Starting phenix.real_space_refine on Fri Jun 27 12:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hc3_34650/06_2025/8hc3_34650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc3_34650/06_2025/8hc3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hc3_34650/06_2025/8hc3_34650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc3_34650/06_2025/8hc3_34650.map" model { file = "/net/cci-nas-00/data/ceres_data/8hc3_34650/06_2025/8hc3_34650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc3_34650/06_2025/8hc3_34650.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.52s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 19.37, per 1000 atoms: 0.61 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: 7.55 Conformation dependent library (CDL) restraints added in 4.3 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: 4.97 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: 16.83 Time building geometry restraints manager: 9.27 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: 18139 17.90 - 35.79: 1409 35.79 - 53.69: 329 53.69 - 71.58: 65 71.58 - 89.48: 23 Dihedral angle restraints: 19965 sinusoidal: 8470 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 19962 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: 0.08 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: 1.070 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: 1.070 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 77.990 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.350 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: 0.030 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 13.395 89.477 12413 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP H 154 HIS 0.005 0.000 HIS B 954 PHE 0.030 0.001 PHE B 275 TYR 0.013 0.001 TYR A 453 ARG 0.011 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 42) link_NAG-ASN : angle 2.83779 ( 126) link_BETA1-4 : bond 0.00450 ( 12) link_BETA1-4 : angle 0.84363 ( 36) hydrogen bonds : bond 0.22839 ( 1013) hydrogen bonds : angle 8.54187 ( 2880) SS BOND : bond 0.00141 ( 52) SS BOND : angle 0.57352 ( 104) covalent geometry : bond 0.00308 (32210) covalent geometry : angle 0.59388 (43821) *********************** 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 : 3.346 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: 0.7239 (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: 0.8779 (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: 0.4149 time to fit residues: 94.8903 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 : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 0.0170 chunk 308 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 356 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN E 27 GLN E 211 ASN D 197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.096960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.073635 restraints weight = 275061.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.072534 restraints weight = 192041.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.072863 restraints weight = 152542.056| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.0818 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= 0.099 Angle : 0.504 9.246 44087 Z= 0.255 Chirality : 0.044 0.377 5128 Planarity : 0.004 0.044 5580 Dihedral : 6.455 58.761 5368 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3890 helix: 1.52 (0.21), residues: 684 sheet: 0.98 (0.17), residues: 853 loop : -0.90 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 64 HIS 0.004 0.001 HIS A1048 PHE 0.015 0.001 PHE C 400 TYR 0.014 0.001 TYR A 266 ARG 0.006 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 42) link_NAG-ASN : angle 2.43011 ( 126) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 0.98512 ( 36) hydrogen bonds : bond 0.03975 ( 1013) hydrogen bonds : angle 6.17546 ( 2880) SS BOND : bond 0.00249 ( 52) SS BOND : angle 0.81462 ( 104) covalent geometry : bond 0.00204 (32210) covalent geometry : angle 0.48570 (43821) *********************** 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 140 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 3.582 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 586 ASP cc_start: 0.7200 (m-30) cc_final: 0.6964 (m-30) REVERT: A 1029 MET cc_start: 0.8611 (tpp) cc_final: 0.8354 (ttm) REVERT: A 1050 MET cc_start: 0.8107 (pmm) cc_final: 0.7636 (pmm) REVERT: B 1138 TYR cc_start: 0.7273 (t80) cc_final: 0.6977 (t80) REVERT: C 242 LEU cc_start: 0.8622 (mm) cc_final: 0.7993 (mp) REVERT: C 740 MET cc_start: 0.7890 (tmm) cc_final: 0.7449 (tmm) REVERT: H 58 PHE cc_start: 0.6885 (m-10) cc_final: 0.6610 (m-10) outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 0.4029 time to fit residues: 97.8072 Evaluate side-chains 99 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 200 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 390 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 291 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 296 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 978 ASN A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 824 ASN B1002 GLN B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN E 37 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS D 200 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.090270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.065311 restraints weight = 250328.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.065312 restraints weight = 151269.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065336 restraints weight = 112095.792| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32316 Z= 0.214 Angle : 0.665 12.445 44087 Z= 0.337 Chirality : 0.047 0.454 5128 Planarity : 0.005 0.069 5580 Dihedral : 6.284 59.282 5368 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.15 % Allowed : 5.43 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 3890 helix: 1.40 (0.21), residues: 681 sheet: 0.77 (0.17), residues: 896 loop : -0.93 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1102 HIS 0.006 0.001 HIS A1064 PHE 0.038 0.002 PHE H 67 TYR 0.021 0.002 TYR B 796 ARG 0.018 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 42) link_NAG-ASN : angle 2.90146 ( 126) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.70457 ( 36) hydrogen bonds : bond 0.04522 ( 1013) hydrogen bonds : angle 5.57271 ( 2880) SS BOND : bond 0.00891 ( 52) SS BOND : angle 1.26578 ( 104) covalent geometry : bond 0.00459 (32210) covalent geometry : angle 0.64395 (43821) *********************** 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 112 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6842 (ttm170) REVERT: A 491 PRO cc_start: 0.5832 (Cg_exo) cc_final: 0.5595 (Cg_endo) REVERT: A 549 THR cc_start: 0.7028 (t) cc_final: 0.6712 (m) REVERT: A 1050 MET cc_start: 0.8835 (pmm) cc_final: 0.7611 (pmm) REVERT: C 740 MET cc_start: 0.7856 (tmm) cc_final: 0.7127 (tmm) REVERT: L 4 MET cc_start: 0.0735 (mmt) cc_final: 0.0513 (mmt) REVERT: L 24 ARG cc_start: 0.5098 (mtm-85) cc_final: 0.4752 (mtp-110) REVERT: L 148 GLN cc_start: 0.7087 (mp10) cc_final: 0.6611 (tp40) outliers start: 5 outliers final: 1 residues processed: 112 average time/residue: 0.4121 time to fit residues: 78.1998 Evaluate side-chains 84 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A1101 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 564 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN L 156 GLN H 3 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.091023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.065078 restraints weight = 265448.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.065521 restraints weight = 149230.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.065528 restraints weight = 105993.390| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32316 Z= 0.108 Angle : 0.520 10.099 44087 Z= 0.260 Chirality : 0.045 0.409 5128 Planarity : 0.004 0.065 5580 Dihedral : 5.718 59.618 5368 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3890 helix: 1.80 (0.21), residues: 668 sheet: 0.57 (0.17), residues: 939 loop : -0.85 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 154 HIS 0.009 0.001 HIS C1048 PHE 0.018 0.001 PHE C 275 TYR 0.016 0.001 TYR E 86 ARG 0.007 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 42) link_NAG-ASN : angle 2.49656 ( 126) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 0.90536 ( 36) hydrogen bonds : bond 0.03449 ( 1013) hydrogen bonds : angle 5.12489 ( 2880) SS BOND : bond 0.00438 ( 52) SS BOND : angle 1.11115 ( 104) covalent geometry : bond 0.00234 (32210) covalent geometry : angle 0.50077 (43821) *********************** 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 109 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 6.224 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 466 ARG cc_start: 0.7217 (ttm170) cc_final: 0.6823 (ttm170) REVERT: A 549 THR cc_start: 0.6492 (t) cc_final: 0.6129 (m) REVERT: A 1050 MET cc_start: 0.8762 (pmm) cc_final: 0.7745 (pmm) REVERT: C 242 LEU cc_start: 0.8855 (mm) cc_final: 0.8560 (mm) REVERT: C 740 MET cc_start: 0.7910 (tmm) cc_final: 0.7195 (tmm) REVERT: L 24 ARG cc_start: 0.5364 (mtm-85) cc_final: 0.4893 (mtp-110) REVERT: L 148 GLN cc_start: 0.6963 (mp10) cc_final: 0.6432 (tp40) outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.5746 time to fit residues: 107.6782 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 : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 277 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 383 optimal weight: 40.0000 chunk 211 optimal weight: 9.9990 chunk 343 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 81 GLN E 148 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.087844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.062929 restraints weight = 218282.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061640 restraints weight = 170292.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061763 restraints weight = 134360.435| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 32316 Z= 0.259 Angle : 0.695 10.169 44087 Z= 0.349 Chirality : 0.047 0.440 5128 Planarity : 0.005 0.085 5580 Dihedral : 6.216 59.491 5368 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 3890 helix: 1.45 (0.21), residues: 665 sheet: 0.24 (0.16), residues: 958 loop : -1.00 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1102 HIS 0.008 0.001 HIS C1048 PHE 0.033 0.002 PHE A 392 TYR 0.021 0.002 TYR B 796 ARG 0.009 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 42) link_NAG-ASN : angle 2.98757 ( 126) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 1.48855 ( 36) hydrogen bonds : bond 0.04268 ( 1013) hydrogen bonds : angle 5.42259 ( 2880) SS BOND : bond 0.00396 ( 52) SS BOND : angle 1.54025 ( 104) covalent geometry : bond 0.00571 (32210) covalent geometry : angle 0.67267 (43821) *********************** 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 : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.7296 (ttm170) cc_final: 0.7020 (ttm170) REVERT: A 549 THR cc_start: 0.7182 (t) cc_final: 0.6783 (m) REVERT: A 1050 MET cc_start: 0.8854 (pmm) cc_final: 0.7536 (pmm) REVERT: C 223 LEU cc_start: 0.9141 (mp) cc_final: 0.8864 (tp) REVERT: C 587 ILE cc_start: 0.9431 (mm) cc_final: 0.9204 (mm) REVERT: C 731 MET cc_start: 0.8844 (pmm) cc_final: 0.8598 (pmm) REVERT: C 740 MET cc_start: 0.8171 (tmm) cc_final: 0.7466 (tmm) REVERT: L 24 ARG cc_start: 0.5589 (mtm-85) cc_final: 0.5123 (mtp-110) REVERT: L 148 GLN cc_start: 0.6408 (mp10) cc_final: 0.6077 (tp40) REVERT: H 83 ARG cc_start: 0.4276 (tmt-80) cc_final: 0.3926 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.4487 time to fit residues: 73.1092 Evaluate side-chains 74 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 45 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 224 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 360 optimal weight: 30.0000 chunk 173 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1083 HIS B1142 GLN C 774 GLN C 907 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 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 = 0.3918 r_free = 0.3918 target = 0.089723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063601 restraints weight = 256536.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.063651 restraints weight = 145520.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.063938 restraints weight = 104887.199| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32316 Z= 0.106 Angle : 0.536 10.874 44087 Z= 0.268 Chirality : 0.045 0.450 5128 Planarity : 0.004 0.058 5580 Dihedral : 5.678 58.844 5368 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 3890 helix: 1.83 (0.21), residues: 658 sheet: 0.28 (0.16), residues: 960 loop : -0.89 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.006 0.001 HIS C1048 PHE 0.017 0.001 PHE A 55 TYR 0.014 0.001 TYR B1067 ARG 0.010 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 42) link_NAG-ASN : angle 2.59572 ( 126) link_BETA1-4 : bond 0.00300 ( 12) link_BETA1-4 : angle 0.83343 ( 36) hydrogen bonds : bond 0.03585 ( 1013) hydrogen bonds : angle 5.03515 ( 2880) SS BOND : bond 0.00338 ( 52) SS BOND : angle 1.05611 ( 104) covalent geometry : bond 0.00232 (32210) covalent geometry : angle 0.51629 (43821) *********************** 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 97 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7973 (tp) cc_final: 0.7687 (mm) REVERT: A 466 ARG cc_start: 0.7299 (ttm170) cc_final: 0.6989 (ttm170) REVERT: A 527 PRO cc_start: 0.6850 (Cg_endo) cc_final: 0.6543 (Cg_exo) REVERT: A 549 THR cc_start: 0.7419 (t) cc_final: 0.7099 (m) REVERT: A 900 MET cc_start: 0.8621 (mmp) cc_final: 0.8406 (mmp) REVERT: A 1050 MET cc_start: 0.8578 (pmm) cc_final: 0.7384 (pmm) REVERT: C 587 ILE cc_start: 0.9454 (mm) cc_final: 0.9240 (mm) REVERT: C 740 MET cc_start: 0.8120 (tmm) cc_final: 0.7091 (tmm) REVERT: L 24 ARG cc_start: 0.5795 (mtm-85) cc_final: 0.4756 (mtp-110) REVERT: L 148 GLN cc_start: 0.6447 (mp10) cc_final: 0.6110 (tp40) REVERT: H 83 ARG cc_start: 0.4307 (tmt-80) cc_final: 0.3848 (mtm-85) REVERT: H 123 PRO cc_start: 0.4980 (Cg_endo) cc_final: 0.4600 (Cg_exo) REVERT: E 174 TYR cc_start: 0.6595 (m-80) cc_final: 0.6249 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.4274 time to fit residues: 70.3362 Evaluate side-chains 75 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 381 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 282 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 919 ASN ** L 199 HIS ** 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 = 0.3843 r_free = 0.3843 target = 0.084999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061436 restraints weight = 203611.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060061 restraints weight = 173406.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060590 restraints weight = 120738.843| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 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 = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32316 Z= 0.175 Angle : 0.590 10.685 44087 Z= 0.296 Chirality : 0.046 0.459 5128 Planarity : 0.004 0.077 5580 Dihedral : 5.792 59.877 5368 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 3890 helix: 1.71 (0.21), residues: 657 sheet: 0.19 (0.16), residues: 989 loop : -0.91 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1102 HIS 0.006 0.001 HIS C1048 PHE 0.014 0.001 PHE C 898 TYR 0.016 0.001 TYR B 451 ARG 0.011 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 42) link_NAG-ASN : angle 2.92951 ( 126) link_BETA1-4 : bond 0.00172 ( 12) link_BETA1-4 : angle 1.09936 ( 36) hydrogen bonds : bond 0.03861 ( 1013) hydrogen bonds : angle 5.13022 ( 2880) SS BOND : bond 0.00345 ( 52) SS BOND : angle 1.41114 ( 104) covalent geometry : bond 0.00384 (32210) covalent geometry : angle 0.56605 (43821) *********************** 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 98 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8080 (tp) cc_final: 0.7648 (mm) REVERT: A 527 PRO cc_start: 0.7374 (Cg_endo) cc_final: 0.7173 (Cg_exo) REVERT: A 549 THR cc_start: 0.7107 (t) cc_final: 0.6824 (m) REVERT: A 1050 MET cc_start: 0.8311 (pmm) cc_final: 0.7225 (pmm) REVERT: B 740 MET cc_start: 0.8757 (tpp) cc_final: 0.7928 (tpt) REVERT: B 900 MET cc_start: 0.8834 (pmm) cc_final: 0.8629 (pmm) REVERT: C 587 ILE cc_start: 0.9468 (mm) cc_final: 0.9253 (mm) REVERT: C 740 MET cc_start: 0.8232 (tmm) cc_final: 0.7298 (tmm) REVERT: L 24 ARG cc_start: 0.5925 (mtm-85) cc_final: 0.4849 (mtp-110) REVERT: L 148 GLN cc_start: 0.6391 (mp10) cc_final: 0.6076 (tp40) REVERT: H 83 ARG cc_start: 0.4114 (tmt-80) cc_final: 0.3559 (mtm-85) REVERT: H 123 PRO cc_start: 0.5021 (Cg_endo) cc_final: 0.4632 (Cg_exo) REVERT: E 4 MET cc_start: -0.0532 (pmm) cc_final: -0.0739 (pmm) REVERT: E 174 TYR cc_start: 0.6695 (m-80) cc_final: 0.6376 (m-80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.5005 time to fit residues: 82.4562 Evaluate side-chains 76 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 387 optimal weight: 40.0000 chunk 291 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 391 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 263 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.086804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.061764 restraints weight = 223164.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060936 restraints weight = 153524.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060853 restraints weight = 134528.161| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32316 Z= 0.153 Angle : 0.571 14.978 44087 Z= 0.286 Chirality : 0.046 0.392 5128 Planarity : 0.004 0.054 5580 Dihedral : 5.670 58.972 5368 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3890 helix: 1.75 (0.21), residues: 657 sheet: 0.20 (0.16), residues: 967 loop : -0.97 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 103 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.001 PHE C 275 TYR 0.012 0.001 TYR C1067 ARG 0.005 0.001 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 42) link_NAG-ASN : angle 2.88481 ( 126) link_BETA1-4 : bond 0.00203 ( 12) link_BETA1-4 : angle 0.85930 ( 36) hydrogen bonds : bond 0.03730 ( 1013) hydrogen bonds : angle 5.06321 ( 2880) SS BOND : bond 0.00285 ( 52) SS BOND : angle 1.21762 ( 104) covalent geometry : bond 0.00338 (32210) covalent geometry : angle 0.54819 (43821) *********************** 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 95 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 4.055 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: 0.8014 (tp) cc_final: 0.7705 (mm) REVERT: A 549 THR cc_start: 0.7098 (t) cc_final: 0.6817 (m) REVERT: A 740 MET cc_start: 0.8305 (mtt) cc_final: 0.8037 (mtt) REVERT: A 900 MET cc_start: 0.8612 (mmp) cc_final: 0.8409 (mmp) REVERT: A 1050 MET cc_start: 0.8514 (pmm) cc_final: 0.7187 (pmm) REVERT: B 740 MET cc_start: 0.8709 (tpp) cc_final: 0.7871 (tpt) REVERT: C 587 ILE cc_start: 0.9428 (mm) cc_final: 0.9220 (mm) REVERT: C 740 MET cc_start: 0.8251 (tmm) cc_final: 0.7345 (tmm) REVERT: C 900 MET cc_start: 0.8685 (mmp) cc_final: 0.8370 (mmm) REVERT: L 24 ARG cc_start: 0.6035 (mtm-85) cc_final: 0.4932 (mmm160) REVERT: L 148 GLN cc_start: 0.6471 (mp10) cc_final: 0.6207 (tp40) REVERT: H 123 PRO cc_start: 0.4830 (Cg_endo) cc_final: 0.4462 (Cg_exo) REVERT: E 174 TYR cc_start: 0.6617 (m-80) cc_final: 0.6318 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.4831 time to fit residues: 80.8315 Evaluate side-chains 68 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 87 optimal weight: 0.2980 chunk 82 optimal weight: 10.0000 chunk 365 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 391 optimal weight: 40.0000 chunk 253 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 357 optimal weight: 9.9990 overall best weight: 4.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 901 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.082659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058895 restraints weight = 233675.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.058672 restraints weight = 132137.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059021 restraints weight = 94487.397| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 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 = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 32316 Z= 0.265 Angle : 0.720 13.652 44087 Z= 0.364 Chirality : 0.049 0.515 5128 Planarity : 0.005 0.056 5580 Dihedral : 6.416 57.849 5368 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3890 helix: 1.26 (0.21), residues: 668 sheet: 0.07 (0.16), residues: 947 loop : -1.18 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1102 HIS 0.007 0.001 HIS C1048 PHE 0.027 0.002 PHE A 906 TYR 0.029 0.002 TYR B 451 ARG 0.005 0.001 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 42) link_NAG-ASN : angle 3.24203 ( 126) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.31147 ( 36) hydrogen bonds : bond 0.04463 ( 1013) hydrogen bonds : angle 5.48106 ( 2880) SS BOND : bond 0.00472 ( 52) SS BOND : angle 1.97026 ( 104) covalent geometry : bond 0.00571 (32210) covalent geometry : angle 0.69362 (43821) *********************** 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 88 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 3.498 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 226 LEU cc_start: 0.8204 (tp) cc_final: 0.7923 (mm) REVERT: A 333 THR cc_start: 0.8025 (m) cc_final: 0.7782 (p) REVERT: A 1050 MET cc_start: 0.8717 (pmm) cc_final: 0.7458 (pmm) REVERT: B 740 MET cc_start: 0.8788 (tpp) cc_final: 0.7952 (tpt) REVERT: C 740 MET cc_start: 0.8309 (tmm) cc_final: 0.7574 (tmm) REVERT: C 900 MET cc_start: 0.8663 (mmp) cc_final: 0.8430 (mmm) REVERT: L 24 ARG cc_start: 0.6077 (mtm-85) cc_final: 0.4949 (mtp-110) REVERT: L 148 GLN cc_start: 0.6557 (mp10) cc_final: 0.6268 (tp40) REVERT: H 83 ARG cc_start: 0.4320 (tmt-80) cc_final: 0.3785 (mtm-85) REVERT: H 123 PRO cc_start: 0.5198 (Cg_endo) cc_final: 0.4783 (Cg_exo) REVERT: E 174 TYR cc_start: 0.6905 (m-80) cc_final: 0.6547 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4400 time to fit residues: 66.0041 Evaluate side-chains 71 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 213 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 208 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 372 optimal weight: 0.0020 chunk 341 optimal weight: 0.2980 chunk 293 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN L 6 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.084822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061638 restraints weight = 221379.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.060374 restraints weight = 147018.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060733 restraints weight = 129836.616| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5565 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= 0.123 Angle : 0.580 13.462 44087 Z= 0.290 Chirality : 0.046 0.507 5128 Planarity : 0.004 0.054 5580 Dihedral : 5.873 58.270 5368 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3890 helix: 1.69 (0.21), residues: 657 sheet: 0.12 (0.16), residues: 972 loop : -1.07 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.009 0.001 HIS C 519 PHE 0.022 0.001 PHE C 275 TYR 0.023 0.001 TYR B 473 ARG 0.004 0.000 ARG L 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 42) link_NAG-ASN : angle 2.88729 ( 126) link_BETA1-4 : bond 0.00244 ( 12) link_BETA1-4 : angle 0.85858 ( 36) hydrogen bonds : bond 0.03873 ( 1013) hydrogen bonds : angle 5.09503 ( 2880) SS BOND : bond 0.00259 ( 52) SS BOND : angle 1.41091 ( 104) covalent geometry : bond 0.00273 (32210) covalent geometry : angle 0.55553 (43821) ********************** 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 91 residues out of total 3443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 3.349 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: symmetry clash REVERT: A 226 LEU cc_start: 0.8054 (tp) cc_final: 0.7742 (mm) REVERT: A 333 THR cc_start: 0.7977 (m) cc_final: 0.7724 (p) REVERT: A 740 MET cc_start: 0.8344 (mtt) cc_final: 0.7976 (mtt) REVERT: A 1050 MET cc_start: 0.8707 (pmm) cc_final: 0.7361 (pmm) REVERT: B 740 MET cc_start: 0.8716 (tpp) cc_final: 0.7938 (tpt) REVERT: C 740 MET cc_start: 0.8293 (tmm) cc_final: 0.7580 (tmm) REVERT: C 900 MET cc_start: 0.8685 (mmp) cc_final: 0.8374 (mmm) REVERT: L 24 ARG cc_start: 0.6064 (mtm-85) cc_final: 0.4962 (mtp-110) REVERT: L 148 GLN cc_start: 0.6479 (mp10) cc_final: 0.6258 (tp40) REVERT: H 123 PRO cc_start: 0.4884 (Cg_endo) cc_final: 0.4494 (Cg_exo) REVERT: E 174 TYR cc_start: 0.6845 (m-80) cc_final: 0.6498 (m-80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.4950 time to fit residues: 76.1683 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 : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 377 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.084128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061097 restraints weight = 221946.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059668 restraints weight = 155303.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060035 restraints weight = 129818.783| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 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 = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32316 Z= 0.164 Angle : 0.599 13.422 44087 Z= 0.299 Chirality : 0.046 0.494 5128 Planarity : 0.004 0.054 5580 Dihedral : 5.851 59.017 5368 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3890 helix: 1.69 (0.21), residues: 657 sheet: 0.14 (0.16), residues: 978 loop : -1.08 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 103 HIS 0.005 0.001 HIS C1048 PHE 0.020 0.001 PHE A 906 TYR 0.019 0.001 TYR B 473 ARG 0.004 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 42) link_NAG-ASN : angle 2.93920 ( 126) link_BETA1-4 : bond 0.00178 ( 12) link_BETA1-4 : angle 0.97430 ( 36) hydrogen bonds : bond 0.03905 ( 1013) hydrogen bonds : angle 5.08415 ( 2880) SS BOND : bond 0.00306 ( 52) SS BOND : angle 1.25756 ( 104) covalent geometry : bond 0.00362 (32210) covalent geometry : angle 0.57575 (43821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9672.10 seconds wall clock time: 174 minutes 24.38 seconds (10464.38 seconds total)