Starting phenix.real_space_refine on Mon Sep 14 09:48:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_24786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_24786.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_24786.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_24786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_24786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_24786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0c_24786/09_2026/7s0c_24786.map" } 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-2.2.1-6174/lib/python3.11/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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 8.78, per 1000 atoms: 0.30 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: 2.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.21 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: 8.64 Time building geometry restraints manager: 3.58 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: 16319 17.88 - 35.75: 1160 35.75 - 53.63: 222 53.63 - 71.50: 47 71.50 - 89.38: 42 Dihedral angle restraints: 17790 sinusoidal: 6694 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 17787 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: 7.410 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.500 Find NCS groups from input model: 0.840 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 13.423 89.379 10499 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 are 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/Z covalent geometry : bond 0.01194 / 0.47 (30255) covalent geometry : angle 0.93453 / 0.51 (41232) SS BOND : bond 0.00555 / 0.32 ( 47) SS BOND : angle 3.06511 / 1.89 ( 94) hydrogen bonds : bond 0.15726 / 10.42 ( 1204) hydrogen bonds : angle 8.27719 / 5.75 ( 3415) Misc. bond : bond 0.33161 / 17.45 ( 1) link_BETA1-4 : bond 0.00708 / 0.50 ( 6) link_BETA1-4 : angle 3.15890 / 1.64 ( 18) link_NAG-ASN : bond 0.00627 / 0.27 ( 25) link_NAG-ASN : angle 3.94130 / 2.40 ( 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 : 1.132 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: 0.1821 time to fit residues: 91.8888 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 : 1.140 ------------------------------------------------------------------------------- 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... B 280 ASN B 762 GLN B 787 GLN A 30 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.191936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.142472 restraints weight = 83740.474| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.74 r_work: 0.3321 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 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 = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 30334 Z= 0.151 Angle : 0.673 12.489 41419 Z= 0.351 Chirality : 0.047 0.297 4836 Planarity : 0.005 0.094 5289 Dihedral : 4.454 53.127 4058 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 0.65 % Allowed : 5.98 % Favored : 93.36 % 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 are not related in a simple way. whole: 0.22 (0.13), residues: 3748 helix: 0.71 (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 0.032 0.002 TYR B 351 PHE 0.024 0.001 PHE H 110 TRP 0.024 0.002 TRP N 96 HIS 0.007 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (30255) covalent geometry : angle 0.65745 / 0.35 (41232) SS BOND : bond 0.00350 / 0.22 ( 47) SS BOND : angle 1.70829 / 1.02 ( 94) hydrogen bonds : bond 0.04456 / 2.90 ( 1204) hydrogen bonds : angle 6.67489 / 4.66 ( 3415) Misc. bond : bond 0.01664 / 0.88 ( 1) link_BETA1-4 : bond 0.00782 / 0.56 ( 6) link_BETA1-4 : angle 2.37917 / 1.21 ( 18) link_NAG-ASN : bond 0.00540 / 0.25 ( 25) link_NAG-ASN : angle 2.69961 / 1.71 ( 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 271 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.6685 (m-10) cc_final: 0.6440 (m-10) REVERT: B 985 ASP cc_start: 0.7607 (m-30) cc_final: 0.7263 (m-30) REVERT: A 403 ARG cc_start: 0.6456 (ptm160) cc_final: 0.5690 (ptt-90) REVERT: C 129 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7520 (mtmm) REVERT: H 96 CYS cc_start: 0.5271 (p) cc_final: 0.4957 (p) REVERT: L 70 ASP cc_start: 0.7065 (m-30) cc_final: 0.6520 (t0) REVERT: M 34 MET cc_start: 0.4066 (tpp) cc_final: 0.3402 (tpp) REVERT: N 4 MET cc_start: 0.4015 (mpp) cc_final: 0.3734 (pmm) REVERT: N 103 LYS cc_start: 0.5760 (mmtm) cc_final: 0.5240 (tttp) outliers start: 19 outliers final: 10 residues processed: 263 average time/residue: 0.1819 time to fit residues: 80.2483 Evaluate side-chains 235 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 30 ASN 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: 3.9990 chunk 261 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 341 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 280 ASN B 774 GLN B 901 GLN B 955 ASN B1011 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN C1106 GLN H 35 HIS H 209 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN M 202 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.184871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136639 restraints weight = 83015.766| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.76 r_work: 0.3200 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 30334 Z= 0.306 Angle : 0.742 14.355 41419 Z= 0.385 Chirality : 0.051 0.323 4836 Planarity : 0.006 0.073 5289 Dihedral : 4.844 52.497 4056 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.51 % Rotamer: Outliers : 1.75 % Allowed : 9.44 % Favored : 88.81 % 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 are not related in a simple way. whole: -0.07 (0.13), residues: 3748 helix: 0.47 (0.19), residues: 720 sheet: 0.57 (0.15), residues: 1067 loop : -0.55 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 346 TYR 0.041 0.002 TYR B 351 PHE 0.023 0.002 PHE A1042 TRP 0.023 0.002 TRP L 96 HIS 0.010 0.002 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.31 (30255) covalent geometry : angle 0.72688 / 0.38 (41232) SS BOND : bond 0.00816 / 0.39 ( 47) SS BOND : angle 2.02442 / 1.21 ( 94) hydrogen bonds : bond 0.04544 / 2.98 ( 1204) hydrogen bonds : angle 6.27492 / 4.36 ( 3415) Misc. bond : bond 0.02461 / 1.30 ( 1) link_BETA1-4 : bond 0.00497 / 0.34 ( 6) link_BETA1-4 : angle 2.64673 / 1.39 ( 18) link_NAG-ASN : bond 0.00539 / 0.28 ( 25) link_NAG-ASN : angle 2.54004 / 1.64 ( 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 296 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: B 436 TRP cc_start: 0.4074 (p90) cc_final: 0.3393 (p90) REVERT: B 985 ASP cc_start: 0.7856 (m-30) cc_final: 0.7479 (m-30) REVERT: A 100 ILE cc_start: 0.6176 (mp) cc_final: 0.5844 (tp) REVERT: A 192 PHE cc_start: 0.7919 (m-10) cc_final: 0.7622 (m-80) REVERT: A 403 ARG cc_start: 0.6429 (ptm160) cc_final: 0.5639 (ptt-90) REVERT: C 129 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7653 (mtmm) REVERT: H 96 CYS cc_start: 0.5576 (p) cc_final: 0.5248 (p) REVERT: H 111 ASP cc_start: 0.7749 (t0) cc_final: 0.7533 (t0) REVERT: L 28 ASP cc_start: 0.7260 (t70) cc_final: 0.6896 (p0) REVERT: L 70 ASP cc_start: 0.7210 (m-30) cc_final: 0.6603 (t0) REVERT: M 34 MET cc_start: 0.4580 (tpp) cc_final: 0.3953 (tpp) REVERT: N 4 MET cc_start: 0.3984 (mpp) cc_final: 0.3732 (pmm) REVERT: N 103 LYS cc_start: 0.5853 (mmtm) cc_final: 0.5179 (tttp) outliers start: 54 outliers final: 41 residues processed: 281 average time/residue: 0.1684 time to fit residues: 80.9700 Evaluate side-chains 260 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL 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 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 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 955 ASN 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 166 CYS 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 29 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 603 ASN 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 119 VAL Chi-restraints excluded: chain L residue 33 LEU 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 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: 0.5980 chunk 375 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 280 ASN B 563 GLN B 955 ASN B1011 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C1071 GLN H 82 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.186987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.138949 restraints weight = 98692.162| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.50 r_work: 0.3187 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 30334 Z= 0.176 Angle : 0.614 12.961 41419 Z= 0.318 Chirality : 0.047 0.298 4836 Planarity : 0.005 0.064 5289 Dihedral : 4.584 52.609 4056 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.47 % Rotamer: Outliers : 2.09 % Allowed : 10.44 % Favored : 87.47 % 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 are not related in a simple way. whole: 0.09 (0.13), residues: 3748 helix: 0.82 (0.19), residues: 704 sheet: 0.62 (0.15), residues: 1052 loop : -0.48 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.038 0.002 TYR B 351 PHE 0.016 0.002 PHE B1121 TRP 0.018 0.001 TRP N 96 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (30255) covalent geometry : angle 0.60075 / 0.31 (41232) SS BOND : bond 0.00371 / 0.26 ( 47) SS BOND : angle 1.59288 / 0.99 ( 94) hydrogen bonds : bond 0.03876 / 2.52 ( 1204) hydrogen bonds : angle 5.95777 / 4.15 ( 3415) Misc. bond : bond 0.02440 / 1.28 ( 1) link_BETA1-4 : bond 0.00831 / 0.60 ( 6) link_BETA1-4 : angle 2.39016 / 1.22 ( 18) link_NAG-ASN : bond 0.00411 / 0.18 ( 25) link_NAG-ASN : angle 2.28370 / 1.46 ( 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 300 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.6941 (m-10) cc_final: 0.6636 (m-10) REVERT: B 985 ASP cc_start: 0.7916 (m-30) cc_final: 0.7599 (m-30) REVERT: B 1130 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7743 (mt) REVERT: A 63 THR cc_start: 0.7888 (m) cc_final: 0.7667 (p) REVERT: A 100 ILE cc_start: 0.6126 (mp) cc_final: 0.5805 (tp) REVERT: A 192 PHE cc_start: 0.7898 (m-10) cc_final: 0.7629 (m-80) REVERT: A 403 ARG cc_start: 0.6223 (ptm160) cc_final: 0.5387 (ptt-90) REVERT: C 129 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7624 (mtpp) REVERT: C 780 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8317 (mm-30) REVERT: H 80 TYR cc_start: 0.6735 (m-80) cc_final: 0.6350 (m-80) REVERT: H 96 CYS cc_start: 0.5512 (p) cc_final: 0.5198 (p) REVERT: H 111 ASP cc_start: 0.7817 (t0) cc_final: 0.7607 (t0) REVERT: H 193 THR cc_start: 0.2654 (OUTLIER) cc_final: 0.2198 (p) REVERT: L 28 ASP cc_start: 0.7300 (t70) cc_final: 0.6958 (p0) REVERT: L 70 ASP cc_start: 0.7218 (m-30) cc_final: 0.6609 (t0) REVERT: M 34 MET cc_start: 0.4677 (tpp) cc_final: 0.4045 (tpp) REVERT: N 103 LYS cc_start: 0.5928 (mmtm) cc_final: 0.5375 (tttp) outliers start: 65 outliers final: 39 residues processed: 286 average time/residue: 0.1596 time to fit residues: 79.0010 Evaluate side-chains 261 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 286 THR 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 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET 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 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 1132 ILE 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 749 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR 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 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: 0.5980 chunk 289 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 320 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 363 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN H 202 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.186882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137288 restraints weight = 85795.648| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.80 r_work: 0.3233 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 30334 Z= 0.161 Angle : 0.587 11.659 41419 Z= 0.304 Chirality : 0.046 0.286 4836 Planarity : 0.005 0.059 5289 Dihedral : 4.469 51.621 4056 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.03 % Allowed : 11.78 % Favored : 86.20 % 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 are not related in a simple way. whole: 0.16 (0.14), residues: 3748 helix: 0.99 (0.20), residues: 698 sheet: 0.59 (0.15), residues: 1065 loop : -0.43 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.033 0.001 TYR B 351 PHE 0.017 0.001 PHE C 592 TRP 0.017 0.001 TRP N 96 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (30255) covalent geometry : angle 0.57469 / 0.30 (41232) SS BOND : bond 0.00335 / 0.24 ( 47) SS BOND : angle 1.48068 / 0.90 ( 94) hydrogen bonds : bond 0.03648 / 2.37 ( 1204) hydrogen bonds : angle 5.73136 / 3.99 ( 3415) Misc. bond : bond 0.02360 / 1.24 ( 1) link_BETA1-4 : bond 0.00805 / 0.58 ( 6) link_BETA1-4 : angle 2.33462 / 1.19 ( 18) link_NAG-ASN : bond 0.00402 / 0.18 ( 25) link_NAG-ASN : angle 2.15241 / 1.37 ( 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 284 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 955 ASN cc_start: 0.8605 (m-40) cc_final: 0.8375 (m-40) REVERT: B 985 ASP cc_start: 0.7790 (m-30) cc_final: 0.7486 (m-30) REVERT: B 1130 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7633 (mt) REVERT: A 63 THR cc_start: 0.7870 (m) cc_final: 0.7669 (p) REVERT: A 100 ILE cc_start: 0.6104 (mp) cc_final: 0.5806 (tp) REVERT: A 192 PHE cc_start: 0.7842 (m-10) cc_final: 0.7608 (m-80) REVERT: A 403 ARG cc_start: 0.6216 (ptm160) cc_final: 0.5341 (ptt-90) REVERT: A 934 ILE cc_start: 0.8612 (mm) cc_final: 0.8407 (mm) REVERT: C 324 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: C 780 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8210 (mm-30) REVERT: H 80 TYR cc_start: 0.6652 (m-80) cc_final: 0.6254 (m-80) REVERT: H 96 CYS cc_start: 0.5492 (p) cc_final: 0.5205 (p) REVERT: H 111 ASP cc_start: 0.7789 (t0) cc_final: 0.7577 (t0) REVERT: H 193 THR cc_start: 0.2591 (OUTLIER) cc_final: 0.2128 (p) REVERT: L 28 ASP cc_start: 0.7265 (t70) cc_final: 0.7065 (t0) REVERT: L 70 ASP cc_start: 0.7207 (m-30) cc_final: 0.6578 (t0) REVERT: M 34 MET cc_start: 0.4498 (tpp) cc_final: 0.4042 (tpp) REVERT: N 103 LYS cc_start: 0.6135 (mmtm) cc_final: 0.5530 (tttp) outliers start: 63 outliers final: 42 residues processed: 268 average time/residue: 0.1622 time to fit residues: 75.2757 Evaluate side-chains 253 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 345 THR 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 791 THR Chi-restraints excluded: chain B residue 900 MET 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 166 CYS Chi-restraints excluded: chain A residue 341 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 826 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 615 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 H residue 28 THR 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 L residue 91 HIS Chi-restraints excluded: chain L residue 96 TRP 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 ************** Weight determination summary: number of chunks: 378 random chunks: chunk 1 optimal weight: 0.9980 chunk 306 optimal weight: 40.0000 chunk 320 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 352 optimal weight: 30.0000 chunk 269 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 293 optimal weight: 0.5980 chunk 193 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 239 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.189221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142265 restraints weight = 85493.904| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.54 r_work: 0.3250 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 30334 Z= 0.173 Angle : 0.584 10.899 41419 Z= 0.303 Chirality : 0.046 0.289 4836 Planarity : 0.005 0.056 5289 Dihedral : 4.441 50.635 4056 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 2.40 % Allowed : 12.18 % Favored : 85.42 % 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 are not related in a simple way. whole: 0.16 (0.14), residues: 3748 helix: 1.09 (0.20), residues: 687 sheet: 0.54 (0.15), residues: 1072 loop : -0.45 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.036 0.001 TYR B 351 PHE 0.020 0.002 PHE C 106 TRP 0.022 0.001 TRP N 96 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (30255) covalent geometry : angle 0.57133 / 0.30 (41232) SS BOND : bond 0.00380 / 0.28 ( 47) SS BOND : angle 1.60735 / 1.04 ( 94) hydrogen bonds : bond 0.03623 / 2.36 ( 1204) hydrogen bonds : angle 5.63210 / 3.93 ( 3415) Misc. bond : bond 0.02310 / 1.22 ( 1) link_BETA1-4 : bond 0.00778 / 0.56 ( 6) link_BETA1-4 : angle 2.35141 / 1.20 ( 18) link_NAG-ASN : bond 0.00385 / 0.17 ( 25) link_NAG-ASN : angle 2.11856 / 1.35 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 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: 75 poor density : 220 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.6782 (m-10) cc_final: 0.6526 (m-10) REVERT: B 955 ASN cc_start: 0.8602 (m-40) cc_final: 0.8393 (m-40) REVERT: B 985 ASP cc_start: 0.7721 (m-30) cc_final: 0.7277 (m-30) REVERT: B 1130 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7729 (mt) REVERT: A 63 THR cc_start: 0.7871 (m) cc_final: 0.7659 (p) REVERT: A 403 ARG cc_start: 0.6281 (ptm160) cc_final: 0.5349 (ptt-90) REVERT: C 780 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8170 (mm-30) REVERT: H 80 TYR cc_start: 0.6731 (m-80) cc_final: 0.6332 (m-80) REVERT: H 96 CYS cc_start: 0.5479 (p) cc_final: 0.5187 (p) REVERT: H 193 THR cc_start: 0.2523 (OUTLIER) cc_final: 0.2087 (p) REVERT: L 28 ASP cc_start: 0.7227 (t70) cc_final: 0.6925 (p0) REVERT: L 70 ASP cc_start: 0.7145 (m-30) cc_final: 0.6563 (t0) REVERT: M 34 MET cc_start: 0.4569 (tpp) cc_final: 0.4218 (tpp) REVERT: N 103 LYS cc_start: 0.6099 (mmtm) cc_final: 0.5481 (tttp) outliers start: 75 outliers final: 55 residues processed: 275 average time/residue: 0.1595 time to fit residues: 75.8407 Evaluate side-chains 259 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 317 ASN Chi-restraints excluded: chain B residue 345 THR 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 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP 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 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 826 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR 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 1040 VAL Chi-restraints excluded: chain H residue 28 THR 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 L residue 91 HIS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain M residue 5 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 372 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 328 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 222 optimal weight: 0.0170 chunk 227 optimal weight: 6.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 901 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.185380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150692 restraints weight = 107332.664| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 6.60 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 30334 Z= 0.194 Angle : 0.600 10.687 41419 Z= 0.310 Chirality : 0.047 0.291 4836 Planarity : 0.005 0.057 5289 Dihedral : 4.519 50.347 4056 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 2.46 % Allowed : 12.09 % Favored : 85.45 % 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 are not related in a simple way. whole: 0.07 (0.14), residues: 3748 helix: 1.01 (0.20), residues: 692 sheet: 0.50 (0.16), residues: 1062 loop : -0.52 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.037 0.001 TYR B 351 PHE 0.019 0.002 PHE A 168 TRP 0.014 0.001 TRP L 96 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (30255) covalent geometry : angle 0.58664 / 0.31 (41232) SS BOND : bond 0.00334 / 0.23 ( 47) SS BOND : angle 1.67004 / 1.09 ( 94) hydrogen bonds : bond 0.03687 / 2.41 ( 1204) hydrogen bonds : angle 5.61141 / 3.92 ( 3415) Misc. bond : bond 0.02307 / 1.21 ( 1) link_BETA1-4 : bond 0.00731 / 0.53 ( 6) link_BETA1-4 : angle 2.36960 / 1.21 ( 18) link_NAG-ASN : bond 0.00398 / 0.19 ( 25) link_NAG-ASN : angle 2.15041 / 1.37 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 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 286 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1130 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7845 (mt) REVERT: A 403 ARG cc_start: 0.6540 (ptm160) cc_final: 0.5859 (ptt-90) REVERT: C 780 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7466 (mm-30) REVERT: C 1017 GLU cc_start: 0.7649 (tp30) cc_final: 0.7449 (tp30) REVERT: H 80 TYR cc_start: 0.6279 (m-80) cc_final: 0.6034 (m-80) REVERT: H 96 CYS cc_start: 0.5017 (p) cc_final: 0.4670 (p) REVERT: H 193 THR cc_start: 0.3076 (OUTLIER) cc_final: 0.2686 (p) outliers start: 77 outliers final: 60 residues processed: 265 average time/residue: 0.1645 time to fit residues: 75.7680 Evaluate side-chains 265 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU 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 196 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 345 THR 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 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 166 CYS 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 C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 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 H residue 28 THR 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 H residue 207 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 283 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 246 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 337 optimal weight: 30.0000 chunk 364 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.1292 > 50:) chunk 187 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 955 ASN B1011 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN L 27 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.186289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.152799 restraints weight = 98998.043| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 6.26 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 30334 Z= 0.151 Angle : 0.575 10.530 41419 Z= 0.297 Chirality : 0.045 0.285 4836 Planarity : 0.004 0.055 5289 Dihedral : 4.421 49.961 4056 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 2.18 % Allowed : 13.03 % Favored : 84.79 % 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 are not related in a simple way. whole: 0.15 (0.14), residues: 3748 helix: 1.13 (0.20), residues: 692 sheet: 0.53 (0.16), residues: 1064 loop : -0.47 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.037 0.001 TYR B 351 PHE 0.018 0.001 PHE A 168 TRP 0.014 0.001 TRP N 96 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (30255) covalent geometry : angle 0.56313 / 0.29 (41232) SS BOND : bond 0.00334 / 0.23 ( 47) SS BOND : angle 1.51816 / 0.96 ( 94) hydrogen bonds : bond 0.03515 / 2.29 ( 1204) hydrogen bonds : angle 5.52317 / 3.86 ( 3415) Misc. bond : bond 0.02295 / 1.21 ( 1) link_BETA1-4 : bond 0.00750 / 0.54 ( 6) link_BETA1-4 : angle 2.32074 / 1.18 ( 18) link_NAG-ASN : bond 0.00375 / 0.16 ( 25) link_NAG-ASN : angle 2.07503 / 1.32 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 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 281 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1130 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7862 (mt) REVERT: A 403 ARG cc_start: 0.6507 (ptm160) cc_final: 0.5887 (ptt-90) REVERT: C 780 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7439 (mm-30) REVERT: C 1017 GLU cc_start: 0.7654 (tp30) cc_final: 0.7434 (tp30) REVERT: H 80 TYR cc_start: 0.6317 (m-80) cc_final: 0.6066 (m-80) REVERT: H 96 CYS cc_start: 0.5024 (p) cc_final: 0.4682 (p) REVERT: H 193 THR cc_start: 0.3112 (OUTLIER) cc_final: 0.2728 (p) outliers start: 68 outliers final: 57 residues processed: 260 average time/residue: 0.1635 time to fit residues: 73.5548 Evaluate side-chains 259 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 ILE 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 320 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 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 786 LYS 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 166 CYS 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 826 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 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 H residue 28 THR 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 H residue 207 ASN Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 334 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 266 optimal weight: 0.7980 chunk 314 optimal weight: 8.9990 chunk 374 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 193 optimal weight: 0.0060 chunk 99 optimal weight: 0.0370 overall best weight: 1.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 437 ASN B 955 ASN B1011 GLN A 360 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.186289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136588 restraints weight = 85050.616| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.78 r_work: 0.3231 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 30334 Z= 0.153 Angle : 0.573 10.070 41419 Z= 0.296 Chirality : 0.045 0.284 4836 Planarity : 0.004 0.056 5289 Dihedral : 4.384 49.503 4056 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 2.27 % Allowed : 13.28 % Favored : 84.45 % 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 are not related in a simple way. whole: 0.18 (0.14), residues: 3748 helix: 1.17 (0.20), residues: 691 sheet: 0.57 (0.16), residues: 1054 loop : -0.47 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.038 0.001 TYR B 351 PHE 0.019 0.001 PHE C 106 TRP 0.017 0.001 TRP M 36 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (30255) covalent geometry : angle 0.56150 / 0.29 (41232) SS BOND : bond 0.00315 / 0.22 ( 47) SS BOND : angle 1.46803 / 0.92 ( 94) hydrogen bonds : bond 0.03487 / 2.28 ( 1204) hydrogen bonds : angle 5.47293 / 3.82 ( 3415) Misc. bond : bond 0.02251 / 1.18 ( 1) link_BETA1-4 : bond 0.00806 / 0.58 ( 6) link_BETA1-4 : angle 2.31870 / 1.18 ( 18) link_NAG-ASN : bond 0.00368 / 0.16 ( 25) link_NAG-ASN : angle 2.04505 / 1.30 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 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 280 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 209 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.6901 (m-10) cc_final: 0.6676 (m-10) REVERT: B 1130 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7770 (mt) REVERT: A 403 ARG cc_start: 0.6327 (ptm160) cc_final: 0.5434 (ptt-90) REVERT: A 455 LEU cc_start: 0.8445 (mt) cc_final: 0.8198 (mt) REVERT: C 239 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: C 780 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8308 (mm-30) REVERT: H 80 TYR cc_start: 0.6744 (m-80) cc_final: 0.6342 (m-80) REVERT: H 96 CYS cc_start: 0.5402 (p) cc_final: 0.5112 (p) REVERT: H 193 THR cc_start: 0.2566 (OUTLIER) cc_final: 0.2175 (p) REVERT: M 161 THR cc_start: 0.4111 (m) cc_final: 0.3644 (p) outliers start: 71 outliers final: 60 residues processed: 260 average time/residue: 0.1613 time to fit residues: 72.3601 Evaluate side-chains 262 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 ILE 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 196 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 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 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 166 CYS 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 826 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 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 785 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 28 THR 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 H residue 207 ASN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 92 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 200 optimal weight: 0.0170 chunk 15 optimal weight: 4.9990 chunk 282 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 111 optimal weight: 7.9990 chunk 267 optimal weight: 0.7980 chunk 339 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C 641 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.189031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136962 restraints weight = 77034.631| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.30 r_work: 0.3299 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 30334 Z= 0.111 Angle : 0.553 9.905 41419 Z= 0.286 Chirality : 0.045 0.280 4836 Planarity : 0.004 0.055 5289 Dihedral : 4.220 48.788 4056 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.81 % Allowed : 14.12 % Favored : 84.08 % 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 are not related in a simple way. whole: 0.30 (0.14), residues: 3748 helix: 1.31 (0.20), residues: 691 sheet: 0.59 (0.16), residues: 1034 loop : -0.36 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.038 0.001 TYR B 351 PHE 0.020 0.001 PHE A 168 TRP 0.023 0.001 TRP L 35 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (30255) covalent geometry : angle 0.54199 / 0.28 (41232) SS BOND : bond 0.00275 / 0.19 ( 47) SS BOND : angle 1.28887 / 0.79 ( 94) hydrogen bonds : bond 0.03276 / 2.13 ( 1204) hydrogen bonds : angle 5.33592 / 3.73 ( 3415) Misc. bond : bond 0.02275 / 1.20 ( 1) link_BETA1-4 : bond 0.00715 / 0.50 ( 6) link_BETA1-4 : angle 2.22427 / 1.12 ( 18) link_NAG-ASN : bond 0.00381 / 0.16 ( 25) link_NAG-ASN : angle 1.95443 / 1.23 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 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 266 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ARG cc_start: 0.7900 (mtp-110) cc_final: 0.7638 (mtm-85) REVERT: B 855 PHE cc_start: 0.6850 (m-10) cc_final: 0.6631 (m-10) REVERT: B 950 ASP cc_start: 0.8138 (m-30) cc_final: 0.7933 (m-30) REVERT: B 1130 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7580 (mt) REVERT: A 403 ARG cc_start: 0.6192 (ptm160) cc_final: 0.5287 (ptt-90) REVERT: C 220 PHE cc_start: 0.7389 (t80) cc_final: 0.7163 (t80) REVERT: C 780 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8179 (mm-30) REVERT: H 80 TYR cc_start: 0.6699 (m-80) cc_final: 0.6279 (m-80) REVERT: H 96 CYS cc_start: 0.5197 (p) cc_final: 0.4943 (p) REVERT: H 193 THR cc_start: 0.2598 (OUTLIER) cc_final: 0.2277 (p) REVERT: M 161 THR cc_start: 0.4042 (m) cc_final: 0.3591 (p) outliers start: 56 outliers final: 44 residues processed: 250 average time/residue: 0.1516 time to fit residues: 66.2378 Evaluate side-chains 239 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU 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 320 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR 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 916 LEU 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 166 CYS 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 826 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 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 785 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 198 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 372 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 291 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 305 optimal weight: 0.0970 chunk 203 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.186719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137470 restraints weight = 86998.589| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.95 r_work: 0.3227 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 30334 Z= 0.151 Angle : 0.566 9.710 41419 Z= 0.292 Chirality : 0.045 0.283 4836 Planarity : 0.004 0.054 5289 Dihedral : 4.246 48.135 4056 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 1.78 % Allowed : 14.15 % Favored : 84.08 % 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 are not related in a simple way. whole: 0.27 (0.14), residues: 3748 helix: 1.24 (0.20), residues: 693 sheet: 0.62 (0.16), residues: 1047 loop : -0.39 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.041 0.001 TYR B 351 PHE 0.031 0.001 PHE C 106 TRP 0.016 0.001 TRP L 96 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (30255) covalent geometry : angle 0.55543 / 0.29 (41232) SS BOND : bond 0.00299 / 0.21 ( 47) SS BOND : angle 1.38154 / 0.85 ( 94) hydrogen bonds : bond 0.03399 / 2.22 ( 1204) hydrogen bonds : angle 5.34122 / 3.73 ( 3415) Misc. bond : bond 0.02275 / 1.20 ( 1) link_BETA1-4 : bond 0.00762 / 0.55 ( 6) link_BETA1-4 : angle 2.26936 / 1.15 ( 18) link_NAG-ASN : bond 0.00363 / 0.15 ( 25) link_NAG-ASN : angle 1.98690 / 1.26 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8094.15 seconds wall clock time: 139 minutes 25.14 seconds (8365.14 seconds total)