Starting phenix.real_space_refine on Thu Mar 5 20:12:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s6l_24879/03_2026/7s6l_24879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s6l_24879/03_2026/7s6l_24879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s6l_24879/03_2026/7s6l_24879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s6l_24879/03_2026/7s6l_24879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s6l_24879/03_2026/7s6l_24879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s6l_24879/03_2026/7s6l_24879.map" } resolution = 4.0 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= -0.001 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 114 5.16 5 C 15773 2.51 5 N 4070 2.21 5 O 4798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 24755 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7688 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 53, 'TRANS': 930} Chain breaks: 9 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 755 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "B" Number of atoms: 7436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7436 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 51, 'TRANS': 897} Chain breaks: 13 Chain: "C" Number of atoms: 7509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7509 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 52, 'TRANS': 908} Chain breaks: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.10, per 1000 atoms: 0.25 Number of scatterers: 24755 At special positions: 0 Unit cell: (129.95, 139.15, 233.45, 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 114 16.00 O 4798 8.00 N 4070 7.00 C 15773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.11 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 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-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 343 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B1134 " " NAG B1305 " - " ASN B1074 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1098 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 51 sheets defined 25.9% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.733A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.936A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.754A 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 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: 3.777A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.515A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.724A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.870A 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 'H' and resid 27 through 30 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.189A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (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 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 5.072A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.468A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.625A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' 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 removed outlier: 4.931A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.827A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.505A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 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 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 removed outlier: 3.968A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.572A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.518A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR B 323 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASN B 542 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.518A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.594A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.417A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.227A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.319A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.533A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.609A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.647A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.647A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.583A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.706A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.443A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.378A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.615A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.571A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.089A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 714 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 719 through 728 removed outlier: 6.345A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD9, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.807A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.898A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.035A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.315A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.913A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.752A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.040A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.040A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.601A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.648A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.835A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.275A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.275A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.756A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3072 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: 7.06 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6598 1.33 - 1.48: 8123 1.48 - 1.62: 10421 1.62 - 1.77: 37 1.77 - 1.91: 119 Bond restraints: 25298 Sorted by residual: bond pdb=" CB LEU B 242 " pdb=" CG LEU B 242 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" CG TYR A 200 " pdb=" CD1 TYR A 200 " ideal model delta sigma weight residual 1.389 1.516 -0.127 2.10e-02 2.27e+03 3.66e+01 bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.392 -0.066 1.10e-02 8.26e+03 3.56e+01 bond pdb=" CG TYR B 200 " pdb=" CD1 TYR B 200 " ideal model delta sigma weight residual 1.389 1.513 -0.124 2.10e-02 2.27e+03 3.47e+01 ... (remaining 25293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 34344 7.28 - 14.55: 66 14.55 - 21.83: 0 21.83 - 29.10: 0 29.10 - 36.38: 1 Bond angle restraints: 34411 Sorted by residual: angle pdb=" C2 NAG B1302 " pdb=" N2 NAG B1302 " pdb=" C7 NAG B1302 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C PRO B 792 " pdb=" N PRO B 793 " pdb=" CA PRO B 793 " ideal model delta sigma weight residual 119.56 128.09 -8.53 1.01e+00 9.80e-01 7.13e+01 angle pdb=" C ILE H 52 " pdb=" N PRO H 52A" pdb=" CA PRO H 52A" ideal model delta sigma weight residual 119.56 128.10 -8.54 1.02e+00 9.61e-01 7.00e+01 angle pdb=" C ASP A1139 " pdb=" N PRO A1140 " pdb=" CA PRO A1140 " ideal model delta sigma weight residual 119.56 128.03 -8.47 1.02e+00 9.61e-01 6.89e+01 angle pdb=" C LYS C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta sigma weight residual 119.56 127.92 -8.36 1.02e+00 9.61e-01 6.71e+01 ... (remaining 34406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14987 17.86 - 35.72: 365 35.72 - 53.57: 85 53.57 - 71.43: 44 71.43 - 89.29: 25 Dihedral angle restraints: 15506 sinusoidal: 6441 harmonic: 9065 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 161.40 -68.40 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 159.46 -66.46 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.69 57.69 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 15503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3005 0.112 - 0.223: 802 0.223 - 0.335: 138 0.335 - 0.446: 54 0.446 - 0.558: 15 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+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 9.77e+01 ... (remaining 4011 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " 0.093 2.00e-02 2.50e+03 9.76e-02 1.19e+02 pdb=" CG ASN B 801 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " -0.151 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.090 2.00e-02 2.50e+03 9.41e-02 1.11e+02 pdb=" CG ASN B 616 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " 0.146 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.077 2.00e-02 2.50e+03 8.22e-02 8.45e+01 pdb=" CG ASN A 616 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.129 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.100 2.00e-02 2.50e+03 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7893 2.85 - 3.36: 23278 3.36 - 3.87: 43222 3.87 - 4.39: 51527 4.39 - 4.90: 81919 Nonbonded interactions: 207839 Sorted by model distance: nonbonded pdb=" N ALA C 520 " pdb=" O ALA C 520 " model vdw 2.336 2.496 nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.395 3.120 nonbonded pdb=" N ALA A 520 " pdb=" O ALA A 520 " model vdw 2.401 2.496 nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.426 2.496 nonbonded pdb=" OD2 ASP A 571 " pdb=" NZ LYS C 964 " model vdw 2.429 3.120 ... (remaining 207834 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 27 through 66 or resid 82 through 113 or resid 116 through \ 134 or resid 166 through 263 or resid 265 through 323 or resid 327 through 442 \ or resid 448 through 454 or resid 462 through 470 or resid 491 through 500 or re \ sid 503 through 676 or resid 690 through 826 or resid 856 through 1304)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 210 or resid 215 through \ 454 or resid 462 through 470 or resid 491 through 826 or resid 856 through 1304 \ )) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 134 or resid 166 through 196 or resid 200 through 210 or resid 215 through 323 \ or resid 327 through 442 or resid 448 through 500 or resid 503 through 826 or re \ sid 856 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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 group one per residue 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.660 Find NCS groups from input model: 0.700 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.020 0.127 25367 Z= 1.040 Angle : 1.747 36.379 34579 Z= 1.171 Chirality : 0.113 0.558 4014 Planarity : 0.009 0.050 4405 Dihedral : 9.975 89.290 9541 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.74 (0.14), residues: 3043 helix: 0.26 (0.18), residues: 681 sheet: 1.09 (0.19), residues: 641 loop : 0.49 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 905 TYR 0.079 0.010 TYR B1067 PHE 0.045 0.006 PHE L 98 TRP 0.044 0.012 TRP H 103 HIS 0.008 0.002 HIS H 100G Details of bonding type rmsd covalent geometry : bond 0.01966 (25298) covalent geometry : angle 1.73750 (34411) SS BOND : bond 0.01699 ( 39) SS BOND : angle 2.78906 ( 78) hydrogen bonds : bond 0.16114 ( 1098) hydrogen bonds : angle 8.48639 ( 3072) link_BETA1-4 : bond 0.06983 ( 7) link_BETA1-4 : angle 4.78611 ( 21) link_NAG-ASN : bond 0.08012 ( 23) link_NAG-ASN : angle 2.84215 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9254 (mt) cc_final: 0.9021 (tp) REVERT: A 759 PHE cc_start: 0.8910 (t80) cc_final: 0.8617 (t80) REVERT: A 869 MET cc_start: 0.9497 (mtm) cc_final: 0.9034 (mtp) REVERT: H 58 MET cc_start: 0.2865 (mpt) cc_final: 0.2228 (tmm) REVERT: H 79 TYR cc_start: 0.8740 (m-80) cc_final: 0.8083 (m-80) REVERT: H 81 GLU cc_start: 0.8369 (tt0) cc_final: 0.8008 (tm-30) REVERT: B 195 LYS cc_start: 0.8831 (pttt) cc_final: 0.8480 (tmtt) REVERT: B 740 MET cc_start: 0.8844 (tpt) cc_final: 0.8353 (tpp) REVERT: B 781 VAL cc_start: 0.9657 (t) cc_final: 0.9332 (m) REVERT: B 1029 MET cc_start: 0.8790 (ttm) cc_final: 0.8553 (tmm) REVERT: C 40 ASP cc_start: 0.9184 (t0) cc_final: 0.8768 (p0) REVERT: C 406 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8355 (mm-30) REVERT: C 759 PHE cc_start: 0.8354 (t80) cc_final: 0.8007 (t80) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.1869 time to fit residues: 45.6109 Evaluate side-chains 72 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 655 HIS A 804 GLN A 914 ASN A 935 GLN A 955 ASN A1005 GLN A1010 GLN A1048 HIS B 439 ASN B 895 GLN B 955 ASN B1011 GLN B1023 ASN B1048 HIS C 334 ASN C 655 HIS C 895 GLN C 955 ASN C1011 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.060036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040325 restraints weight = 199082.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038560 restraints weight = 105774.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038818 restraints weight = 69527.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038986 restraints weight = 54548.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.039223 restraints weight = 47528.069| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 25367 Z= 0.254 Angle : 0.741 9.527 34579 Z= 0.384 Chirality : 0.046 0.268 4014 Planarity : 0.004 0.039 4405 Dihedral : 5.726 51.640 3954 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 0.55 % Allowed : 2.52 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.94 (0.15), residues: 3043 helix: 1.84 (0.20), residues: 675 sheet: 0.65 (0.18), residues: 759 loop : 0.18 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 408 TYR 0.031 0.002 TYR B1067 PHE 0.030 0.002 PHE C 338 TRP 0.027 0.003 TRP B 886 HIS 0.007 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00563 (25298) covalent geometry : angle 0.72598 (34411) SS BOND : bond 0.00579 ( 39) SS BOND : angle 1.21399 ( 78) hydrogen bonds : bond 0.05622 ( 1098) hydrogen bonds : angle 6.83744 ( 3072) link_BETA1-4 : bond 0.00461 ( 7) link_BETA1-4 : angle 2.69134 ( 21) link_NAG-ASN : bond 0.00715 ( 23) link_NAG-ASN : angle 2.84658 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9441 (mt) cc_final: 0.9214 (mp) REVERT: A 869 MET cc_start: 0.9411 (mtm) cc_final: 0.9149 (mtt) REVERT: A 900 MET cc_start: 0.9288 (mtp) cc_final: 0.9020 (mtt) REVERT: H 58 MET cc_start: 0.4454 (mpt) cc_final: 0.3580 (tmm) REVERT: B 390 LEU cc_start: 0.8290 (mm) cc_final: 0.8033 (mm) REVERT: B 436 TRP cc_start: 0.7768 (t60) cc_final: 0.7161 (t60) REVERT: B 731 MET cc_start: 0.8610 (ttm) cc_final: 0.8390 (ttm) REVERT: B 740 MET cc_start: 0.9055 (tpt) cc_final: 0.8792 (tpp) REVERT: B 781 VAL cc_start: 0.9563 (t) cc_final: 0.9218 (m) REVERT: B 869 MET cc_start: 0.9421 (mtp) cc_final: 0.9093 (mtp) REVERT: C 40 ASP cc_start: 0.9142 (t0) cc_final: 0.8832 (p0) REVERT: C 406 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8317 (mm-30) outliers start: 15 outliers final: 4 residues processed: 89 average time/residue: 0.1537 time to fit residues: 23.4259 Evaluate side-chains 63 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 146 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A1023 ASN L 53 ASN L 89 GLN B 895 GLN B 957 GLN B1010 GLN C 207 HIS C1113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.059787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041216 restraints weight = 198467.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.039264 restraints weight = 106188.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039683 restraints weight = 69931.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.039951 restraints weight = 51567.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.040096 restraints weight = 43500.368| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25367 Z= 0.165 Angle : 0.610 11.904 34579 Z= 0.315 Chirality : 0.044 0.334 4014 Planarity : 0.004 0.033 4405 Dihedral : 5.084 53.303 3952 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 0.51 % Allowed : 2.82 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.96 (0.15), residues: 3043 helix: 2.06 (0.20), residues: 678 sheet: 0.54 (0.18), residues: 746 loop : 0.15 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.024 0.002 TYR B1067 PHE 0.038 0.002 PHE A 759 TRP 0.016 0.002 TRP B 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00357 (25298) covalent geometry : angle 0.60124 (34411) SS BOND : bond 0.00437 ( 39) SS BOND : angle 0.82668 ( 78) hydrogen bonds : bond 0.04690 ( 1098) hydrogen bonds : angle 6.11328 ( 3072) link_BETA1-4 : bond 0.00468 ( 7) link_BETA1-4 : angle 1.85162 ( 21) link_NAG-ASN : bond 0.00305 ( 23) link_NAG-ASN : angle 2.03610 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9525 (mt) cc_final: 0.9300 (mp) REVERT: A 1029 MET cc_start: 0.9678 (tpp) cc_final: 0.9357 (tpp) REVERT: H 48 MET cc_start: 0.5755 (mmm) cc_final: 0.5496 (mmm) REVERT: H 58 MET cc_start: 0.4338 (mpt) cc_final: 0.3562 (ttt) REVERT: B 697 MET cc_start: 0.8742 (pmm) cc_final: 0.8475 (pmm) REVERT: B 731 MET cc_start: 0.8587 (ttm) cc_final: 0.8355 (ttm) REVERT: B 740 MET cc_start: 0.9068 (tpt) cc_final: 0.8858 (tpp) REVERT: B 869 MET cc_start: 0.9399 (mtp) cc_final: 0.9033 (mtp) REVERT: C 40 ASP cc_start: 0.9102 (t0) cc_final: 0.8826 (p0) outliers start: 14 outliers final: 4 residues processed: 73 average time/residue: 0.1495 time to fit residues: 19.1823 Evaluate side-chains 54 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 781 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 83 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 284 optimal weight: 0.0570 chunk 12 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B1088 HIS B1113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.059671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.040986 restraints weight = 196810.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.037207 restraints weight = 102816.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037375 restraints weight = 69863.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037560 restraints weight = 55140.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.037847 restraints weight = 48538.201| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25367 Z= 0.125 Angle : 0.545 10.108 34579 Z= 0.283 Chirality : 0.043 0.183 4014 Planarity : 0.004 0.037 4405 Dihedral : 4.861 52.169 3952 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.30 % Favored : 97.63 % Rotamer: Outliers : 0.48 % Allowed : 3.40 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.94 (0.15), residues: 3043 helix: 2.31 (0.21), residues: 655 sheet: 0.42 (0.18), residues: 729 loop : 0.12 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 509 TYR 0.030 0.001 TYR B1067 PHE 0.026 0.001 PHE A 759 TRP 0.036 0.002 TRP L 35 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00268 (25298) covalent geometry : angle 0.53420 (34411) SS BOND : bond 0.00279 ( 39) SS BOND : angle 1.27699 ( 78) hydrogen bonds : bond 0.04183 ( 1098) hydrogen bonds : angle 5.85370 ( 3072) link_BETA1-4 : bond 0.00311 ( 7) link_BETA1-4 : angle 1.63108 ( 21) link_NAG-ASN : bond 0.00233 ( 23) link_NAG-ASN : angle 1.92449 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9510 (mt) cc_final: 0.9279 (mp) REVERT: A 763 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9538 (mp) REVERT: A 869 MET cc_start: 0.9207 (mtt) cc_final: 0.8822 (mpp) REVERT: A 1029 MET cc_start: 0.9684 (tpp) cc_final: 0.9304 (tpp) REVERT: H 58 MET cc_start: 0.4403 (mpt) cc_final: 0.3647 (ttt) REVERT: B 697 MET cc_start: 0.9032 (pmm) cc_final: 0.8561 (pmm) REVERT: B 731 MET cc_start: 0.8505 (ttm) cc_final: 0.8288 (ttm) REVERT: B 869 MET cc_start: 0.9375 (mtp) cc_final: 0.9019 (mtp) REVERT: B 1001 LEU cc_start: 0.9825 (tp) cc_final: 0.9608 (pp) REVERT: C 40 ASP cc_start: 0.9068 (t0) cc_final: 0.8776 (p0) REVERT: C 869 MET cc_start: 0.9469 (mtm) cc_final: 0.8620 (mtm) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 0.1750 time to fit residues: 19.6162 Evaluate side-chains 61 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A1005 GLN L 37 GLN B 439 ASN B 655 HIS C 954 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.039149 restraints weight = 199306.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.037089 restraints weight = 103923.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037314 restraints weight = 68699.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037562 restraints weight = 54098.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037658 restraints weight = 46602.652| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 25367 Z= 0.235 Angle : 0.633 7.788 34579 Z= 0.323 Chirality : 0.043 0.166 4014 Planarity : 0.004 0.041 4405 Dihedral : 5.025 51.219 3952 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 0.69 % Allowed : 3.95 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.66 (0.15), residues: 3043 helix: 1.98 (0.20), residues: 666 sheet: 0.30 (0.19), residues: 733 loop : -0.07 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 509 TYR 0.022 0.002 TYR B1067 PHE 0.024 0.002 PHE B 906 TRP 0.045 0.002 TRP L 35 HIS 0.007 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00514 (25298) covalent geometry : angle 0.62316 (34411) SS BOND : bond 0.00301 ( 39) SS BOND : angle 1.16328 ( 78) hydrogen bonds : bond 0.04368 ( 1098) hydrogen bonds : angle 5.94772 ( 3072) link_BETA1-4 : bond 0.00152 ( 7) link_BETA1-4 : angle 1.72563 ( 21) link_NAG-ASN : bond 0.00568 ( 23) link_NAG-ASN : angle 2.20729 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9596 (mt) cc_final: 0.9360 (mp) REVERT: A 869 MET cc_start: 0.9363 (mtt) cc_final: 0.9160 (mtm) REVERT: A 1029 MET cc_start: 0.9746 (tpp) cc_final: 0.9378 (tpp) REVERT: H 58 MET cc_start: 0.4441 (mpt) cc_final: 0.3590 (ttt) REVERT: B 387 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9073 (mm) REVERT: B 697 MET cc_start: 0.9053 (pmm) cc_final: 0.8390 (pmm) REVERT: B 731 MET cc_start: 0.8587 (ttm) cc_final: 0.8374 (ttm) REVERT: B 869 MET cc_start: 0.9376 (mtp) cc_final: 0.9048 (mtp) REVERT: C 40 ASP cc_start: 0.9104 (t0) cc_final: 0.8565 (m-30) outliers start: 19 outliers final: 10 residues processed: 68 average time/residue: 0.1644 time to fit residues: 19.2415 Evaluate side-chains 60 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 225 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 89 optimal weight: 0.0470 chunk 216 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 954 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 = 0.3460 r_free = 0.3460 target = 0.058716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.040225 restraints weight = 197297.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.037645 restraints weight = 101305.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037903 restraints weight = 67374.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038159 restraints weight = 51891.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.038335 restraints weight = 44164.879| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25367 Z= 0.128 Angle : 0.537 9.886 34579 Z= 0.275 Chirality : 0.043 0.165 4014 Planarity : 0.004 0.040 4405 Dihedral : 4.772 52.767 3952 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 0.62 % Allowed : 4.17 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.80 (0.15), residues: 3043 helix: 2.26 (0.21), residues: 660 sheet: 0.31 (0.19), residues: 733 loop : -0.02 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 509 TYR 0.023 0.001 TYR B1067 PHE 0.025 0.001 PHE A 759 TRP 0.036 0.002 TRP L 35 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00281 (25298) covalent geometry : angle 0.52534 (34411) SS BOND : bond 0.00238 ( 39) SS BOND : angle 1.57272 ( 78) hydrogen bonds : bond 0.03998 ( 1098) hydrogen bonds : angle 5.68100 ( 3072) link_BETA1-4 : bond 0.00232 ( 7) link_BETA1-4 : angle 1.45647 ( 21) link_NAG-ASN : bond 0.00236 ( 23) link_NAG-ASN : angle 1.83476 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9599 (mt) cc_final: 0.9367 (mp) REVERT: A 869 MET cc_start: 0.9304 (mtt) cc_final: 0.8889 (mpp) REVERT: A 1029 MET cc_start: 0.9726 (tpp) cc_final: 0.9332 (tpp) REVERT: H 58 MET cc_start: 0.4808 (mpt) cc_final: 0.4056 (ttt) REVERT: H 79 TYR cc_start: 0.8478 (m-80) cc_final: 0.8253 (m-80) REVERT: B 387 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8960 (mm) REVERT: B 697 MET cc_start: 0.9084 (pmm) cc_final: 0.8460 (pmm) REVERT: B 731 MET cc_start: 0.8536 (ttm) cc_final: 0.8316 (ttm) REVERT: B 869 MET cc_start: 0.9372 (mtp) cc_final: 0.9042 (mtp) REVERT: B 1001 LEU cc_start: 0.9822 (tp) cc_final: 0.9609 (pp) REVERT: B 1029 MET cc_start: 0.9388 (tpp) cc_final: 0.9084 (tpp) REVERT: C 40 ASP cc_start: 0.9127 (t0) cc_final: 0.8732 (p0) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.1822 time to fit residues: 20.8367 Evaluate side-chains 59 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 143 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A1005 GLN A1088 HIS A1108 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.058559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038733 restraints weight = 200633.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.036762 restraints weight = 108842.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037102 restraints weight = 73258.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037353 restraints weight = 57818.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.037559 restraints weight = 50393.303| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25367 Z= 0.133 Angle : 0.524 7.790 34579 Z= 0.270 Chirality : 0.042 0.165 4014 Planarity : 0.004 0.038 4405 Dihedral : 4.569 51.927 3952 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 0.69 % Allowed : 4.46 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.83 (0.15), residues: 3043 helix: 2.40 (0.21), residues: 654 sheet: 0.33 (0.19), residues: 718 loop : -0.03 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 509 TYR 0.021 0.001 TYR B1067 PHE 0.017 0.001 PHE A 759 TRP 0.036 0.002 TRP L 35 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00294 (25298) covalent geometry : angle 0.51400 (34411) SS BOND : bond 0.00380 ( 39) SS BOND : angle 1.37676 ( 78) hydrogen bonds : bond 0.03798 ( 1098) hydrogen bonds : angle 5.52107 ( 3072) link_BETA1-4 : bond 0.00216 ( 7) link_BETA1-4 : angle 1.37547 ( 21) link_NAG-ASN : bond 0.00238 ( 23) link_NAG-ASN : angle 1.77572 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9618 (mt) cc_final: 0.9386 (mp) REVERT: A 740 MET cc_start: 0.9266 (tpp) cc_final: 0.8947 (tpp) REVERT: A 869 MET cc_start: 0.9312 (mtt) cc_final: 0.8889 (mpp) REVERT: A 1029 MET cc_start: 0.9733 (tpp) cc_final: 0.9331 (tpp) REVERT: H 58 MET cc_start: 0.4761 (mpt) cc_final: 0.4036 (ttt) REVERT: B 387 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8910 (mm) REVERT: B 697 MET cc_start: 0.9034 (pmm) cc_final: 0.8383 (pmm) REVERT: B 869 MET cc_start: 0.9364 (mtp) cc_final: 0.9035 (mtp) REVERT: B 1001 LEU cc_start: 0.9817 (tp) cc_final: 0.9617 (pp) REVERT: B 1029 MET cc_start: 0.9401 (tpp) cc_final: 0.9096 (tpp) REVERT: C 40 ASP cc_start: 0.9137 (t0) cc_final: 0.8817 (p0) REVERT: C 979 ASP cc_start: 0.9530 (m-30) cc_final: 0.9251 (t0) outliers start: 19 outliers final: 12 residues processed: 68 average time/residue: 0.1729 time to fit residues: 19.7272 Evaluate side-chains 61 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 181 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 303 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN A1119 ASN H 39 GLN L 38 GLN C 613 GLN C 641 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.057630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.038702 restraints weight = 203733.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.037283 restraints weight = 107754.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 87)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036795 restraints weight = 73044.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.036985 restraints weight = 56382.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037051 restraints weight = 47858.147| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 25367 Z= 0.235 Angle : 0.619 7.858 34579 Z= 0.313 Chirality : 0.043 0.183 4014 Planarity : 0.004 0.041 4405 Dihedral : 4.898 49.855 3952 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 0.66 % Allowed : 4.79 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.62 (0.15), residues: 3043 helix: 2.18 (0.21), residues: 655 sheet: 0.26 (0.19), residues: 734 loop : -0.19 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 509 TYR 0.020 0.002 TYR H 79 PHE 0.020 0.002 PHE B 906 TRP 0.046 0.002 TRP L 35 HIS 0.008 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00515 (25298) covalent geometry : angle 0.60927 (34411) SS BOND : bond 0.00300 ( 39) SS BOND : angle 1.23486 ( 78) hydrogen bonds : bond 0.04142 ( 1098) hydrogen bonds : angle 5.78758 ( 3072) link_BETA1-4 : bond 0.00145 ( 7) link_BETA1-4 : angle 1.55146 ( 21) link_NAG-ASN : bond 0.00548 ( 23) link_NAG-ASN : angle 2.09666 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9606 (mt) cc_final: 0.9350 (mp) REVERT: A 740 MET cc_start: 0.9262 (tpp) cc_final: 0.8927 (tpp) REVERT: A 1029 MET cc_start: 0.9744 (tpp) cc_final: 0.9492 (tpp) REVERT: H 58 MET cc_start: 0.4430 (mpt) cc_final: 0.3613 (ttt) REVERT: H 79 TYR cc_start: 0.8527 (m-10) cc_final: 0.8215 (m-80) REVERT: H 94 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6197 (mpp-170) REVERT: B 387 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9020 (mm) REVERT: B 697 MET cc_start: 0.9067 (pmm) cc_final: 0.8364 (pmm) REVERT: B 869 MET cc_start: 0.9319 (mtp) cc_final: 0.9028 (mtp) REVERT: B 1029 MET cc_start: 0.9473 (tpp) cc_final: 0.9130 (tpp) REVERT: C 40 ASP cc_start: 0.9049 (t0) cc_final: 0.8630 (p0) REVERT: C 979 ASP cc_start: 0.9510 (m-30) cc_final: 0.9278 (t0) outliers start: 18 outliers final: 13 residues processed: 63 average time/residue: 0.1742 time to fit residues: 18.7118 Evaluate side-chains 61 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 137 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 954 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 = 0.3432 r_free = 0.3432 target = 0.057943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.038987 restraints weight = 201960.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.036641 restraints weight = 105975.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036950 restraints weight = 70808.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037118 restraints weight = 55733.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.037319 restraints weight = 49113.978| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25367 Z= 0.166 Angle : 0.554 12.763 34579 Z= 0.282 Chirality : 0.043 0.181 4014 Planarity : 0.004 0.039 4405 Dihedral : 4.777 51.400 3952 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.85 % Rotamer: Outliers : 0.77 % Allowed : 4.90 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.64 (0.15), residues: 3043 helix: 2.18 (0.21), residues: 667 sheet: 0.27 (0.19), residues: 720 loop : -0.19 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 509 TYR 0.021 0.001 TYR B1067 PHE 0.025 0.001 PHE A 888 TRP 0.042 0.002 TRP L 35 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00366 (25298) covalent geometry : angle 0.54552 (34411) SS BOND : bond 0.00250 ( 39) SS BOND : angle 1.08575 ( 78) hydrogen bonds : bond 0.03938 ( 1098) hydrogen bonds : angle 5.62894 ( 3072) link_BETA1-4 : bond 0.00151 ( 7) link_BETA1-4 : angle 1.38161 ( 21) link_NAG-ASN : bond 0.00308 ( 23) link_NAG-ASN : angle 1.86428 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9610 (mt) cc_final: 0.9358 (mp) REVERT: A 740 MET cc_start: 0.9278 (tpp) cc_final: 0.8932 (tpp) REVERT: A 1029 MET cc_start: 0.9742 (tpp) cc_final: 0.9481 (tpp) REVERT: H 58 MET cc_start: 0.4390 (mpt) cc_final: 0.3600 (ttt) REVERT: H 94 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6057 (mpp-170) REVERT: B 387 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8962 (mm) REVERT: B 697 MET cc_start: 0.9074 (pmm) cc_final: 0.8347 (pmm) REVERT: B 869 MET cc_start: 0.9329 (mtp) cc_final: 0.9057 (mtp) REVERT: B 1029 MET cc_start: 0.9449 (tpp) cc_final: 0.9118 (tpp) REVERT: C 40 ASP cc_start: 0.9037 (t0) cc_final: 0.8603 (p0) REVERT: C 979 ASP cc_start: 0.9513 (m-30) cc_final: 0.9286 (t0) outliers start: 21 outliers final: 16 residues processed: 63 average time/residue: 0.1662 time to fit residues: 17.8685 Evaluate side-chains 64 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 225 optimal weight: 0.0570 chunk 291 optimal weight: 4.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 954 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 = 0.3430 r_free = 0.3430 target = 0.057894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.039266 restraints weight = 202335.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037088 restraints weight = 107783.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037408 restraints weight = 74221.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.037577 restraints weight = 56111.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037787 restraints weight = 47586.168| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25367 Z= 0.162 Angle : 0.556 17.504 34579 Z= 0.282 Chirality : 0.042 0.181 4014 Planarity : 0.004 0.043 4405 Dihedral : 4.695 50.393 3952 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 0.62 % Allowed : 5.16 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.65 (0.15), residues: 3043 helix: 2.26 (0.21), residues: 660 sheet: 0.28 (0.19), residues: 717 loop : -0.19 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 509 TYR 0.020 0.001 TYR B1067 PHE 0.028 0.001 PHE B 888 TRP 0.040 0.002 TRP L 35 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00359 (25298) covalent geometry : angle 0.54791 (34411) SS BOND : bond 0.00238 ( 39) SS BOND : angle 1.03210 ( 78) hydrogen bonds : bond 0.03887 ( 1098) hydrogen bonds : angle 5.56683 ( 3072) link_BETA1-4 : bond 0.00142 ( 7) link_BETA1-4 : angle 1.36594 ( 21) link_NAG-ASN : bond 0.00322 ( 23) link_NAG-ASN : angle 1.85916 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9611 (mt) cc_final: 0.9355 (mp) REVERT: A 740 MET cc_start: 0.9256 (tpp) cc_final: 0.8928 (tpp) REVERT: A 1029 MET cc_start: 0.9728 (tpp) cc_final: 0.9464 (tpp) REVERT: H 58 MET cc_start: 0.4390 (mpt) cc_final: 0.3594 (ttt) REVERT: H 94 ARG cc_start: 0.6757 (ptp90) cc_final: 0.6182 (mpp-170) REVERT: B 387 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8840 (mm) REVERT: B 697 MET cc_start: 0.9072 (pmm) cc_final: 0.8372 (pmm) REVERT: B 869 MET cc_start: 0.9324 (mtp) cc_final: 0.9032 (mtp) REVERT: B 1029 MET cc_start: 0.9471 (tpp) cc_final: 0.9122 (tpp) REVERT: C 40 ASP cc_start: 0.9052 (t0) cc_final: 0.8670 (p0) outliers start: 17 outliers final: 15 residues processed: 63 average time/residue: 0.1659 time to fit residues: 17.8380 Evaluate side-chains 60 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 286 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 250 optimal weight: 0.0870 chunk 198 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 277 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN A1113 GLN ** C 954 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 = 0.3446 r_free = 0.3446 target = 0.058419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039681 restraints weight = 200105.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037105 restraints weight = 105190.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037485 restraints weight = 69708.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.037545 restraints weight = 54423.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037731 restraints weight = 48506.508| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25367 Z= 0.109 Angle : 0.521 17.737 34579 Z= 0.265 Chirality : 0.043 0.171 4014 Planarity : 0.004 0.040 4405 Dihedral : 4.545 51.867 3952 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 0.69 % Allowed : 5.16 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.77 (0.15), residues: 3043 helix: 2.43 (0.21), residues: 655 sheet: 0.27 (0.19), residues: 723 loop : -0.10 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.021 0.001 TYR B1067 PHE 0.028 0.001 PHE B 888 TRP 0.032 0.002 TRP L 35 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00239 (25298) covalent geometry : angle 0.51273 (34411) SS BOND : bond 0.00203 ( 39) SS BOND : angle 1.10556 ( 78) hydrogen bonds : bond 0.03728 ( 1098) hydrogen bonds : angle 5.42708 ( 3072) link_BETA1-4 : bond 0.00262 ( 7) link_BETA1-4 : angle 1.25129 ( 21) link_NAG-ASN : bond 0.00177 ( 23) link_NAG-ASN : angle 1.70070 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5727.71 seconds wall clock time: 99 minutes 9.87 seconds (5949.87 seconds total)