Starting phenix.real_space_refine on Sun Jul 5 02:46:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s6l_24879/07_2026/7s6l_24879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s6l_24879/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s6l_24879/07_2026/7s6l_24879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s6l_24879/07_2026/7s6l_24879.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s6l_24879/07_2026/7s6l_24879.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s6l_24879/07_2026/7s6l_24879.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s6l_24879/07_2026/7s6l_24879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s6l_24879/07_2026/7s6l_24879.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 5.27, per 1000 atoms: 0.21 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: 2.24 Conformation dependent library (CDL) restraints added in 960.1 milliseconds 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: 1.03 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: 7.69 Time building geometry restraints manager: 2.97 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: 14382 17.86 - 35.72: 344 35.72 - 53.57: 81 53.57 - 71.43: 44 71.43 - 89.29: 25 Dihedral angle restraints: 14876 sinusoidal: 5811 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 14873 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: 5.300 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.770 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 10.103 89.290 8911 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/Z covalent geometry : bond 0.01966 / 1.03 (25298) covalent geometry : angle 1.73750 / 1.17 (34411) SS BOND : bond 0.01699 / 1.05 ( 39) SS BOND : angle 2.78906 / 1.86 ( 78) hydrogen bonds : bond 0.16114 / 10.48 ( 1098) hydrogen bonds : angle 8.48639 / 5.93 ( 3072) link_BETA1-4 : bond 0.06983 / 4.43 ( 7) link_BETA1-4 : angle 4.78611 / 2.82 ( 21) link_NAG-ASN : bond 0.08012 / 4.85 ( 23) link_NAG-ASN : angle 2.84215 / 1.86 ( 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 : 1.105 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: 0.1652 time to fit residues: 40.5325 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 : 0.943 ------------------------------------------------------------------------------- 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... 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3504 r_free = 0.3504 target = 0.060068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040147 restraints weight = 199062.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.038540 restraints weight = 105869.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038953 restraints weight = 71147.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.039249 restraints weight = 56352.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.039469 restraints weight = 48021.275| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 25367 Z= 0.254 Angle : 0.741 9.703 34579 Z= 0.384 Chirality : 0.046 0.329 4014 Planarity : 0.005 0.038 4405 Dihedral : 5.173 24.494 3324 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.16 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: 0.93 (0.15), residues: 3043 helix: 1.82 (0.20), residues: 675 sheet: 0.65 (0.18), residues: 759 loop : 0.17 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.031 0.002 TYR B1067 PHE 0.029 0.002 PHE C 338 TRP 0.041 0.003 TRP B 886 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 (25298) covalent geometry : angle 0.72699 / 0.38 (34411) SS BOND : bond 0.00993 / 0.41 ( 39) SS BOND : angle 1.15436 / 0.72 ( 78) hydrogen bonds : bond 0.05616 / 3.60 ( 1098) hydrogen bonds : angle 6.86235 / 4.75 ( 3072) link_BETA1-4 : bond 0.00438 / 0.22 ( 7) link_BETA1-4 : angle 2.58532 / 1.48 ( 21) link_NAG-ASN : bond 0.00823 / 0.47 ( 23) link_NAG-ASN : angle 2.82771 / 1.80 ( 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 92 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.922 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: 0.9459 (mt) cc_final: 0.9224 (mp) REVERT: A 752 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9202 (mp) REVERT: A 869 MET cc_start: 0.9392 (mtm) cc_final: 0.9160 (mtt) REVERT: A 900 MET cc_start: 0.9290 (mtp) cc_final: 0.9022 (mtt) REVERT: H 58 MET cc_start: 0.4452 (mpt) cc_final: 0.3564 (tmm) REVERT: B 425 LEU cc_start: 0.8277 (tp) cc_final: 0.8067 (tp) REVERT: B 436 TRP cc_start: 0.8114 (t60) cc_final: 0.7643 (t60) REVERT: B 731 MET cc_start: 0.8529 (ttm) cc_final: 0.8312 (ttm) REVERT: B 740 MET cc_start: 0.9011 (tpt) cc_final: 0.8751 (tpp) REVERT: B 781 VAL cc_start: 0.9559 (t) cc_final: 0.9238 (m) REVERT: B 869 MET cc_start: 0.9383 (mtp) cc_final: 0.9081 (mtp) REVERT: B 900 MET cc_start: 0.9131 (mtm) cc_final: 0.8918 (mtt) REVERT: C 40 ASP cc_start: 0.9114 (t0) cc_final: 0.8843 (p0) REVERT: C 406 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8309 (mm-30) outliers start: 15 outliers final: 3 residues processed: 88 average time/residue: 0.1374 time to fit residues: 20.7807 Evaluate side-chains 62 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain B residue 888 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 146 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 0.0570 chunk 221 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 overall best weight: 2.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1023 ASN L 53 ASN L 89 GLN B 895 GLN B 957 GLN B1010 GLN C 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.059693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.040138 restraints weight = 198691.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038408 restraints weight = 105477.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038750 restraints weight = 68769.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.038909 restraints weight = 53676.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039128 restraints weight = 47134.688| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 25367 Z= 0.177 Angle : 0.611 12.497 34579 Z= 0.316 Chirality : 0.044 0.338 4014 Planarity : 0.004 0.033 4405 Dihedral : 4.710 20.305 3322 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.77 % Rotamer: Outliers : 0.51 % Allowed : 3.00 % Favored : 96.49 % 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: 0.91 (0.15), residues: 3043 helix: 2.01 (0.20), residues: 678 sheet: 0.52 (0.18), residues: 746 loop : 0.12 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.026 0.002 TYR B1067 PHE 0.036 0.002 PHE A 759 TRP 0.018 0.002 TRP L 35 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (25298) covalent geometry : angle 0.60325 / 0.31 (34411) SS BOND : bond 0.00291 / 0.18 ( 39) SS BOND : angle 0.84220 / 0.53 ( 78) hydrogen bonds : bond 0.04750 / 3.07 ( 1098) hydrogen bonds : angle 6.18598 / 4.28 ( 3072) link_BETA1-4 : bond 0.00406 / 0.29 ( 7) link_BETA1-4 : angle 1.67208 / 0.95 ( 21) link_NAG-ASN : bond 0.00320 / 0.18 ( 23) link_NAG-ASN : angle 2.01869 / 1.26 ( 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 78 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9538 (mt) cc_final: 0.9314 (mp) REVERT: A 1029 MET cc_start: 0.9671 (tpp) cc_final: 0.9366 (tpp) REVERT: H 48 MET cc_start: 0.5853 (mmm) cc_final: 0.5589 (mmm) REVERT: H 58 MET cc_start: 0.4371 (mpt) cc_final: 0.3593 (ttt) REVERT: B 697 MET cc_start: 0.8774 (pmm) cc_final: 0.8477 (pmm) REVERT: B 731 MET cc_start: 0.8594 (ttm) cc_final: 0.8359 (ttm) REVERT: B 740 MET cc_start: 0.9048 (tpt) cc_final: 0.8848 (tpp) REVERT: B 869 MET cc_start: 0.9402 (mtp) cc_final: 0.9061 (mtp) REVERT: C 40 ASP cc_start: 0.9094 (t0) cc_final: 0.8824 (p0) REVERT: C 697 MET cc_start: 0.8675 (ttm) cc_final: 0.8315 (ttt) outliers start: 14 outliers final: 3 residues processed: 72 average time/residue: 0.1634 time to fit residues: 20.4211 Evaluate side-chains 55 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 83 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN A1005 GLN B 655 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.058158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.039009 restraints weight = 200487.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.037393 restraints weight = 106317.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037743 restraints weight = 70163.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037956 restraints weight = 53898.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038183 restraints weight = 46958.865| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 25367 Z= 0.256 Angle : 0.665 8.816 34579 Z= 0.339 Chirality : 0.044 0.160 4014 Planarity : 0.004 0.035 4405 Dihedral : 4.774 19.331 3322 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 0.69 % Allowed : 3.62 % Favored : 95.69 % 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: 0.61 (0.15), residues: 3043 helix: 1.86 (0.20), residues: 666 sheet: 0.30 (0.18), residues: 756 loop : -0.08 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 509 TYR 0.028 0.002 TYR B1067 PHE 0.026 0.002 PHE C 759 TRP 0.039 0.002 TRP L 35 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (25298) covalent geometry : angle 0.65355 / 0.34 (34411) SS BOND : bond 0.00366 / 0.23 ( 39) SS BOND : angle 1.61000 / 0.98 ( 78) hydrogen bonds : bond 0.04521 / 2.92 ( 1098) hydrogen bonds : angle 6.17399 / 4.27 ( 3072) link_BETA1-4 : bond 0.00375 / 0.28 ( 7) link_BETA1-4 : angle 1.69547 / 0.94 ( 21) link_NAG-ASN : bond 0.00612 / 0.38 ( 23) link_NAG-ASN : angle 2.21499 / 1.44 ( 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 72 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9595 (mt) cc_final: 0.9364 (mp) REVERT: A 869 MET cc_start: 0.9353 (mtt) cc_final: 0.8982 (mpp) REVERT: A 1029 MET cc_start: 0.9679 (tpp) cc_final: 0.9334 (tpp) REVERT: H 58 MET cc_start: 0.4438 (mpt) cc_final: 0.3651 (ttt) REVERT: B 697 MET cc_start: 0.9066 (pmm) cc_final: 0.8492 (pmm) REVERT: B 731 MET cc_start: 0.8593 (ttm) cc_final: 0.8351 (ttm) REVERT: B 740 MET cc_start: 0.9145 (tpt) cc_final: 0.8927 (tpp) REVERT: B 869 MET cc_start: 0.9399 (mtp) cc_final: 0.9085 (mtp) REVERT: B 1029 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8934 (tmm) REVERT: C 40 ASP cc_start: 0.9088 (t0) cc_final: 0.8575 (m-30) outliers start: 19 outliers final: 10 residues processed: 68 average time/residue: 0.1714 time to fit residues: 19.5063 Evaluate side-chains 58 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 718 PHE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL 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: 8.9990 chunk 45 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 151 optimal weight: 0.0060 chunk 185 optimal weight: 6.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 ASN 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 = 0.3473 r_free = 0.3473 target = 0.059085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040371 restraints weight = 196359.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037894 restraints weight = 101422.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.038143 restraints weight = 68094.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038457 restraints weight = 52543.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038592 restraints weight = 44278.554| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25367 Z= 0.115 Angle : 0.529 9.736 34579 Z= 0.274 Chirality : 0.043 0.185 4014 Planarity : 0.004 0.036 4405 Dihedral : 4.410 18.517 3322 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.67 % Rotamer: Outliers : 0.62 % Allowed : 4.06 % Favored : 95.32 % 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: 0.79 (0.15), residues: 3043 helix: 2.24 (0.21), residues: 660 sheet: 0.23 (0.18), residues: 743 loop : 0.04 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 509 TYR 0.025 0.001 TYR B1067 PHE 0.020 0.001 PHE A 759 TRP 0.043 0.002 TRP L 35 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (25298) covalent geometry : angle 0.52178 / 0.27 (34411) SS BOND : bond 0.00223 / 0.14 ( 39) SS BOND : angle 1.07289 / 0.65 ( 78) hydrogen bonds : bond 0.03987 / 2.57 ( 1098) hydrogen bonds : angle 5.73893 / 3.98 ( 3072) link_BETA1-4 : bond 0.00300 / 0.20 ( 7) link_BETA1-4 : angle 1.25862 / 0.71 ( 21) link_NAG-ASN : bond 0.00228 / 0.12 ( 23) link_NAG-ASN : angle 1.62795 / 1.04 ( 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 75 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9576 (mt) cc_final: 0.9345 (mp) REVERT: A 869 MET cc_start: 0.9289 (mtt) cc_final: 0.8894 (mpp) REVERT: A 1029 MET cc_start: 0.9725 (tpp) cc_final: 0.9351 (tpp) REVERT: H 58 MET cc_start: 0.4387 (mpt) cc_final: 0.3548 (ttt) REVERT: B 387 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9089 (mm) REVERT: B 697 MET cc_start: 0.9059 (pmm) cc_final: 0.8502 (pmm) REVERT: B 869 MET cc_start: 0.9385 (mtp) cc_final: 0.9065 (mtp) REVERT: B 1001 LEU cc_start: 0.9818 (tp) cc_final: 0.9606 (pp) REVERT: C 40 ASP cc_start: 0.9106 (t0) cc_final: 0.8762 (p0) outliers start: 17 outliers final: 10 residues processed: 72 average time/residue: 0.1752 time to fit residues: 20.6186 Evaluate side-chains 61 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU 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 C residue 408 ARG Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 225 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN C1113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.040233 restraints weight = 199178.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036696 restraints weight = 106110.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.036794 restraints weight = 72916.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037082 restraints weight = 56197.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037191 restraints weight = 48531.083| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25367 Z= 0.123 Angle : 0.522 9.409 34579 Z= 0.269 Chirality : 0.043 0.168 4014 Planarity : 0.004 0.035 4405 Dihedral : 4.282 18.399 3322 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 0.51 % Allowed : 4.61 % Favored : 94.88 % 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: 0.85 (0.15), residues: 3043 helix: 2.36 (0.21), residues: 655 sheet: 0.32 (0.19), residues: 721 loop : 0.02 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 509 TYR 0.024 0.001 TYR B 369 PHE 0.018 0.001 PHE B 377 TRP 0.042 0.002 TRP L 35 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (25298) covalent geometry : angle 0.51451 / 0.27 (34411) SS BOND : bond 0.00227 / 0.14 ( 39) SS BOND : angle 0.97426 / 0.60 ( 78) hydrogen bonds : bond 0.03859 / 2.47 ( 1098) hydrogen bonds : angle 5.58828 / 3.87 ( 3072) link_BETA1-4 : bond 0.00209 / 0.13 ( 7) link_BETA1-4 : angle 1.21753 / 0.68 ( 21) link_NAG-ASN : bond 0.00231 / 0.13 ( 23) link_NAG-ASN : angle 1.65925 / 1.09 ( 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 67 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9593 (mt) cc_final: 0.9361 (mp) REVERT: A 869 MET cc_start: 0.9283 (mtt) cc_final: 0.8901 (mpp) REVERT: A 1029 MET cc_start: 0.9711 (tpp) cc_final: 0.9304 (tpp) REVERT: H 58 MET cc_start: 0.4768 (mpt) cc_final: 0.4020 (ttt) REVERT: H 79 TYR cc_start: 0.8498 (m-80) cc_final: 0.8253 (m-80) REVERT: H 80 MET cc_start: 0.3960 (ptm) cc_final: 0.3156 (ptm) REVERT: B 387 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8965 (mm) REVERT: B 697 MET cc_start: 0.9078 (pmm) cc_final: 0.8511 (pmm) REVERT: B 869 MET cc_start: 0.9357 (mtp) cc_final: 0.9057 (mtp) REVERT: B 1001 LEU cc_start: 0.9815 (tp) cc_final: 0.9613 (pp) REVERT: C 40 ASP cc_start: 0.9090 (t0) cc_final: 0.8753 (p0) outliers start: 14 outliers final: 11 residues processed: 65 average time/residue: 0.1595 time to fit residues: 17.8157 Evaluate side-chains 58 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 C residue 189 LEU Chi-restraints excluded: chain C residue 781 VAL 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: 0.7980 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 chunk 248 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN A1088 HIS A1108 ASN C 641 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.039677 restraints weight = 201230.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035920 restraints weight = 105855.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.036240 restraints weight = 72628.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036417 restraints weight = 57578.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.036585 restraints weight = 50308.392| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25367 Z= 0.179 Angle : 0.559 7.529 34579 Z= 0.286 Chirality : 0.042 0.172 4014 Planarity : 0.004 0.037 4405 Dihedral : 4.351 23.457 3322 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 0.77 % Allowed : 4.86 % Favored : 94.37 % 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: 0.76 (0.15), residues: 3043 helix: 2.31 (0.21), residues: 654 sheet: 0.33 (0.19), residues: 733 loop : -0.10 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 509 TYR 0.017 0.001 TYR C1067 PHE 0.017 0.001 PHE B 906 TRP 0.038 0.002 TRP L 35 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (25298) covalent geometry : angle 0.55238 / 0.28 (34411) SS BOND : bond 0.00289 / 0.19 ( 39) SS BOND : angle 0.90610 / 0.57 ( 78) hydrogen bonds : bond 0.03956 / 2.55 ( 1098) hydrogen bonds : angle 5.66680 / 3.93 ( 3072) link_BETA1-4 : bond 0.00136 / 0.09 ( 7) link_BETA1-4 : angle 1.29979 / 0.72 ( 21) link_NAG-ASN : bond 0.00387 / 0.23 ( 23) link_NAG-ASN : angle 1.78332 / 1.17 ( 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 71 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9590 (mt) cc_final: 0.9353 (mp) REVERT: A 869 MET cc_start: 0.9347 (mtt) cc_final: 0.8952 (mpp) REVERT: A 1029 MET cc_start: 0.9739 (tpp) cc_final: 0.9338 (tpp) REVERT: H 58 MET cc_start: 0.4766 (mpt) cc_final: 0.4028 (ttt) REVERT: B 387 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9016 (mm) REVERT: B 697 MET cc_start: 0.9077 (pmm) cc_final: 0.8396 (pmm) REVERT: B 869 MET cc_start: 0.9319 (mtp) cc_final: 0.9013 (mtp) REVERT: C 40 ASP cc_start: 0.9130 (t0) cc_final: 0.8761 (p0) REVERT: C 979 ASP cc_start: 0.9547 (m-30) cc_final: 0.9271 (t0) outliers start: 21 outliers final: 13 residues processed: 68 average time/residue: 0.1847 time to fit residues: 21.0075 Evaluate side-chains 62 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 303 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN L 38 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.058004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.039746 restraints weight = 201779.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035987 restraints weight = 105191.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.036034 restraints weight = 73648.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.036307 restraints weight = 57560.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036475 restraints weight = 50292.849| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 25367 Z= 0.178 Angle : 0.568 14.960 34579 Z= 0.289 Chirality : 0.043 0.181 4014 Planarity : 0.004 0.036 4405 Dihedral : 4.371 19.633 3322 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.85 % Rotamer: Outliers : 0.69 % Allowed : 5.08 % 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: 0.64 (0.15), residues: 3043 helix: 2.15 (0.21), residues: 660 sheet: 0.28 (0.19), residues: 731 loop : -0.17 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 509 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE A 888 TRP 0.034 0.002 TRP L 35 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (25298) covalent geometry : angle 0.55677 / 0.29 (34411) SS BOND : bond 0.00257 / 0.16 ( 39) SS BOND : angle 1.73761 / 1.03 ( 78) hydrogen bonds : bond 0.03960 / 2.57 ( 1098) hydrogen bonds : angle 5.65323 / 3.93 ( 3072) link_BETA1-4 : bond 0.00134 / 0.08 ( 7) link_BETA1-4 : angle 1.26286 / 0.70 ( 21) link_NAG-ASN : bond 0.00361 / 0.21 ( 23) link_NAG-ASN : angle 1.77157 / 1.18 ( 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 67 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9614 (mt) cc_final: 0.9359 (mp) REVERT: A 740 MET cc_start: 0.9157 (tpp) cc_final: 0.8919 (tpp) REVERT: A 869 MET cc_start: 0.9363 (mtt) cc_final: 0.8955 (mpp) REVERT: A 1029 MET cc_start: 0.9740 (tpp) cc_final: 0.9487 (tpp) REVERT: H 58 MET cc_start: 0.4776 (mpt) cc_final: 0.4016 (ttt) REVERT: B 387 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 697 MET cc_start: 0.9056 (pmm) cc_final: 0.8303 (pmm) REVERT: B 869 MET cc_start: 0.9339 (mtp) cc_final: 0.9054 (mtp) REVERT: B 1029 MET cc_start: 0.9508 (tpp) cc_final: 0.9186 (tpp) REVERT: C 40 ASP cc_start: 0.9045 (t0) cc_final: 0.8687 (p0) REVERT: C 979 ASP cc_start: 0.9508 (m-30) cc_final: 0.9256 (t0) outliers start: 19 outliers final: 13 residues processed: 63 average time/residue: 0.1707 time to fit residues: 18.2958 Evaluate side-chains 61 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 137 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 129 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 0.0010 chunk 222 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 overall best weight: 0.5706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.058848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.039930 restraints weight = 199642.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037481 restraints weight = 104209.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037666 restraints weight = 71118.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037930 restraints weight = 55741.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038140 restraints weight = 47889.760| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25367 Z= 0.099 Angle : 0.513 9.373 34579 Z= 0.264 Chirality : 0.043 0.167 4014 Planarity : 0.004 0.037 4405 Dihedral : 4.166 19.020 3322 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 0.48 % Allowed : 5.23 % Favored : 94.30 % 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: 0.82 (0.15), residues: 3043 helix: 2.42 (0.21), residues: 654 sheet: 0.28 (0.19), residues: 729 loop : -0.03 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.020 0.001 TYR B1067 PHE 0.027 0.001 PHE A 888 TRP 0.032 0.002 TRP L 35 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (25298) covalent geometry : angle 0.50406 / 0.26 (34411) SS BOND : bond 0.00211 / 0.13 ( 39) SS BOND : angle 1.41865 / 0.84 ( 78) hydrogen bonds : bond 0.03703 / 2.39 ( 1098) hydrogen bonds : angle 5.37728 / 3.74 ( 3072) link_BETA1-4 : bond 0.00333 / 0.17 ( 7) link_BETA1-4 : angle 1.17275 / 0.66 ( 21) link_NAG-ASN : bond 0.00165 / 0.09 ( 23) link_NAG-ASN : angle 1.50721 / 1.00 ( 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 66 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9610 (mt) cc_final: 0.9359 (mp) REVERT: A 740 MET cc_start: 0.9134 (tpp) cc_final: 0.8515 (tpt) REVERT: A 869 MET cc_start: 0.9330 (mtt) cc_final: 0.8931 (mpp) REVERT: A 1029 MET cc_start: 0.9728 (tpp) cc_final: 0.9320 (tpp) REVERT: H 58 MET cc_start: 0.4345 (mpt) cc_final: 0.3553 (ttt) REVERT: H 79 TYR cc_start: 0.8466 (m-80) cc_final: 0.8222 (m-80) REVERT: B 387 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 697 MET cc_start: 0.9033 (pmm) cc_final: 0.8331 (pmm) REVERT: B 869 MET cc_start: 0.9330 (mtp) cc_final: 0.9038 (mtp) REVERT: B 1029 MET cc_start: 0.9328 (tpp) cc_final: 0.9086 (tpp) REVERT: C 40 ASP cc_start: 0.9074 (t0) cc_final: 0.8806 (p0) REVERT: C 979 ASP cc_start: 0.9513 (m-30) cc_final: 0.9280 (t0) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.1576 time to fit residues: 16.5240 Evaluate side-chains 57 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR 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 137 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 252 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN A1119 ASN B 926 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.057469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.038620 restraints weight = 204088.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035918 restraints weight = 107393.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.036184 restraints weight = 72375.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036360 restraints weight = 58500.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036508 restraints weight = 50532.717| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 25367 Z= 0.250 Angle : 0.631 9.125 34579 Z= 0.318 Chirality : 0.043 0.187 4014 Planarity : 0.004 0.040 4405 Dihedral : 4.418 21.169 3322 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 0.48 % Allowed : 5.67 % Favored : 93.86 % 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: 0.55 (0.15), residues: 3043 helix: 2.09 (0.21), residues: 660 sheet: 0.22 (0.19), residues: 735 loop : -0.23 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 94 TYR 0.018 0.002 TYR C1067 PHE 0.028 0.002 PHE A 888 TRP 0.032 0.002 TRP L 35 HIS 0.008 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (25298) covalent geometry : angle 0.62119 / 0.32 (34411) SS BOND : bond 0.00308 / 0.19 ( 39) SS BOND : angle 1.44417 / 0.86 ( 78) hydrogen bonds : bond 0.04061 / 2.64 ( 1098) hydrogen bonds : angle 5.72045 / 3.97 ( 3072) link_BETA1-4 : bond 0.00150 / 0.10 ( 7) link_BETA1-4 : angle 1.34146 / 0.75 ( 21) link_NAG-ASN : bond 0.00574 / 0.34 ( 23) link_NAG-ASN : angle 1.97158 / 1.31 ( 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 59 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9616 (mt) cc_final: 0.9358 (mp) REVERT: A 740 MET cc_start: 0.9198 (tpp) cc_final: 0.8922 (tpp) REVERT: A 869 MET cc_start: 0.9405 (mtt) cc_final: 0.8981 (mpp) REVERT: A 1029 MET cc_start: 0.9745 (tpp) cc_final: 0.9474 (tpp) REVERT: H 58 MET cc_start: 0.4394 (mpt) cc_final: 0.3595 (ttt) REVERT: H 94 ARG cc_start: 0.6883 (mpp80) cc_final: 0.6268 (mpp80) REVERT: B 387 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 697 MET cc_start: 0.9071 (pmm) cc_final: 0.8327 (pmm) REVERT: B 869 MET cc_start: 0.9325 (mtp) cc_final: 0.9029 (mtp) REVERT: B 1029 MET cc_start: 0.9455 (tpp) cc_final: 0.9214 (tpp) REVERT: C 40 ASP cc_start: 0.9075 (t0) cc_final: 0.8581 (p0) REVERT: C 979 ASP cc_start: 0.9529 (m-30) cc_final: 0.9323 (t0) outliers start: 13 outliers final: 11 residues processed: 57 average time/residue: 0.1614 time to fit residues: 15.3604 Evaluate side-chains 58 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 63 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 250 optimal weight: 30.0000 chunk 198 optimal weight: 0.0040 chunk 260 optimal weight: 7.9990 chunk 277 optimal weight: 0.0170 chunk 172 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 135 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 0.4630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.058593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.039255 restraints weight = 199378.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037094 restraints weight = 106429.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037490 restraints weight = 71894.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037716 restraints weight = 55475.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.037814 restraints weight = 47566.479| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25367 Z= 0.098 Angle : 0.522 14.063 34579 Z= 0.266 Chirality : 0.043 0.235 4014 Planarity : 0.004 0.037 4405 Dihedral : 4.176 19.058 3322 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 0.51 % Allowed : 5.70 % Favored : 93.78 % 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 (0.16), residues: 3043 helix: 2.41 (0.21), residues: 654 sheet: 0.30 (0.19), residues: 718 loop : -0.06 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.019 0.001 TYR B1067 PHE 0.029 0.001 PHE B 888 TRP 0.030 0.002 TRP L 35 HIS 0.002 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (25298) covalent geometry : angle 0.51416 / 0.26 (34411) SS BOND : bond 0.00205 / 0.12 ( 39) SS BOND : angle 1.30928 / 0.78 ( 78) hydrogen bonds : bond 0.03722 / 2.41 ( 1098) hydrogen bonds : angle 5.38376 / 3.75 ( 3072) link_BETA1-4 : bond 0.00283 / 0.18 ( 7) link_BETA1-4 : angle 1.20307 / 0.68 ( 21) link_NAG-ASN : bond 0.00178 / 0.09 ( 23) link_NAG-ASN : angle 1.55411 / 1.04 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5238.20 seconds wall clock time: 90 minutes 57.58 seconds (5457.58 seconds total)