Starting phenix.real_space_refine on Mon Aug 25 17:37:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0c_24786/08_2025/7s0c_24786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0c_24786/08_2025/7s0c_24786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s0c_24786/08_2025/7s0c_24786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0c_24786/08_2025/7s0c_24786.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0c_24786/08_2025/7s0c_24786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0c_24786/08_2025/7s0c_24786.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 127 5.16 5 C 18808 2.51 5 N 4891 2.21 5 O 5772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29598 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7393 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 8, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 7724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7715 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 54, 'TRANS': 949} Chain breaks: 9 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 80 Conformer: "B" Number of residues, atoms: 1004, 7715 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 54, 'TRANS': 949} Chain breaks: 9 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 80 bond proxies already assigned to first conformer: 7877 Chain: "C" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7393 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 8, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "H" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1674 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Chain: "L" Number of atoms: 1653 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1682 Chain: "M" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1674 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Chain: "N" Number of atoms: 1653 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1682 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.40 Time building chain proxies: 9.26, per 1000 atoms: 0.31 Number of scatterers: 29598 At special positions: 0 Unit cell: (166.848, 135.564, 225.94, 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 127 16.00 O 5772 8.00 N 4891 7.00 C 18808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG BCYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG ACYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG BCYS N 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, 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-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1134 " " NAG A1305 " - " ASN A1098 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C 801 " " NAG D 1 " - " ASN B 331 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN C 717 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7150 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 64 sheets defined 22.4% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.691A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.559A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 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: 3.723A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.527A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.513A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.711A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.861A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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 removed outlier: 3.542A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.847A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.863A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.247A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.601A 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 removed outlier: 3.559A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.605A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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: 3.611A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.677A 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 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.541A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.195A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.858A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.694A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.596A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.799A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.562A 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 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.575A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) 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 removed outlier: 3.722A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.850A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.075A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.630A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.622A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.009A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.528A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.557A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.595A pdb=" N THR M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 168 No H-bonds generated for 'chain 'M' and resid 166 through 168' Processing helix chain 'M' and resid 197 through 199 No H-bonds generated for 'chain 'M' and resid 197 through 199' Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.025A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 removed outlier: 3.561A pdb=" N LYS N 126 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 188 removed outlier: 3.576A pdb=" N LYS N 188 " --> pdb=" O ALA N 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.782A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.094A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.690A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.166A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.820A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.896A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.335A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.400A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.400A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.432A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.789A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.718A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.181A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.030A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.431A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.830A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.962A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.340A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.340A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.460A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.553A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.776A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.002A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.622A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.020A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.318A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR C 660 " --> pdb=" O SER C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.874A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.361A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.700A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.515A pdb=" N HIS H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.660A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.660A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.555A pdb=" N LYS H 219 " --> pdb=" O CYS H 206 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.645A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 62 through 63 removed outlier: 3.576A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.531A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE L 116 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AG1, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.565A pdb=" N HIS M 35 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 130 through 134 removed outlier: 3.974A pdb=" N GLY M 149 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 130 through 134 removed outlier: 3.974A pdb=" N GLY M 149 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 161 through 164 removed outlier: 3.675A pdb=" N LYS M 219 " --> pdb=" O CYS M 206 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.579A pdb=" N LEU N 11 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR N 86 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL N 104 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 23 through 24 Processing sheet with id=AG8, first strand: chain 'N' and resid 62 through 63 Processing sheet with id=AG9, first strand: chain 'N' and resid 114 through 118 removed outlier: 3.703A pdb=" N SER N 114 " --> pdb=" O ASN N 137 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN N 137 " --> pdb=" O SER N 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE N 116 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA N 130 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 153 through 155 removed outlier: 4.609A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) 1255 hydrogen bonds defined for protein. 3415 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: 6.42 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.21: 1 1.21 - 1.53: 26598 1.53 - 1.84: 3649 1.84 - 2.15: 5 2.15 - 2.46: 2 Bond restraints: 30255 Sorted by residual: bond pdb=" CD2 TYR B 351 " pdb=" CE2 TYR B 351 " ideal model delta sigma weight residual 1.382 2.461 -1.079 3.00e-02 1.11e+03 1.29e+03 bond pdb=" CD1 TYR B 351 " pdb=" CE1 TYR B 351 " ideal model delta sigma weight residual 1.382 2.207 -0.825 3.00e-02 1.11e+03 7.57e+02 bond pdb=" CE2 TYR B 351 " pdb=" CZ TYR B 351 " ideal model delta sigma weight residual 1.378 1.970 -0.592 2.40e-02 1.74e+03 6.08e+02 bond pdb=" CE1 TYR B 351 " pdb=" CZ TYR B 351 " ideal model delta sigma weight residual 1.378 1.880 -0.502 2.40e-02 1.74e+03 4.38e+02 bond pdb=" CG TYR B 351 " pdb=" CD2 TYR B 351 " ideal model delta sigma weight residual 1.389 1.809 -0.420 2.10e-02 2.27e+03 4.00e+02 ... (remaining 30250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 41170 6.26 - 12.52: 51 12.52 - 18.78: 8 18.78 - 25.03: 1 25.03 - 31.29: 2 Bond angle restraints: 41232 Sorted by residual: angle pdb=" C LEU M 102 " pdb=" N ALA M 103 " pdb=" CA ALA M 103 " ideal model delta sigma weight residual 122.56 153.85 -31.29 1.50e+00 4.44e-01 4.35e+02 angle pdb=" N PRO N 59 " pdb=" CD PRO N 59 " pdb=" CG PRO N 59 " ideal model delta sigma weight residual 103.20 74.86 28.34 1.50e+00 4.44e-01 3.57e+02 angle pdb=" CA PRO N 59 " pdb=" CB PRO N 59 " pdb=" CG PRO N 59 " ideal model delta sigma weight residual 104.50 83.72 20.78 1.90e+00 2.77e-01 1.20e+02 angle pdb=" CA LEU M 102 " pdb=" C LEU M 102 " pdb=" O LEU M 102 " ideal model delta sigma weight residual 120.51 107.08 13.43 1.43e+00 4.89e-01 8.82e+01 angle pdb=" CA PRO N 59 " pdb=" N PRO N 59 " pdb=" CD PRO N 59 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 ... (remaining 41227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 16897 17.88 - 35.75: 1204 35.75 - 53.63: 240 53.63 - 71.50: 58 71.50 - 89.38: 42 Dihedral angle restraints: 18441 sinusoidal: 7345 harmonic: 11096 Sorted by residual: dihedral pdb=" CA ALA B1070 " pdb=" C ALA B1070 " pdb=" N GLN B1071 " pdb=" CA GLN B1071 " ideal model delta harmonic sigma weight residual -180.00 -127.94 -52.06 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 175.79 -82.79 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -159.53 73.53 1 1.00e+01 1.00e-02 6.88e+01 ... (remaining 18438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4678 0.123 - 0.246: 149 0.246 - 0.369: 6 0.369 - 0.491: 2 0.491 - 0.614: 1 Chirality restraints: 4836 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.44e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 4833 not shown) Planarity restraints: 5314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 119 " 0.116 5.00e-02 4.00e+02 1.72e-01 4.71e+01 pdb=" N PRO L 120 " -0.297 5.00e-02 4.00e+02 pdb=" CA PRO L 120 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO L 120 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 119 " -0.097 5.00e-02 4.00e+02 1.43e-01 3.29e+01 pdb=" N PRO N 120 " 0.248 5.00e-02 4.00e+02 pdb=" CA PRO N 120 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO N 120 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 567 " 0.460 9.50e-02 1.11e+02 2.08e-01 3.27e+01 pdb=" NE ARG B 567 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 567 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG B 567 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 567 " 0.001 2.00e-02 2.50e+03 ... (remaining 5311 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 109 2.44 - 3.06: 19232 3.06 - 3.67: 43120 3.67 - 4.29: 63917 4.29 - 4.90: 108729 Nonbonded interactions: 235107 Sorted by model distance: nonbonded pdb=" OH TYR B 351 " pdb=" O ARG M 100 " model vdw 1.826 3.040 nonbonded pdb=" OD1 ASN B 280 " pdb=" OG1 THR B 286 " model vdw 1.996 3.040 nonbonded pdb=" OE2 GLU B 725 " pdb=" NE2 HIS B1064 " model vdw 2.093 3.120 nonbonded pdb=" OG1 THR A 859 " pdb=" OD2 ASP C 614 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.116 3.040 ... (remaining 235102 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 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 280 or (resid 281 and (name N or n \ ame CA or name C or name O or name CB )) or resid 282 through 339 or (resid 340 \ and (name N or name CA or name C or name O or name CB )) or resid 341 through 34 \ 5 or (resid 346 and (name N or name CA or name C or name O or name CB )) or resi \ d 347 through 348 or (resid 349 and (name N or name CA or name C or name O or na \ me CB )) or resid 350 through 397 or (resid 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 402 or (resid 403 and (name N or n \ ame CA or name C or name O or name CB )) or resid 404 or (resid 405 through 407 \ and (name N or name CA or name C or name O or name CB )) or resid 408 through 41 \ 3 or (resid 414 through 415 and (name N or name CA or name C or name O or name C \ B )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or na \ me CB )) or resid 418 through 419 or (resid 420 and (name N or name CA or name C \ or name O or name CB )) or resid 421 through 423 or (resid 424 and (name N or n \ ame CA or name C or name O or name CB )) or resid 425 through 426 or (resid 427 \ through 428 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 9 through 440 or (resid 441 and (name N or name CA or name C or name O or name C \ B )) or resid 442 through 443 or resid 449 through 453 or (resid 454 and (name N \ or name CA or name C or name O or name CB )) or resid 491 or (resid 492 through \ 493 and (name N or name CA or name C or name O or name CB )) or resid 494 throu \ gh 497 or (resid 498 and (name N or name CA or name C or name O or name CB )) or \ resid 499 through 500 or resid 503 through 515 or (resid 516 and (name N or nam \ e CA or name C or name O or name CB )) or resid 517 through 527 or (resid 528 th \ rough 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 1304)) selection = (chain 'B' and (resid 27 through 66 or resid 80 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 194 or (resid 195 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 245 or resid 261 through 331 or (resid 332 through 333 and ( \ name N or name CA or name C or name O or name CB )) or resid 334 through 518 or \ resid 520 through 620 or resid 641 through 1304)) selection = (chain 'C' and (resid 27 through 66 or resid 80 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 194 or (resid 195 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 245 or resid 261 through 331 or (resid 332 through 333 and ( \ name N or name CA or name C or name O or name CB )) or resid 334 through 518 or \ resid 520 through 620 or resid 641 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = (chain 'L' and (resid 1 through 193 or resid 195 through 214)) selection = (chain 'N' and (resid 1 through 193 or resid 195 through 214)) } 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=0.04 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.940 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.012 1.079 30334 Z= 0.507 Angle : 0.961 31.293 41419 Z= 0.515 Chirality : 0.057 0.614 4836 Planarity : 0.010 0.208 5289 Dihedral : 13.412 89.379 11150 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.08 % Favored : 94.74 % Rotamer: Outliers : 0.19 % Allowed : 0.44 % Favored : 99.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.13), residues: 3748 helix: -0.09 (0.17), residues: 727 sheet: 0.68 (0.15), residues: 1050 loop : -0.72 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.003 ARG B 567 TYR 0.055 0.003 TYR B 351 PHE 0.049 0.002 PHE M 105 TRP 0.042 0.003 TRP L 96 HIS 0.010 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.01194 (30255) covalent geometry : angle 0.93453 (41232) SS BOND : bond 0.00555 ( 47) SS BOND : angle 3.06511 ( 94) hydrogen bonds : bond 0.15726 ( 1204) hydrogen bonds : angle 8.27719 ( 3415) Misc. bond : bond 0.33161 ( 1) link_BETA1-4 : bond 0.00708 ( 6) link_BETA1-4 : angle 3.15890 ( 18) link_NAG-ASN : bond 0.00627 ( 25) link_NAG-ASN : angle 3.94130 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 300 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.6464 (ptm160) cc_final: 0.5634 (ptt-90) REVERT: C 129 LYS cc_start: 0.7412 (mtmm) cc_final: 0.7155 (mtmm) REVERT: H 96 CYS cc_start: 0.5145 (p) cc_final: 0.4718 (p) REVERT: L 3 GLN cc_start: 0.7810 (mp10) cc_final: 0.7469 (pm20) REVERT: L 70 ASP cc_start: 0.6718 (m-30) cc_final: 0.6437 (t0) REVERT: N 103 LYS cc_start: 0.5355 (mmtm) cc_final: 0.4826 (tttp) outliers start: 4 outliers final: 1 residues processed: 302 average time/residue: 0.1740 time to fit residues: 87.2588 Evaluate side-chains 232 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 762 GLN B 787 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 613 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 90 GLN ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.191870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143417 restraints weight = 83655.691| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.86 r_work: 0.3319 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 30334 Z= 0.150 Angle : 0.668 12.134 41419 Z= 0.349 Chirality : 0.047 0.322 4836 Planarity : 0.005 0.093 5289 Dihedral : 6.199 59.551 4709 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.15 % Favored : 96.69 % Rotamer: Outliers : 0.62 % Allowed : 6.08 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.13), residues: 3748 helix: 0.73 (0.19), residues: 735 sheet: 0.83 (0.15), residues: 1049 loop : -0.41 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.035 0.002 TYR B 351 PHE 0.022 0.001 PHE H 110 TRP 0.024 0.002 TRP N 96 HIS 0.008 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00339 (30255) covalent geometry : angle 0.65234 (41232) SS BOND : bond 0.00351 ( 47) SS BOND : angle 1.69441 ( 94) hydrogen bonds : bond 0.04323 ( 1204) hydrogen bonds : angle 6.61860 ( 3415) Misc. bond : bond 0.03223 ( 1) link_BETA1-4 : bond 0.00837 ( 6) link_BETA1-4 : angle 2.47048 ( 18) link_NAG-ASN : bond 0.00525 ( 25) link_NAG-ASN : angle 2.72972 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.6755 (m-10) cc_final: 0.6498 (m-10) REVERT: B 985 ASP cc_start: 0.7610 (m-30) cc_final: 0.7268 (m-30) REVERT: A 403 ARG cc_start: 0.6435 (ptm160) cc_final: 0.5673 (ptt-90) REVERT: C 129 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7534 (mtmm) REVERT: H 96 CYS cc_start: 0.5313 (p) cc_final: 0.5026 (p) REVERT: L 70 ASP cc_start: 0.7065 (m-30) cc_final: 0.6513 (t0) REVERT: M 34 MET cc_start: 0.4031 (tpp) cc_final: 0.3390 (tpp) REVERT: M 46 GLU cc_start: 0.5917 (tp30) cc_final: 0.5699 (tp30) REVERT: N 4 MET cc_start: 0.3967 (mpp) cc_final: 0.3748 (pmm) REVERT: N 103 LYS cc_start: 0.5734 (mmtm) cc_final: 0.5215 (tttp) outliers start: 18 outliers final: 9 residues processed: 265 average time/residue: 0.1559 time to fit residues: 68.8700 Evaluate side-chains 232 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 131 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 163 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 292 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 chunk 341 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 774 GLN B 955 ASN B1011 GLN A 30 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN C1106 GLN L 38 GLN L 137 ASN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.189049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140841 restraints weight = 83263.089| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.83 r_work: 0.3254 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 30334 Z= 0.194 Angle : 0.638 13.585 41419 Z= 0.332 Chirality : 0.047 0.292 4836 Planarity : 0.005 0.072 5289 Dihedral : 5.791 59.312 4707 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 1.37 % Allowed : 8.79 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.13), residues: 3748 helix: 0.81 (0.19), residues: 719 sheet: 0.73 (0.15), residues: 1053 loop : -0.40 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.037 0.002 TYR B 351 PHE 0.018 0.002 PHE B 643 TRP 0.020 0.002 TRP L 96 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00466 (30255) covalent geometry : angle 0.62360 (41232) SS BOND : bond 0.00479 ( 47) SS BOND : angle 1.63847 ( 94) hydrogen bonds : bond 0.03959 ( 1204) hydrogen bonds : angle 6.08443 ( 3415) Misc. bond : bond 0.02521 ( 1) link_BETA1-4 : bond 0.00834 ( 6) link_BETA1-4 : angle 2.49916 ( 18) link_NAG-ASN : bond 0.00481 ( 25) link_NAG-ASN : angle 2.44688 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 436 TRP cc_start: 0.4033 (p90) cc_final: 0.3403 (p90) REVERT: B 855 PHE cc_start: 0.6740 (m-10) cc_final: 0.6511 (m-10) REVERT: B 985 ASP cc_start: 0.7714 (m-30) cc_final: 0.7319 (m-30) REVERT: A 403 ARG cc_start: 0.6170 (ptm160) cc_final: 0.5362 (ptt-90) REVERT: C 129 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7585 (mtmm) REVERT: C 943 SER cc_start: 0.7872 (p) cc_final: 0.7533 (t) REVERT: H 96 CYS cc_start: 0.5341 (p) cc_final: 0.5119 (p) REVERT: L 70 ASP cc_start: 0.7185 (m-30) cc_final: 0.6578 (t0) REVERT: M 34 MET cc_start: 0.4471 (tpp) cc_final: 0.4218 (tpt) REVERT: N 4 MET cc_start: 0.4010 (mpp) cc_final: 0.3650 (pmm) REVERT: N 103 LYS cc_start: 0.5763 (mmtm) cc_final: 0.5222 (tttp) outliers start: 42 outliers final: 30 residues processed: 278 average time/residue: 0.1728 time to fit residues: 80.6418 Evaluate side-chains 258 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 132 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 41 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 375 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 563 GLN B 901 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C1071 GLN H 35 HIS H 209 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.186033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140386 restraints weight = 98547.399| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 4.34 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 30334 Z= 0.236 Angle : 0.651 12.778 41419 Z= 0.338 Chirality : 0.048 0.299 4836 Planarity : 0.005 0.064 5289 Dihedral : 5.773 59.884 4707 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 2.12 % Allowed : 10.25 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.13), residues: 3748 helix: 0.78 (0.19), residues: 698 sheet: 0.63 (0.15), residues: 1055 loop : -0.49 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 346 TYR 0.038 0.002 TYR B 351 PHE 0.034 0.002 PHE A 168 TRP 0.018 0.002 TRP L 96 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00575 (30255) covalent geometry : angle 0.63630 (41232) SS BOND : bond 0.00398 ( 47) SS BOND : angle 1.72559 ( 94) hydrogen bonds : bond 0.04038 ( 1204) hydrogen bonds : angle 5.94734 ( 3415) Misc. bond : bond 0.02574 ( 1) link_BETA1-4 : bond 0.00814 ( 6) link_BETA1-4 : angle 2.55528 ( 18) link_NAG-ASN : bond 0.00462 ( 25) link_NAG-ASN : angle 2.41436 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 237 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1130 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7806 (mt) REVERT: A 192 PHE cc_start: 0.7401 (m-10) cc_final: 0.7111 (m-80) REVERT: A 403 ARG cc_start: 0.6355 (ptm160) cc_final: 0.5990 (ptt-90) REVERT: C 780 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7455 (mm-30) REVERT: H 96 CYS cc_start: 0.5016 (p) cc_final: 0.4686 (p) REVERT: H 193 THR cc_start: 0.3393 (OUTLIER) cc_final: 0.3012 (p) outliers start: 66 outliers final: 49 residues processed: 288 average time/residue: 0.1725 time to fit residues: 85.4625 Evaluate side-chains 266 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 132 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 57 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 219 optimal weight: 0.6980 chunk 320 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 173 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 363 optimal weight: 40.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.187632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138274 restraints weight = 85730.100| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.76 r_work: 0.3248 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 30334 Z= 0.148 Angle : 0.578 11.200 41419 Z= 0.300 Chirality : 0.046 0.281 4836 Planarity : 0.005 0.059 5289 Dihedral : 5.475 59.559 4707 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 2.03 % Allowed : 11.53 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.14), residues: 3748 helix: 1.02 (0.20), residues: 698 sheet: 0.66 (0.15), residues: 1062 loop : -0.41 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 237 TYR 0.035 0.001 TYR B 351 PHE 0.019 0.001 PHE B 347 TRP 0.017 0.001 TRP N 96 HIS 0.003 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00349 (30255) covalent geometry : angle 0.56444 (41232) SS BOND : bond 0.00330 ( 47) SS BOND : angle 1.46965 ( 94) hydrogen bonds : bond 0.03602 ( 1204) hydrogen bonds : angle 5.71025 ( 3415) Misc. bond : bond 0.02316 ( 1) link_BETA1-4 : bond 0.00841 ( 6) link_BETA1-4 : angle 2.50043 ( 18) link_NAG-ASN : bond 0.00407 ( 25) link_NAG-ASN : angle 2.23703 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: B 855 PHE cc_start: 0.6802 (m-10) cc_final: 0.6526 (m-10) REVERT: B 1130 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7736 (mt) REVERT: A 192 PHE cc_start: 0.7801 (m-10) cc_final: 0.7548 (m-80) REVERT: A 403 ARG cc_start: 0.6181 (ptm160) cc_final: 0.5249 (ptt-90) REVERT: A 934 ILE cc_start: 0.8603 (mm) cc_final: 0.8396 (mm) REVERT: C 129 LYS cc_start: 0.7808 (mtmm) cc_final: 0.6912 (ttmm) REVERT: C 324 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: C 780 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8177 (mm-30) REVERT: H 96 CYS cc_start: 0.5410 (p) cc_final: 0.5119 (p) outliers start: 63 outliers final: 40 residues processed: 277 average time/residue: 0.1564 time to fit residues: 74.5295 Evaluate side-chains 255 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 132 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.8767 > 50: distance: 64 - 69: 34.650 distance: 69 - 70: 59.961 distance: 70 - 71: 17.846 distance: 70 - 73: 46.905 distance: 71 - 72: 40.258 distance: 71 - 75: 22.461 distance: 73 - 74: 36.451 distance: 75 - 76: 43.075 distance: 76 - 77: 19.600 distance: 76 - 79: 41.830 distance: 77 - 78: 20.592 distance: 77 - 86: 22.699 distance: 79 - 80: 45.104 distance: 80 - 81: 45.241 distance: 81 - 82: 19.775 distance: 82 - 83: 28.346 distance: 83 - 84: 11.012 distance: 83 - 85: 27.163 distance: 86 - 87: 39.601 distance: 87 - 88: 12.330 distance: 87 - 90: 19.652 distance: 88 - 89: 36.522 distance: 88 - 97: 25.826 distance: 90 - 91: 22.228 distance: 91 - 93: 15.263 distance: 92 - 94: 6.895 distance: 93 - 95: 23.660 distance: 94 - 96: 19.096 distance: 95 - 96: 23.319 distance: 97 - 98: 17.252 distance: 98 - 99: 24.667 distance: 98 - 101: 33.422 distance: 99 - 100: 34.832 distance: 99 - 103: 7.481 distance: 100 - 166: 26.593 distance: 101 - 102: 40.640 distance: 103 - 104: 15.031 distance: 104 - 105: 60.758 distance: 105 - 106: 55.481 distance: 105 - 107: 19.423 distance: 107 - 108: 16.150 distance: 108 - 109: 25.413 distance: 108 - 111: 37.506 distance: 109 - 110: 30.386 distance: 109 - 113: 28.452 distance: 111 - 112: 57.587 distance: 113 - 114: 10.086 distance: 114 - 115: 37.491 distance: 115 - 116: 30.456 distance: 115 - 117: 43.448 distance: 117 - 118: 26.305 distance: 118 - 119: 44.972 distance: 118 - 121: 39.799 distance: 119 - 120: 22.859 distance: 119 - 123: 24.858 distance: 121 - 122: 56.619 distance: 123 - 124: 20.593 distance: 124 - 125: 19.034 distance: 125 - 126: 17.160 distance: 125 - 127: 21.040 distance: 127 - 128: 21.217 distance: 128 - 129: 11.108 distance: 128 - 131: 13.233 distance: 129 - 130: 10.245 distance: 129 - 134: 10.461 distance: 131 - 132: 8.140 distance: 131 - 133: 7.937