' and (resid 17 through 255 or resid 257 through 441 or resid 450 throu \ gh 618 or resid 641 through 827 or resid 851 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.400 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.696 28867 Z= 1.190 Angle : 1.860 49.321 39364 Z= 1.216 Chirality : 0.116 1.109 4569 Planarity : 0.008 0.089 4997 Dihedral : 10.457 89.756 10962 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.32 % Allowed : 0.68 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.13), residues: 3461 helix: 0.67 (0.18), residues: 677 sheet: 1.02 (0.18), residues: 814 loop : 0.13 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 454 TYR 0.077 0.008 TYR C 37 PHE 0.036 0.006 PHE B 58 TRP 0.056 0.010 TRP B 258 HIS 0.007 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.02175 (28778) covalent geometry : angle 1.84888 (39144) SS BOND : bond 0.12087 ( 47) SS BOND : angle 3.50569 ( 94) hydrogen bonds : bond 0.16609 ( 1187) hydrogen bonds : angle 8.09224 ( 3303) link_BETA1-4 : bond 0.06813 ( 6) link_BETA1-4 : angle 4.71580 ( 18) link_BETA1-6 : bond 0.05491 ( 1) link_BETA1-6 : angle 3.38275 ( 3) link_NAG-ASN : bond 0.07884 ( 35) link_NAG-ASN : angle 2.68264 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 386 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 VAL cc_start: 0.9100 (p) cc_final: 0.8853 (m) REVERT: H 48 MET cc_start: 0.8429 (mtp) cc_final: 0.7413 (mtm) REVERT: H 75 THR cc_start: 0.8258 (p) cc_final: 0.8004 (p) REVERT: H 82 LEU cc_start: 0.7411 (tp) cc_final: 0.7015 (tp) REVERT: H 86 ASP cc_start: 0.7823 (m-30) cc_final: 0.7434 (m-30) REVERT: H 99 ASP cc_start: 0.6598 (t0) cc_final: 0.6240 (p0) REVERT: L 5 THR cc_start: 0.9193 (m) cc_final: 0.8986 (p) REVERT: L 24 ARG cc_start: 0.9218 (ttm170) cc_final: 0.9008 (tmm160) REVERT: L 35 TRP cc_start: 0.7041 (m100) cc_final: 0.5978 (m100) REVERT: L 42 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8299 (mp10) REVERT: L 58 ILE cc_start: 0.8083 (tt) cc_final: 0.7146 (tt) REVERT: L 95 LEU cc_start: 0.7817 (tp) cc_final: 0.7595 (tp) REVERT: L 102 THR cc_start: 0.7465 (p) cc_final: 0.7187 (p) REVERT: C 33 THR cc_start: 0.7788 (p) cc_final: 0.7438 (t) REVERT: C 153 MET cc_start: 0.4619 (ptt) cc_final: 0.2890 (pmm) REVERT: C 988 GLU cc_start: 0.8592 (tp30) cc_final: 0.8186 (tp30) REVERT: C 1005 GLN cc_start: 0.8507 (tp40) cc_final: 0.7961 (tm-30) REVERT: B 79 PHE cc_start: 0.4446 (m-10) cc_final: 0.4224 (m-80) REVERT: E 39 GLN cc_start: 0.5577 (tt0) cc_final: 0.5273 (tt0) REVERT: E 75 THR cc_start: 0.8642 (p) cc_final: 0.8332 (m) REVERT: E 79 PHE cc_start: 0.8138 (m-80) cc_final: 0.7612 (m-10) REVERT: E 94 LEU cc_start: 0.6860 (mt) cc_final: 0.6643 (mp) REVERT: E 99 ASP cc_start: 0.6558 (t0) cc_final: 0.6274 (t0) REVERT: F 47 LEU cc_start: 0.9159 (mt) cc_final: 0.8909 (mp) outliers start: 10 outliers final: 3 residues processed: 395 average time/residue: 0.2079 time to fit residues: 123.3032 Evaluate side-chains 219 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain F residue 46 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 90 HIS A 134 GLN A 188 ASN A1002 GLN C 49 HIS B 239 GLN B 655 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.085866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.059644 restraints weight = 97188.444| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.63 r_work: 0.3190 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28867 Z= 0.174 Angle : 0.793 38.594 39364 Z= 0.392 Chirality : 0.048 0.304 4569 Planarity : 0.005 0.050 4997 Dihedral : 6.076 54.853 4660 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.07 % Allowed : 4.24 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3461 helix: 2.49 (0.20), residues: 651 sheet: 0.71 (0.18), residues: 849 loop : -0.36 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.028 0.002 TYR L 91 PHE 0.036 0.002 PHE F 83 TRP 0.030 0.002 TRP E 98 HIS 0.009 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00374 (28778) covalent geometry : angle 0.77709 (39144) SS BOND : bond 0.00401 ( 47) SS BOND : angle 1.24484 ( 94) hydrogen bonds : bond 0.06109 ( 1187) hydrogen bonds : angle 6.32438 ( 3303) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 2.34672 ( 18) link_BETA1-6 : bond 0.00316 ( 1) link_BETA1-6 : angle 1.71013 ( 3) link_NAG-ASN : bond 0.00545 ( 35) link_NAG-ASN : angle 2.81470 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 VAL cc_start: 0.8819 (t) cc_final: 0.8613 (p) REVERT: H 66 ARG cc_start: 0.7506 (mtm110) cc_final: 0.7268 (mtm-85) REVERT: H 72 ASP cc_start: 0.8357 (t0) cc_final: 0.7871 (t0) REVERT: H 75 THR cc_start: 0.8510 (p) cc_final: 0.8077 (p) REVERT: H 80 MET cc_start: 0.7861 (tmm) cc_final: 0.7592 (tmm) REVERT: H 82 LEU cc_start: 0.8344 (mt) cc_final: 0.7801 (mt) REVERT: L 35 TRP cc_start: 0.6786 (m100) cc_final: 0.6100 (m100) REVERT: L 37 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7814 (tp40) REVERT: A 519 HIS cc_start: 0.6818 (t-90) cc_final: 0.6491 (t-90) REVERT: A 544 ASN cc_start: 0.8587 (t0) cc_final: 0.7960 (t0) REVERT: C 88 ASP cc_start: 0.8779 (m-30) cc_final: 0.8400 (p0) REVERT: C 153 MET cc_start: 0.5148 (ptt) cc_final: 0.3222 (pmm) REVERT: C 278 LYS cc_start: 0.8680 (tttt) cc_final: 0.8432 (ttmm) REVERT: B 79 PHE cc_start: 0.4651 (m-80) cc_final: 0.4374 (m-80) REVERT: B 376 THR cc_start: 0.8844 (m) cc_final: 0.8301 (p) REVERT: E 12 LYS cc_start: 0.7249 (mmtt) cc_final: 0.7028 (mmtt) REVERT: E 23 LYS cc_start: 0.7063 (tptp) cc_final: 0.6856 (tptp) REVERT: E 82 LEU cc_start: 0.6728 (mp) cc_final: 0.6208 (mt) REVERT: E 99 ASP cc_start: 0.6722 (t0) cc_final: 0.5563 (t0) REVERT: F 45 ARG cc_start: 0.7775 (tpt-90) cc_final: 0.7346 (tpt-90) REVERT: F 54 ARG cc_start: 0.7997 (ptp90) cc_final: 0.7344 (ptp-110) REVERT: F 75 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7425 (mm) REVERT: F 79 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6784 (mp0) outliers start: 33 outliers final: 17 residues processed: 301 average time/residue: 0.1963 time to fit residues: 91.3948 Evaluate side-chains 222 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 94 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 166 optimal weight: 30.0000 chunk 262 optimal weight: 3.9990 chunk 326 optimal weight: 1.9990 chunk 328 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN A 125 ASN A1048 HIS C 218 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 97 GLN F 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.087566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.058315 restraints weight = 102443.978| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.70 r_work: 0.3083 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28867 Z= 0.184 Angle : 0.651 11.285 39364 Z= 0.339 Chirality : 0.047 0.458 4569 Planarity : 0.004 0.067 4997 Dihedral : 5.554 54.985 4660 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 1.23 % Allowed : 5.70 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3461 helix: 2.69 (0.20), residues: 663 sheet: 0.48 (0.17), residues: 876 loop : -0.49 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1019 TYR 0.027 0.002 TYR E 102 PHE 0.024 0.002 PHE A 888 TRP 0.014 0.001 TRP E 98 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00414 (28778) covalent geometry : angle 0.63864 (39144) SS BOND : bond 0.00299 ( 47) SS BOND : angle 1.06039 ( 94) hydrogen bonds : bond 0.05505 ( 1187) hydrogen bonds : angle 5.83453 ( 3303) link_BETA1-4 : bond 0.00597 ( 6) link_BETA1-4 : angle 1.66186 ( 18) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 2.30671 ( 3) link_NAG-ASN : bond 0.00494 ( 35) link_NAG-ASN : angle 2.28378 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.8029 (tmm) cc_final: 0.7546 (tmm) REVERT: H 82 LEU cc_start: 0.8368 (mt) cc_final: 0.7830 (mt) REVERT: H 91 TYR cc_start: 0.8086 (m-80) cc_final: 0.7846 (m-80) REVERT: A 519 HIS cc_start: 0.7169 (t-90) cc_final: 0.6727 (t-90) REVERT: C 88 ASP cc_start: 0.8827 (m-30) cc_final: 0.8477 (p0) REVERT: C 104 TRP cc_start: 0.8151 (m-90) cc_final: 0.7798 (m-90) REVERT: C 153 MET cc_start: 0.5169 (ptt) cc_final: 0.3060 (pmm) REVERT: B 79 PHE cc_start: 0.4910 (m-80) cc_final: 0.4651 (m-80) REVERT: B 376 THR cc_start: 0.8834 (m) cc_final: 0.8347 (p) REVERT: B 674 TYR cc_start: 0.5404 (m-80) cc_final: 0.5195 (m-80) REVERT: B 740 MET cc_start: 0.8807 (tpt) cc_final: 0.8489 (tpp) REVERT: B 940 SER cc_start: 0.9079 (m) cc_final: 0.8875 (p) REVERT: B 1005 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8243 (tm-30) REVERT: E 12 LYS cc_start: 0.7252 (mmtt) cc_final: 0.7038 (mmtt) REVERT: E 80 MET cc_start: 0.8215 (tmm) cc_final: 0.7995 (tpt) REVERT: E 82 LEU cc_start: 0.6384 (mp) cc_final: 0.5979 (mt) REVERT: F 54 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7513 (ptp-110) outliers start: 38 outliers final: 24 residues processed: 242 average time/residue: 0.1951 time to fit residues: 73.9093 Evaluate side-chains 217 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 124 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 38 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN B 394 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN E 97 GLN F 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.086487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.057217 restraints weight = 102003.377| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.68 r_work: 0.3059 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28867 Z= 0.190 Angle : 0.635 15.234 39364 Z= 0.326 Chirality : 0.046 0.301 4569 Planarity : 0.004 0.060 4997 Dihedral : 5.378 57.164 4660 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.83 % Favored : 97.05 % Rotamer: Outliers : 1.52 % Allowed : 6.67 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3461 helix: 2.83 (0.20), residues: 650 sheet: 0.42 (0.17), residues: 898 loop : -0.66 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 66 TYR 0.022 0.002 TYR F 49 PHE 0.022 0.002 PHE A 888 TRP 0.011 0.001 TRP L 35 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00436 (28778) covalent geometry : angle 0.62455 (39144) SS BOND : bond 0.00303 ( 47) SS BOND : angle 0.98705 ( 94) hydrogen bonds : bond 0.05170 ( 1187) hydrogen bonds : angle 5.64739 ( 3303) link_BETA1-4 : bond 0.00310 ( 6) link_BETA1-4 : angle 1.38282 ( 18) link_BETA1-6 : bond 0.00178 ( 1) link_BETA1-6 : angle 1.49296 ( 3) link_NAG-ASN : bond 0.00303 ( 35) link_NAG-ASN : angle 2.10980 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8197 (mttp) REVERT: H 80 MET cc_start: 0.8071 (tmm) cc_final: 0.7742 (tmm) REVERT: H 82 LEU cc_start: 0.8502 (mt) cc_final: 0.8073 (mt) REVERT: H 90 TYR cc_start: 0.8975 (m-80) cc_final: 0.8693 (m-80) REVERT: H 91 TYR cc_start: 0.8232 (m-80) cc_final: 0.7832 (m-80) REVERT: H 95 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7599 (ptm-80) REVERT: A 519 HIS cc_start: 0.7386 (t-90) cc_final: 0.6875 (t-90) REVERT: C 153 MET cc_start: 0.5354 (ptt) cc_final: 0.3086 (pmm) REVERT: B 79 PHE cc_start: 0.4962 (m-80) cc_final: 0.4739 (m-80) REVERT: B 376 THR cc_start: 0.8899 (m) cc_final: 0.8419 (p) REVERT: B 380 TYR cc_start: 0.8909 (m-80) cc_final: 0.8623 (m-80) REVERT: B 740 MET cc_start: 0.8824 (tpt) cc_final: 0.8592 (tpp) REVERT: B 940 SER cc_start: 0.9127 (m) cc_final: 0.8904 (p) REVERT: B 1005 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8224 (tm-30) REVERT: F 49 TYR cc_start: 0.4334 (m-10) cc_final: 0.4108 (m-10) REVERT: F 54 ARG cc_start: 0.8143 (ptp90) cc_final: 0.7753 (ptp-110) REVERT: F 62 PHE cc_start: 0.8595 (m-80) cc_final: 0.8382 (m-80) outliers start: 47 outliers final: 27 residues processed: 251 average time/residue: 0.1935 time to fit residues: 75.8931 Evaluate side-chains 225 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 218 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 349 optimal weight: 0.8980 chunk 251 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 309 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 39 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.086833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.057730 restraints weight = 101694.511| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.67 r_work: 0.3147 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28867 Z= 0.147 Angle : 0.598 14.144 39364 Z= 0.308 Chirality : 0.045 0.293 4569 Planarity : 0.004 0.046 4997 Dihedral : 5.168 51.137 4658 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.71 % Rotamer: Outliers : 1.23 % Allowed : 7.61 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3461 helix: 2.95 (0.20), residues: 649 sheet: 0.38 (0.17), residues: 905 loop : -0.71 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 38 TYR 0.017 0.001 TYR B1067 PHE 0.029 0.001 PHE H 29 TRP 0.033 0.001 TRP L 96 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00330 (28778) covalent geometry : angle 0.58684 (39144) SS BOND : bond 0.00327 ( 47) SS BOND : angle 1.19713 ( 94) hydrogen bonds : bond 0.04854 ( 1187) hydrogen bonds : angle 5.47307 ( 3303) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 1.33926 ( 18) link_BETA1-6 : bond 0.00007 ( 1) link_BETA1-6 : angle 2.09261 ( 3) link_NAG-ASN : bond 0.00336 ( 35) link_NAG-ASN : angle 2.02172 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8217 (mttp) REVERT: H 82 LEU cc_start: 0.8501 (mt) cc_final: 0.8112 (mt) REVERT: H 91 TYR cc_start: 0.8242 (m-80) cc_final: 0.7834 (m-80) REVERT: H 95 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7483 (ptm-80) REVERT: L 96 TRP cc_start: 0.7613 (m-10) cc_final: 0.7266 (m-10) REVERT: A 519 HIS cc_start: 0.7395 (t-90) cc_final: 0.6957 (t-90) REVERT: C 153 MET cc_start: 0.5345 (ptt) cc_final: 0.3344 (pmm) REVERT: B 18 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7794 (mp) REVERT: B 376 THR cc_start: 0.8879 (m) cc_final: 0.8401 (p) REVERT: B 380 TYR cc_start: 0.8879 (m-80) cc_final: 0.8546 (m-80) REVERT: B 740 MET cc_start: 0.8846 (tpt) cc_final: 0.8612 (tpp) REVERT: B 1005 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8134 (tm-30) REVERT: E 12 LYS cc_start: 0.7399 (mmtt) cc_final: 0.7196 (mmtt) REVERT: F 54 ARG cc_start: 0.8108 (ptp90) cc_final: 0.7786 (ptp-110) REVERT: F 62 PHE cc_start: 0.8560 (m-80) cc_final: 0.8245 (m-80) outliers start: 38 outliers final: 24 residues processed: 236 average time/residue: 0.2007 time to fit residues: 73.6358 Evaluate side-chains 219 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 187 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 304 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 226 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.083828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056774 restraints weight = 98739.181| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.60 r_work: 0.3154 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28867 Z= 0.146 Angle : 0.594 14.605 39364 Z= 0.305 Chirality : 0.044 0.293 4569 Planarity : 0.004 0.054 4997 Dihedral : 5.064 51.735 4658 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % Rotamer: Outliers : 1.39 % Allowed : 7.96 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3461 helix: 2.99 (0.20), residues: 647 sheet: 0.39 (0.17), residues: 894 loop : -0.74 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 66 TYR 0.019 0.001 TYR C1067 PHE 0.040 0.002 PHE B 79 TRP 0.031 0.001 TRP B 353 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00330 (28778) covalent geometry : angle 0.58257 (39144) SS BOND : bond 0.00333 ( 47) SS BOND : angle 1.39959 ( 94) hydrogen bonds : bond 0.04697 ( 1187) hydrogen bonds : angle 5.37123 ( 3303) link_BETA1-4 : bond 0.00322 ( 6) link_BETA1-4 : angle 1.16143 ( 18) link_BETA1-6 : bond 0.00303 ( 1) link_BETA1-6 : angle 1.50110 ( 3) link_NAG-ASN : bond 0.00305 ( 35) link_NAG-ASN : angle 1.91141 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8198 (ttmt) REVERT: H 39 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: H 82 LEU cc_start: 0.8371 (mt) cc_final: 0.7903 (mt) REVERT: H 91 TYR cc_start: 0.8202 (m-80) cc_final: 0.7730 (m-80) REVERT: H 95 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7568 (ptm-80) REVERT: L 100 GLN cc_start: 0.7707 (mp10) cc_final: 0.7494 (mp10) REVERT: A 519 HIS cc_start: 0.7503 (t-90) cc_final: 0.7043 (t-90) REVERT: C 153 MET cc_start: 0.5197 (ptt) cc_final: 0.3221 (pmm) REVERT: B 376 THR cc_start: 0.8875 (m) cc_final: 0.8425 (p) REVERT: B 380 TYR cc_start: 0.8868 (m-80) cc_final: 0.8588 (m-80) REVERT: B 740 MET cc_start: 0.8865 (tpt) cc_final: 0.8632 (tpp) REVERT: B 1005 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8120 (tm-30) REVERT: F 54 ARG cc_start: 0.8097 (ptp90) cc_final: 0.7798 (ptp-110) outliers start: 43 outliers final: 31 residues processed: 231 average time/residue: 0.1925 time to fit residues: 69.2434 Evaluate side-chains 227 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 139 optimal weight: 0.3980 chunk 303 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 0.0040 chunk 176 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.085986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.058095 restraints weight = 96802.736| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.85 r_work: 0.3157 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28867 Z= 0.119 Angle : 0.577 14.405 39364 Z= 0.294 Chirality : 0.044 0.292 4569 Planarity : 0.004 0.050 4997 Dihedral : 4.915 52.815 4658 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.06 % Favored : 96.79 % Rotamer: Outliers : 1.29 % Allowed : 8.48 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3461 helix: 3.06 (0.20), residues: 649 sheet: 0.46 (0.17), residues: 883 loop : -0.75 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 66 TYR 0.026 0.001 TYR F 49 PHE 0.033 0.001 PHE B 79 TRP 0.025 0.001 TRP B 353 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00263 (28778) covalent geometry : angle 0.56644 (39144) SS BOND : bond 0.00231 ( 47) SS BOND : angle 1.12881 ( 94) hydrogen bonds : bond 0.04400 ( 1187) hydrogen bonds : angle 5.23550 ( 3303) link_BETA1-4 : bond 0.00378 ( 6) link_BETA1-4 : angle 1.15426 ( 18) link_BETA1-6 : bond 0.00130 ( 1) link_BETA1-6 : angle 2.06369 ( 3) link_NAG-ASN : bond 0.00301 ( 35) link_NAG-ASN : angle 1.87409 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8134 (ttmt) REVERT: H 80 MET cc_start: 0.7958 (tmm) cc_final: 0.7442 (tmm) REVERT: H 81 GLU cc_start: 0.8320 (tp30) cc_final: 0.8010 (tp30) REVERT: H 82 LEU cc_start: 0.7985 (mt) cc_final: 0.7610 (mt) REVERT: H 91 TYR cc_start: 0.8198 (m-80) cc_final: 0.7759 (m-80) REVERT: H 95 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7529 (ptm-80) REVERT: A 519 HIS cc_start: 0.7582 (t-90) cc_final: 0.7096 (t-90) REVERT: C 153 MET cc_start: 0.5134 (ptt) cc_final: 0.3224 (pmm) REVERT: C 342 PHE cc_start: 0.8678 (p90) cc_final: 0.8255 (p90) REVERT: B 376 THR cc_start: 0.8832 (m) cc_final: 0.8355 (p) REVERT: B 380 TYR cc_start: 0.8865 (m-80) cc_final: 0.8537 (m-80) REVERT: B 740 MET cc_start: 0.8868 (tpt) cc_final: 0.8648 (tpp) REVERT: B 1005 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8107 (tm-30) REVERT: F 54 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7769 (ptp-110) outliers start: 40 outliers final: 28 residues processed: 228 average time/residue: 0.2007 time to fit residues: 71.5507 Evaluate side-chains 219 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 201 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 338 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 655 HIS B 388 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.081910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.055640 restraints weight = 98855.597| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.55 r_work: 0.3066 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 28867 Z= 0.212 Angle : 0.649 14.897 39364 Z= 0.327 Chirality : 0.045 0.278 4569 Planarity : 0.004 0.070 4997 Dihedral : 5.080 52.788 4658 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.98 % Rotamer: Outliers : 1.33 % Allowed : 8.48 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3461 helix: 2.82 (0.20), residues: 659 sheet: 0.31 (0.17), residues: 922 loop : -0.88 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 102 TYR 0.031 0.002 TYR C 421 PHE 0.034 0.002 PHE B 79 TRP 0.019 0.001 TRP B 353 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00491 (28778) covalent geometry : angle 0.63982 (39144) SS BOND : bond 0.00307 ( 47) SS BOND : angle 1.14391 ( 94) hydrogen bonds : bond 0.04995 ( 1187) hydrogen bonds : angle 5.34919 ( 3303) link_BETA1-4 : bond 0.00325 ( 6) link_BETA1-4 : angle 1.06195 ( 18) link_BETA1-6 : bond 0.00364 ( 1) link_BETA1-6 : angle 1.55151 ( 3) link_NAG-ASN : bond 0.00320 ( 35) link_NAG-ASN : angle 1.94021 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8228 (ttmt) REVERT: H 19 LYS cc_start: 0.8416 (tppp) cc_final: 0.8095 (tppt) REVERT: H 39 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8077 (tp40) REVERT: H 82 LEU cc_start: 0.8265 (mt) cc_final: 0.7909 (mt) REVERT: H 91 TYR cc_start: 0.8271 (m-80) cc_final: 0.7791 (m-80) REVERT: H 95 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7649 (ptm-80) REVERT: L 91 TYR cc_start: 0.5601 (t80) cc_final: 0.5202 (t80) REVERT: A 516 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 519 HIS cc_start: 0.7701 (t-90) cc_final: 0.6919 (t-90) REVERT: A 1019 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8604 (ttp80) REVERT: C 153 MET cc_start: 0.5079 (ptt) cc_final: 0.3164 (pmm) REVERT: C 342 PHE cc_start: 0.8642 (p90) cc_final: 0.8187 (p90) REVERT: B 376 THR cc_start: 0.8832 (m) cc_final: 0.8414 (p) REVERT: B 380 TYR cc_start: 0.8878 (m-80) cc_final: 0.8515 (m-10) REVERT: B 740 MET cc_start: 0.9010 (tpt) cc_final: 0.8771 (tpp) REVERT: B 1005 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8175 (tm-30) REVERT: E 80 MET cc_start: 0.7278 (tpt) cc_final: 0.6948 (tpt) REVERT: F 45 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7484 (mtt90) REVERT: F 54 ARG cc_start: 0.8151 (ptp90) cc_final: 0.7686 (ptp-110) outliers start: 41 outliers final: 33 residues processed: 219 average time/residue: 0.1956 time to fit residues: 67.1246 Evaluate side-chains 220 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 159 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 325 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 chunk 194 optimal weight: 0.6980 chunk 196 optimal weight: 0.0270 chunk 284 optimal weight: 0.0770 chunk 177 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.060289 restraints weight = 101804.245| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.67 r_work: 0.3104 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28867 Z= 0.106 Angle : 0.589 15.946 39364 Z= 0.295 Chirality : 0.044 0.291 4569 Planarity : 0.004 0.054 4997 Dihedral : 4.855 53.190 4658 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 1.13 % Allowed : 9.09 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3461 helix: 3.16 (0.20), residues: 644 sheet: 0.46 (0.17), residues: 896 loop : -0.79 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 995 TYR 0.035 0.001 TYR C 421 PHE 0.033 0.001 PHE B 79 TRP 0.024 0.001 TRP B 353 HIS 0.003 0.000 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00225 (28778) covalent geometry : angle 0.58173 (39144) SS BOND : bond 0.00222 ( 47) SS BOND : angle 1.00239 ( 94) hydrogen bonds : bond 0.04248 ( 1187) hydrogen bonds : angle 5.13021 ( 3303) link_BETA1-4 : bond 0.00408 ( 6) link_BETA1-4 : angle 0.99357 ( 18) link_BETA1-6 : bond 0.00425 ( 1) link_BETA1-6 : angle 1.19357 ( 3) link_NAG-ASN : bond 0.00341 ( 35) link_NAG-ASN : angle 1.73227 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (ttmt) REVERT: H 19 LYS cc_start: 0.8311 (tppp) cc_final: 0.7956 (tppt) REVERT: H 39 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7988 (tp40) REVERT: H 91 TYR cc_start: 0.8219 (m-80) cc_final: 0.7858 (m-80) REVERT: H 95 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7615 (ptm-80) REVERT: L 91 TYR cc_start: 0.5463 (t80) cc_final: 0.5051 (t80) REVERT: A 516 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6485 (tm-30) REVERT: A 519 HIS cc_start: 0.7703 (t-90) cc_final: 0.6878 (t-90) REVERT: C 153 MET cc_start: 0.4932 (ptt) cc_final: 0.3059 (pmm) REVERT: C 342 PHE cc_start: 0.8638 (p90) cc_final: 0.8214 (p90) REVERT: B 380 TYR cc_start: 0.8862 (m-80) cc_final: 0.8564 (m-80) REVERT: B 740 MET cc_start: 0.8823 (tpt) cc_final: 0.8609 (tpp) REVERT: B 855 PHE cc_start: 0.8419 (m-80) cc_final: 0.8201 (m-80) REVERT: B 1002 GLN cc_start: 0.8635 (tp40) cc_final: 0.8422 (tm-30) REVERT: B 1005 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8112 (tm-30) REVERT: F 45 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7360 (mtt90) REVERT: F 54 ARG cc_start: 0.8014 (ptp90) cc_final: 0.7727 (ptp-110) outliers start: 35 outliers final: 28 residues processed: 218 average time/residue: 0.2010 time to fit residues: 68.5154 Evaluate side-chains 219 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 169 optimal weight: 20.0000 chunk 306 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 343 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN A 125 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.081796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055586 restraints weight = 98443.796| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.53 r_work: 0.3107 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28867 Z= 0.230 Angle : 0.658 16.005 39364 Z= 0.331 Chirality : 0.046 0.276 4569 Planarity : 0.004 0.050 4997 Dihedral : 5.046 51.628 4658 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.33 % Favored : 95.52 % Rotamer: Outliers : 1.17 % Allowed : 9.29 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3461 helix: 2.87 (0.20), residues: 658 sheet: 0.26 (0.17), residues: 935 loop : -0.97 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 66 TYR 0.035 0.002 TYR C 421 PHE 0.038 0.002 PHE H 29 TRP 0.019 0.001 TRP B 353 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00539 (28778) covalent geometry : angle 0.64940 (39144) SS BOND : bond 0.00303 ( 47) SS BOND : angle 1.08968 ( 94) hydrogen bonds : bond 0.04954 ( 1187) hydrogen bonds : angle 5.27813 ( 3303) link_BETA1-4 : bond 0.00217 ( 6) link_BETA1-4 : angle 0.99324 ( 18) link_BETA1-6 : bond 0.00093 ( 1) link_BETA1-6 : angle 1.60592 ( 3) link_NAG-ASN : bond 0.00303 ( 35) link_NAG-ASN : angle 1.89994 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: H 19 LYS cc_start: 0.8302 (tppp) cc_final: 0.7922 (tppt) REVERT: H 38 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8275 (ttm110) REVERT: H 39 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7980 (tp40) REVERT: H 80 MET cc_start: 0.8210 (tmm) cc_final: 0.7901 (tmm) REVERT: H 91 TYR cc_start: 0.8347 (m-80) cc_final: 0.7991 (m-80) REVERT: H 95 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7840 (ttp80) REVERT: L 69 THR cc_start: 0.8680 (p) cc_final: 0.8374 (t) REVERT: L 91 TYR cc_start: 0.5436 (t80) cc_final: 0.5197 (t80) REVERT: A 516 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6420 (tm-30) REVERT: A 519 HIS cc_start: 0.7838 (t-90) cc_final: 0.7105 (t-90) REVERT: C 153 MET cc_start: 0.5015 (ptt) cc_final: 0.3046 (pmm) REVERT: C 342 PHE cc_start: 0.8619 (p90) cc_final: 0.8203 (p90) REVERT: C 353 TRP cc_start: 0.3973 (t-100) cc_final: 0.3701 (t-100) REVERT: B 380 TYR cc_start: 0.8896 (m-80) cc_final: 0.8540 (m-10) REVERT: B 740 MET cc_start: 0.8996 (tpt) cc_final: 0.8734 (tpp) REVERT: B 855 PHE cc_start: 0.8306 (m-80) cc_final: 0.8049 (m-80) REVERT: B 1002 GLN cc_start: 0.8687 (tp40) cc_final: 0.8464 (tm-30) REVERT: B 1005 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8163 (tm-30) REVERT: E 12 LYS cc_start: 0.7827 (tptt) cc_final: 0.7445 (tptt) REVERT: E 23 LYS cc_start: 0.6577 (tptp) cc_final: 0.6348 (tptp) REVERT: F 45 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7361 (mtt90) REVERT: F 54 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7650 (ptp-110) outliers start: 36 outliers final: 32 residues processed: 208 average time/residue: 0.1988 time to fit residues: 64.4337 Evaluate side-chains 218 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 189 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.085327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.058351 restraints weight = 97393.867| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.76 r_work: 0.3142 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28867 Z= 0.128 Angle : 0.592 16.903 39364 Z= 0.297 Chirality : 0.044 0.284 4569 Planarity : 0.004 0.048 4997 Dihedral : 4.932 52.329 4658 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.27 % Rotamer: Outliers : 1.17 % Allowed : 9.42 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3461 helix: 3.09 (0.20), residues: 645 sheet: 0.33 (0.17), residues: 901 loop : -0.92 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 66 TYR 0.035 0.001 TYR C 421 PHE 0.034 0.001 PHE H 29 TRP 0.023 0.001 TRP B 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00289 (28778) covalent geometry : angle 0.58383 (39144) SS BOND : bond 0.00247 ( 47) SS BOND : angle 0.99547 ( 94) hydrogen bonds : bond 0.04435 ( 1187) hydrogen bonds : angle 5.14864 ( 3303) link_BETA1-4 : bond 0.00346 ( 6) link_BETA1-4 : angle 0.93471 ( 18) link_BETA1-6 : bond 0.00261 ( 1) link_BETA1-6 : angle 1.30287 ( 3) link_NAG-ASN : bond 0.00278 ( 35) link_NAG-ASN : angle 1.73756 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7926.24 seconds wall clock time: 135 minutes 59.12 seconds (8159.12 seconds total)