Starting phenix.real_space_refine on Mon Jul 6 01:26:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc3_34650/07_2026/8hc3_34650.map" } resolution = 4.35 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= 0.003 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 137 5.16 5 C 20039 2.51 5 N 5185 2.21 5 O 6136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31497 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain: "H" Number of atoms: 1591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 bond proxies already assigned to first conformer: 1619 Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain: "D" Number of atoms: 1591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 bond proxies already assigned to first conformer: 1619 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.19, per 1000 atoms: 0.23 Number of scatterers: 31497 At special positions: 0 Unit cell: (146.85, 140.25, 247.5, 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 137 16.00 O 6136 8.00 N 5185 7.00 C 20039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 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=2.04 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 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 C 15 " - pdb=" SG CYS C 136 " 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 215 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 215 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " 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=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7396 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 67 sheets defined 19.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.894A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.526A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 388' Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.994A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.743A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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 781 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.838A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.844A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.048A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.928A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.556A pdb=" N PHE B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.869A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.807A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.739A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.950A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.813A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.534A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.819A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.517A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.853A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.361A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.588A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.691A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.835A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.513A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.895A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.505A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.033A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.839A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 removed outlier: 3.841A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.899A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.655A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 185 through 189 Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.170A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.590A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.729A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.864A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.581A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.920A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 4.256A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.760A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 removed outlier: 4.199A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 584 through 585 removed outlier: 3.671A pdb=" N PHE C 43 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 567 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.897A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 3.737A pdb=" N ILE C 788 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.901A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.901A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.118A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.653A pdb=" N ILE A 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.918A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 55 removed outlier: 4.134A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 Processing sheet with id=AC3, first strand: chain 'B' and resid 135 through 141 removed outlier: 10.887A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.690A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.679A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 511 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.651A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.422A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.833A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.833A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.031A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.990A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.475A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.019A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 140 through 142 removed outlier: 4.027A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 318 removed outlier: 3.783A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 359 removed outlier: 4.034A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.539A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.656A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.811A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.679A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 3.849A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.742A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.905A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.509A pdb=" N GLU L 106 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.685A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.587A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 149 through 151 Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.209A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR H 77 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.835A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.835A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 94 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.647A pdb=" N LEU H 138 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 182 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.647A pdb=" N LEU H 138 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 182 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.357A pdb=" N THR H 151 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN H 199 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 153 " --> pdb=" O ASN H 197 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS H 200 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.712A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 7 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.680A pdb=" N VAL E 11 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU E 106 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR E 103 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN E 37 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.583A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.612A pdb=" N CYS E 195 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.176A pdb=" N VAL D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 23 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 20 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 80 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 77 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN D 72 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.429A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 50 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 58 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.429A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D 101 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.971A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 181 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.971A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 194 through 200 removed outlier: 4.508A pdb=" N TYR D 194 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS D 196 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 209 " --> pdb=" O CYS D 196 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 2880 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: 8.41 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9991 1.35 - 1.47: 8027 1.47 - 1.59: 14022 1.59 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 32210 Sorted by residual: bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" C PHE L 119 " pdb=" N PRO L 120 " ideal model delta sigma weight residual 1.331 1.347 -0.016 8.70e-03 1.32e+04 3.44e+00 ... (remaining 32205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 43195 2.25 - 4.50: 545 4.50 - 6.75: 69 6.75 - 9.01: 9 9.01 - 11.26: 3 Bond angle restraints: 43821 Sorted by residual: angle pdb=" CB MET B 697 " pdb=" CG MET B 697 " pdb=" SD MET B 697 " ideal model delta sigma weight residual 112.70 123.96 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.46 127.48 -5.02 1.41e+00 5.03e-01 1.27e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.04 -4.34 1.22e+00 6.72e-01 1.26e+01 angle pdb=" C PHE L 119 " pdb=" N PRO L 120 " pdb=" CA PRO L 120 " ideal model delta sigma weight residual 119.66 117.09 2.57 7.30e-01 1.88e+00 1.24e+01 angle pdb=" C LYS H 143 " pdb=" N ASP H 144 " pdb=" CA ASP H 144 " ideal model delta sigma weight residual 122.46 127.41 -4.95 1.41e+00 5.03e-01 1.23e+01 ... (remaining 43816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 17134 17.90 - 35.79: 1360 35.79 - 53.69: 266 53.69 - 71.58: 48 71.58 - 89.48: 23 Dihedral angle restraints: 18831 sinusoidal: 7336 harmonic: 11495 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -171.37 85.37 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.85 82.15 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 174.60 -81.60 1 1.00e+01 1.00e-02 8.20e+01 ... (remaining 18828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4616 0.085 - 0.169: 502 0.169 - 0.254: 4 0.254 - 0.339: 2 0.339 - 0.424: 4 Chirality restraints: 5128 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 5125 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 148 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO H 149 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO H 149 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 149 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO C 330 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.018 2.00e-02 2.50e+03 1.66e-02 3.42e+00 pdb=" CG ASN B 61 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " 0.018 2.00e-02 2.50e+03 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2249 2.74 - 3.28: 29290 3.28 - 3.82: 51897 3.82 - 4.36: 57017 4.36 - 4.90: 99733 Nonbonded interactions: 240186 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.206 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG B 328 " pdb=" OD1 ASP B 578 " model vdw 2.274 3.120 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.276 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.291 3.040 ... (remaining 240181 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 1 through 16 or resid 18 through 217)) selection = (chain 'H' and (resid 1 through 16 or resid 18 through 217)) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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=0.02 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.120 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.003 0.046 32316 Z= 0.157 Angle : 0.612 12.257 44087 Z= 0.295 Chirality : 0.047 0.424 5128 Planarity : 0.004 0.054 5580 Dihedral : 13.275 89.477 11279 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 3890 helix: 0.89 (0.20), residues: 686 sheet: 0.95 (0.18), residues: 863 loop : -1.03 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1019 TYR 0.013 0.001 TYR A 453 PHE 0.030 0.001 PHE B 275 TRP 0.007 0.001 TRP H 154 HIS 0.005 0.000 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (32210) covalent geometry : angle 0.59388 / 0.29 (43821) SS BOND : bond 0.00141 / 0.09 ( 52) SS BOND : angle 0.57352 / 0.38 ( 104) hydrogen bonds : bond 0.22839 / 15.23 ( 1013) hydrogen bonds : angle 8.54187 / 5.83 ( 2880) link_BETA1-4 : bond 0.00450 / 0.25 ( 12) link_BETA1-4 : angle 0.84363 / 0.58 ( 36) link_NAG-ASN : bond 0.00666 / 0.46 ( 42) link_NAG-ASN : angle 2.83779 / 2.02 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.7611 (pmm) cc_final: 0.7285 (pmm) REVERT: B 1031 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7241 (tp30) REVERT: B 1138 TYR cc_start: 0.7300 (t80) cc_final: 0.6946 (t80) REVERT: C 740 MET cc_start: 0.7737 (tmm) cc_final: 0.6751 (tmm) REVERT: C 878 LEU cc_start: 0.9308 (mt) cc_final: 0.9002 (mt) REVERT: C 900 MET cc_start: 0.9152 (mmp) cc_final: 0.8780 (mpp) REVERT: D 149 PRO cc_start: -0.3270 (Cg_endo) cc_final: -0.3785 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1834 time to fit residues: 41.8264 Evaluate side-chains 100 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 978 ASN A1002 GLN A1101 HIS B 360 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 804 GLN B 824 ASN B 955 ASN B1002 GLN B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 188 ASN C 505 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C1106 GLN L 156 GLN H 3 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 37 GLN E 211 ASN D 35 HIS D 200 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.086344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.061750 restraints weight = 246985.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061812 restraints weight = 153567.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.061841 restraints weight = 104236.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062134 restraints weight = 98733.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062358 restraints weight = 78589.883| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 32316 Z= 0.319 Angle : 0.834 11.014 44087 Z= 0.423 Chirality : 0.052 0.414 5128 Planarity : 0.006 0.056 5580 Dihedral : 4.583 22.489 4234 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 0.41 % Allowed : 7.69 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.13), residues: 3890 helix: 0.90 (0.20), residues: 673 sheet: 0.50 (0.17), residues: 914 loop : -1.09 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 457 TYR 0.030 0.003 TYR A 266 PHE 0.042 0.003 PHE B 201 TRP 0.025 0.002 TRP A1102 HIS 0.009 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.32 (32210) covalent geometry : angle 0.81263 / 0.42 (43821) SS BOND : bond 0.00513 / 0.34 ( 52) SS BOND : angle 1.43098 / 1.00 ( 104) hydrogen bonds : bond 0.05271 / 3.41 ( 1013) hydrogen bonds : angle 6.24142 / 4.28 ( 2880) link_BETA1-4 : bond 0.00501 / 0.25 ( 12) link_BETA1-4 : angle 2.32795 / 1.64 ( 36) link_NAG-ASN : bond 0.00760 / 0.50 ( 42) link_NAG-ASN : angle 3.25035 / 2.33 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6957 (ttm170) REVERT: A 491 PRO cc_start: 0.6116 (Cg_exo) cc_final: 0.5906 (Cg_endo) REVERT: A 500 THR cc_start: 0.6226 (OUTLIER) cc_final: 0.6016 (p) REVERT: A 549 THR cc_start: 0.7198 (t) cc_final: 0.6916 (m) REVERT: A 1050 MET cc_start: 0.8891 (pmm) cc_final: 0.7530 (pmm) REVERT: C 191 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 740 MET cc_start: 0.7938 (tmm) cc_final: 0.7338 (tmm) REVERT: L 24 ARG cc_start: 0.5603 (mtm-85) cc_final: 0.5049 (mtp-110) REVERT: D 149 PRO cc_start: -0.3100 (Cg_endo) cc_final: -0.3397 (Cg_exo) outliers start: 14 outliers final: 7 residues processed: 126 average time/residue: 0.1851 time to fit residues: 40.0089 Evaluate side-chains 87 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 195 optimal weight: 3.9990 chunk 188 optimal weight: 0.0770 chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 211 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 309 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 342 optimal weight: 20.0000 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 784 GLN B 955 ASN B1002 GLN B1083 HIS C 907 ASN H 3 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.090435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.064510 restraints weight = 252750.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064323 restraints weight = 147010.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064681 restraints weight = 109034.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.064779 restraints weight = 95827.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065010 restraints weight = 86361.492| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32316 Z= 0.138 Angle : 0.563 10.570 44087 Z= 0.284 Chirality : 0.046 0.444 5128 Planarity : 0.004 0.075 5580 Dihedral : 3.963 19.955 4234 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 3890 helix: 1.52 (0.21), residues: 668 sheet: 0.41 (0.16), residues: 950 loop : -0.98 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 328 TYR 0.012 0.001 TYR D 79 PHE 0.018 0.001 PHE C 490 TRP 0.013 0.001 TRP A 64 HIS 0.007 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (32210) covalent geometry : angle 0.54201 / 0.28 (43821) SS BOND : bond 0.00397 / 0.26 ( 52) SS BOND : angle 1.21622 / 0.88 ( 104) hydrogen bonds : bond 0.04104 / 2.70 ( 1013) hydrogen bonds : angle 5.54456 / 3.80 ( 2880) link_BETA1-4 : bond 0.00261 / 0.13 ( 12) link_BETA1-4 : angle 1.03254 / 0.73 ( 36) link_NAG-ASN : bond 0.00507 / 0.35 ( 42) link_NAG-ASN : angle 2.65776 / 1.95 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7979 (tp) cc_final: 0.7690 (mm) REVERT: A 466 ARG cc_start: 0.7257 (ttm170) cc_final: 0.6901 (ttm170) REVERT: A 491 PRO cc_start: 0.5959 (Cg_exo) cc_final: 0.5720 (Cg_endo) REVERT: A 549 THR cc_start: 0.6919 (t) cc_final: 0.6623 (m) REVERT: A 1050 MET cc_start: 0.8861 (pmm) cc_final: 0.7684 (pmm) REVERT: B 900 MET cc_start: 0.9055 (pmm) cc_final: 0.8800 (pmm) REVERT: C 587 ILE cc_start: 0.9468 (mm) cc_final: 0.9254 (mm) REVERT: C 731 MET cc_start: 0.9183 (pmm) cc_final: 0.8959 (pmm) REVERT: C 740 MET cc_start: 0.7916 (tmm) cc_final: 0.7087 (tmm) REVERT: L 24 ARG cc_start: 0.5541 (mtm-85) cc_final: 0.4993 (mtp-110) REVERT: H 83 ARG cc_start: 0.4121 (tmt-80) cc_final: 0.3338 (mtm-85) REVERT: D 149 PRO cc_start: -0.3529 (Cg_endo) cc_final: -0.3985 (Cg_exo) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.2011 time to fit residues: 36.0210 Evaluate side-chains 78 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 63 optimal weight: 3.9990 chunk 332 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 14 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN L 89 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.082876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.059602 restraints weight = 241907.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.058533 restraints weight = 152918.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058908 restraints weight = 128006.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059164 restraints weight = 102459.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.059233 restraints weight = 94722.931| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 32316 Z= 0.336 Angle : 0.839 11.717 44087 Z= 0.423 Chirality : 0.051 0.481 5128 Planarity : 0.006 0.061 5580 Dihedral : 5.109 27.767 4234 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.17 % Allowed : 5.05 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 3890 helix: 0.74 (0.20), residues: 674 sheet: 0.04 (0.16), residues: 961 loop : -1.29 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 357 TYR 0.026 0.003 TYR B 796 PHE 0.055 0.003 PHE A 392 TRP 0.023 0.002 TRP A1102 HIS 0.009 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.34 (32210) covalent geometry : angle 0.81332 / 0.42 (43821) SS BOND : bond 0.00601 / 0.38 ( 52) SS BOND : angle 1.82977 / 1.26 ( 104) hydrogen bonds : bond 0.05086 / 3.31 ( 1013) hydrogen bonds : angle 6.04934 / 4.15 ( 2880) link_BETA1-4 : bond 0.00531 / 0.31 ( 12) link_BETA1-4 : angle 1.83887 / 1.19 ( 36) link_NAG-ASN : bond 0.00941 / 0.60 ( 42) link_NAG-ASN : angle 3.51196 / 2.49 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8271 (tp) cc_final: 0.7850 (mm) REVERT: A 1050 MET cc_start: 0.8853 (pmm) cc_final: 0.7962 (pmm) REVERT: B 740 MET cc_start: 0.8744 (tpp) cc_final: 0.7926 (tpt) REVERT: B 1029 MET cc_start: 0.9354 (tmm) cc_final: 0.9066 (tmm) REVERT: C 740 MET cc_start: 0.8111 (tmm) cc_final: 0.7315 (tmm) REVERT: L 24 ARG cc_start: 0.5651 (mtm-85) cc_final: 0.5129 (mtp-110) REVERT: H 83 ARG cc_start: 0.4617 (tmt-80) cc_final: 0.3757 (mtm-85) REVERT: E 174 TYR cc_start: 0.6814 (m-80) cc_final: 0.6538 (m-80) REVERT: D 149 PRO cc_start: -0.3751 (Cg_endo) cc_final: -0.4236 (Cg_exo) outliers start: 6 outliers final: 2 residues processed: 95 average time/residue: 0.2121 time to fit residues: 33.6364 Evaluate side-chains 68 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 356 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 220 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 352 optimal weight: 0.0670 chunk 194 optimal weight: 0.0170 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.088011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060878 restraints weight = 284694.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059104 restraints weight = 195355.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059709 restraints weight = 160274.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059923 restraints weight = 112390.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060050 restraints weight = 100171.329| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32316 Z= 0.119 Angle : 0.581 11.660 44087 Z= 0.291 Chirality : 0.046 0.490 5128 Planarity : 0.004 0.056 5580 Dihedral : 4.304 21.405 4234 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.06 % Allowed : 1.80 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 3890 helix: 1.53 (0.21), residues: 659 sheet: 0.06 (0.16), residues: 955 loop : -1.12 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 328 TYR 0.023 0.001 TYR D 59 PHE 0.025 0.001 PHE B 543 TRP 0.012 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (32210) covalent geometry : angle 0.55640 / 0.29 (43821) SS BOND : bond 0.00296 / 0.20 ( 52) SS BOND : angle 1.51717 / 0.89 ( 104) hydrogen bonds : bond 0.03957 / 2.57 ( 1013) hydrogen bonds : angle 5.36952 / 3.69 ( 2880) link_BETA1-4 : bond 0.00293 / 0.16 ( 12) link_BETA1-4 : angle 0.86830 / 0.60 ( 36) link_NAG-ASN : bond 0.00597 / 0.38 ( 42) link_NAG-ASN : angle 2.85294 / 2.05 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7969 (tp) cc_final: 0.7662 (mm) REVERT: A 1050 MET cc_start: 0.8274 (pmm) cc_final: 0.7350 (pmm) REVERT: B 740 MET cc_start: 0.8663 (tpp) cc_final: 0.7833 (tpt) REVERT: C 587 ILE cc_start: 0.9376 (mm) cc_final: 0.9158 (mm) REVERT: C 740 MET cc_start: 0.8236 (tmm) cc_final: 0.7333 (tmm) REVERT: L 24 ARG cc_start: 0.6083 (mtm-85) cc_final: 0.5502 (mtp-110) REVERT: E 174 TYR cc_start: 0.6492 (m-80) cc_final: 0.6273 (m-80) REVERT: D 149 PRO cc_start: -0.2938 (Cg_endo) cc_final: -0.3538 (Cg_exo) outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.2055 time to fit residues: 33.4567 Evaluate side-chains 65 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 105 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 269 optimal weight: 8.9990 chunk 265 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.084882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061598 restraints weight = 249587.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060375 restraints weight = 154792.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060881 restraints weight = 117039.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060811 restraints weight = 101033.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060992 restraints weight = 94172.564| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32316 Z= 0.160 Angle : 0.594 11.732 44087 Z= 0.297 Chirality : 0.046 0.474 5128 Planarity : 0.004 0.059 5580 Dihedral : 4.267 23.200 4234 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 3890 helix: 1.50 (0.21), residues: 663 sheet: 0.13 (0.16), residues: 962 loop : -1.11 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 328 TYR 0.014 0.001 TYR B 796 PHE 0.021 0.001 PHE B 543 TRP 0.009 0.001 TRP A 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (32210) covalent geometry : angle 0.56894 / 0.29 (43821) SS BOND : bond 0.00347 / 0.23 ( 52) SS BOND : angle 1.36268 / 0.91 ( 104) hydrogen bonds : bond 0.03927 / 2.56 ( 1013) hydrogen bonds : angle 5.27056 / 3.63 ( 2880) link_BETA1-4 : bond 0.00178 / 0.10 ( 12) link_BETA1-4 : angle 1.03064 / 0.68 ( 36) link_NAG-ASN : bond 0.00539 / 0.36 ( 42) link_NAG-ASN : angle 2.98117 / 2.09 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.6993 (t) cc_final: 0.6667 (m) REVERT: A 1050 MET cc_start: 0.8677 (pmm) cc_final: 0.7301 (pmm) REVERT: B 740 MET cc_start: 0.8728 (tpp) cc_final: 0.7944 (tpt) REVERT: C 740 MET cc_start: 0.8229 (tmm) cc_final: 0.7629 (tmm) REVERT: L 24 ARG cc_start: 0.5997 (mtm-85) cc_final: 0.4920 (mtp-110) REVERT: H 83 ARG cc_start: 0.4501 (tmt-80) cc_final: 0.4072 (mtm-85) REVERT: E 174 TYR cc_start: 0.6779 (m-80) cc_final: 0.6436 (m-80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2163 time to fit residues: 31.2559 Evaluate side-chains 69 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 277 optimal weight: 4.9990 chunk 338 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 284 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 241 optimal weight: 0.5980 chunk 314 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 309 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 339 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** E 148 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 = 0.3890 r_free = 0.3890 target = 0.087741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.064612 restraints weight = 255868.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.063455 restraints weight = 191767.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064126 restraints weight = 147189.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064081 restraints weight = 113824.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064114 restraints weight = 110440.109| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32316 Z= 0.109 Angle : 0.543 10.824 44087 Z= 0.271 Chirality : 0.045 0.448 5128 Planarity : 0.004 0.056 5580 Dihedral : 4.043 20.500 4234 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 3890 helix: 1.82 (0.21), residues: 652 sheet: 0.15 (0.16), residues: 960 loop : -1.04 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.016 0.001 TYR H 59 PHE 0.018 0.001 PHE C 275 TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (32210) covalent geometry : angle 0.52090 / 0.27 (43821) SS BOND : bond 0.00239 / 0.16 ( 52) SS BOND : angle 1.16208 / 0.76 ( 104) hydrogen bonds : bond 0.03614 / 2.35 ( 1013) hydrogen bonds : angle 5.04364 / 3.47 ( 2880) link_BETA1-4 : bond 0.00244 / 0.13 ( 12) link_BETA1-4 : angle 0.81730 / 0.55 ( 36) link_NAG-ASN : bond 0.00502 / 0.34 ( 42) link_NAG-ASN : angle 2.74423 / 1.91 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.6983 (t) cc_final: 0.6645 (m) REVERT: A 1050 MET cc_start: 0.8692 (pmm) cc_final: 0.7297 (pmm) REVERT: B 740 MET cc_start: 0.8622 (tpp) cc_final: 0.7837 (tpt) REVERT: B 1029 MET cc_start: 0.9257 (tmm) cc_final: 0.9048 (tmm) REVERT: C 740 MET cc_start: 0.8168 (tmm) cc_final: 0.7553 (tmm) REVERT: L 24 ARG cc_start: 0.5848 (mtm-85) cc_final: 0.4739 (mtp-110) REVERT: E 174 TYR cc_start: 0.6997 (m-80) cc_final: 0.6526 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2109 time to fit residues: 33.2826 Evaluate side-chains 65 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 178 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 312 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 305 optimal weight: 0.0870 chunk 113 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 235 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 148 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 = 0.3906 r_free = 0.3906 target = 0.088292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.061012 restraints weight = 276894.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059776 restraints weight = 185587.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060057 restraints weight = 157816.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.060203 restraints weight = 124205.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060237 restraints weight = 112533.121| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32316 Z= 0.094 Angle : 0.528 10.407 44087 Z= 0.263 Chirality : 0.045 0.420 5128 Planarity : 0.004 0.056 5580 Dihedral : 3.855 20.040 4234 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3890 helix: 1.93 (0.21), residues: 654 sheet: 0.40 (0.16), residues: 945 loop : -1.02 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.020 0.001 TYR B 495 PHE 0.017 0.001 PHE C 275 TRP 0.011 0.001 TRP B 64 HIS 0.004 0.000 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (32210) covalent geometry : angle 0.50784 / 0.26 (43821) SS BOND : bond 0.00219 / 0.15 ( 52) SS BOND : angle 0.94068 / 0.62 ( 104) hydrogen bonds : bond 0.03381 / 2.20 ( 1013) hydrogen bonds : angle 4.90950 / 3.40 ( 2880) link_BETA1-4 : bond 0.00324 / 0.18 ( 12) link_BETA1-4 : angle 0.80059 / 0.54 ( 36) link_NAG-ASN : bond 0.00499 / 0.34 ( 42) link_NAG-ASN : angle 2.60833 / 1.80 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8006 (m) cc_final: 0.7804 (p) REVERT: A 549 THR cc_start: 0.7047 (t) cc_final: 0.6787 (m) REVERT: A 1050 MET cc_start: 0.8670 (pmm) cc_final: 0.7264 (pmm) REVERT: C 740 MET cc_start: 0.8234 (tmm) cc_final: 0.7595 (tmm) REVERT: L 24 ARG cc_start: 0.6159 (mtm-85) cc_final: 0.5296 (mtp-110) REVERT: E 174 TYR cc_start: 0.6443 (m-80) cc_final: 0.6218 (m-80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1937 time to fit residues: 30.4186 Evaluate side-chains 63 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 343 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 385 optimal weight: 40.0000 chunk 366 optimal weight: 40.0000 chunk 68 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN H 81 GLN E 92 ASN ** E 148 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 = 0.3812 r_free = 0.3812 target = 0.084191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061561 restraints weight = 261341.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061124 restraints weight = 165369.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061422 restraints weight = 129979.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061440 restraints weight = 103107.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061783 restraints weight = 99125.719| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32316 Z= 0.181 Angle : 0.605 14.009 44087 Z= 0.302 Chirality : 0.046 0.413 5128 Planarity : 0.004 0.056 5580 Dihedral : 4.128 22.519 4234 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 3890 helix: 1.77 (0.21), residues: 654 sheet: 0.20 (0.16), residues: 973 loop : -1.02 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 905 TYR 0.021 0.001 TYR A 741 PHE 0.016 0.001 PHE H 67 TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (32210) covalent geometry : angle 0.58238 / 0.30 (43821) SS BOND : bond 0.00333 / 0.21 ( 52) SS BOND : angle 1.20913 / 0.83 ( 104) hydrogen bonds : bond 0.03863 / 2.52 ( 1013) hydrogen bonds : angle 5.09853 / 3.52 ( 2880) link_BETA1-4 : bond 0.00169 / 0.10 ( 12) link_BETA1-4 : angle 1.04877 / 0.68 ( 36) link_NAG-ASN : bond 0.00577 / 0.38 ( 42) link_NAG-ASN : angle 2.94306 / 2.13 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8288 (m) cc_final: 0.7996 (p) REVERT: A 549 THR cc_start: 0.7125 (t) cc_final: 0.6830 (m) REVERT: A 740 MET cc_start: 0.8485 (mtt) cc_final: 0.8072 (mtt) REVERT: A 1050 MET cc_start: 0.8896 (pmm) cc_final: 0.7422 (pmm) REVERT: B 473 TYR cc_start: 0.2393 (t80) cc_final: 0.2173 (t80) REVERT: B 731 MET cc_start: 0.8473 (pmm) cc_final: 0.8129 (ptm) REVERT: B 740 MET cc_start: 0.8699 (tpp) cc_final: 0.7918 (tpt) REVERT: B 869 MET cc_start: 0.8984 (ptp) cc_final: 0.8665 (ptp) REVERT: B 1050 MET cc_start: 0.8609 (ppp) cc_final: 0.8383 (ppp) REVERT: C 740 MET cc_start: 0.8214 (tmm) cc_final: 0.7606 (tmm) REVERT: L 24 ARG cc_start: 0.5982 (mtm-85) cc_final: 0.4869 (mtp-110) REVERT: E 174 TYR cc_start: 0.6962 (m-80) cc_final: 0.6499 (m-80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1887 time to fit residues: 27.7885 Evaluate side-chains 66 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 342 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 330 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN H 81 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 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 = 0.3824 r_free = 0.3824 target = 0.084645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061241 restraints weight = 225736.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060146 restraints weight = 143776.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.060347 restraints weight = 121979.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060152 restraints weight = 120299.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060282 restraints weight = 100115.662| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32316 Z= 0.135 Angle : 0.567 13.163 44087 Z= 0.283 Chirality : 0.045 0.463 5128 Planarity : 0.004 0.055 5580 Dihedral : 4.069 21.083 4234 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.13), residues: 3890 helix: 1.84 (0.21), residues: 656 sheet: 0.24 (0.16), residues: 969 loop : -1.02 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG A 346 TYR 0.013 0.001 TYR C 873 PHE 0.023 0.001 PHE C 906 TRP 0.014 0.001 TRP B 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (32210) covalent geometry : angle 0.54399 / 0.28 (43821) SS BOND : bond 0.00255 / 0.17 ( 52) SS BOND : angle 1.31351 / 0.80 ( 104) hydrogen bonds : bond 0.03646 / 2.37 ( 1013) hydrogen bonds : angle 4.98498 / 3.45 ( 2880) link_BETA1-4 : bond 0.00228 / 0.13 ( 12) link_BETA1-4 : angle 0.90090 / 0.60 ( 36) link_NAG-ASN : bond 0.00516 / 0.34 ( 42) link_NAG-ASN : angle 2.84313 / 2.24 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.7988 (m) cc_final: 0.7731 (p) REVERT: A 549 THR cc_start: 0.7036 (t) cc_final: 0.6714 (m) REVERT: A 740 MET cc_start: 0.8492 (mtt) cc_final: 0.8239 (mtt) REVERT: A 1050 MET cc_start: 0.8758 (pmm) cc_final: 0.7490 (pmm) REVERT: B 731 MET cc_start: 0.8493 (pmm) cc_final: 0.8237 (ptm) REVERT: B 740 MET cc_start: 0.8649 (tpp) cc_final: 0.7874 (tpt) REVERT: C 740 MET cc_start: 0.8253 (tmm) cc_final: 0.7624 (tmm) REVERT: L 24 ARG cc_start: 0.6097 (mtm-85) cc_final: 0.5074 (mtp-110) REVERT: E 174 TYR cc_start: 0.6813 (m-80) cc_final: 0.6443 (m-80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1915 time to fit residues: 27.1582 Evaluate side-chains 63 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 209 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 338 optimal weight: 0.3980 chunk 270 optimal weight: 1.9990 chunk 321 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 148 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 = 0.3842 r_free = 0.3842 target = 0.085401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.062054 restraints weight = 225667.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060815 restraints weight = 139128.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061260 restraints weight = 108366.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061318 restraints weight = 89075.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061454 restraints weight = 82486.864| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32316 Z= 0.097 Angle : 0.537 12.975 44087 Z= 0.267 Chirality : 0.045 0.453 5128 Planarity : 0.004 0.055 5580 Dihedral : 3.906 21.889 4234 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 3890 helix: 1.99 (0.21), residues: 653 sheet: 0.33 (0.16), residues: 974 loop : -0.97 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 346 TYR 0.015 0.001 TYR B1067 PHE 0.018 0.001 PHE C 906 TRP 0.013 0.001 TRP B 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (32210) covalent geometry : angle 0.51490 / 0.26 (43821) SS BOND : bond 0.00280 / 0.17 ( 52) SS BOND : angle 1.20829 / 0.74 ( 104) hydrogen bonds : bond 0.03455 / 2.24 ( 1013) hydrogen bonds : angle 4.82370 / 3.34 ( 2880) link_BETA1-4 : bond 0.00291 / 0.16 ( 12) link_BETA1-4 : angle 0.80495 / 0.55 ( 36) link_NAG-ASN : bond 0.00528 / 0.35 ( 42) link_NAG-ASN : angle 2.69686 / 2.08 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4967.65 seconds wall clock time: 87 minutes 36.07 seconds (5256.07 seconds total)