Starting phenix.real_space_refine on Mon Jul 6 21:07:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hca_34657/07_2026/8hca_34657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hca_34657/07_2026/8hca_34657.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/8hca_34657/07_2026/8hca_34657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hca_34657/07_2026/8hca_34657.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hca_34657/07_2026/8hca_34657.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hca_34657/07_2026/8hca_34657.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hca_34657/07_2026/8hca_34657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hca_34657/07_2026/8hca_34657.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4818 atoms to isotropic. 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 156 5.16 5 C 22344 2.51 5 N 5802 2.21 5 O 6885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35187 Number of models: 1 Model: "" Number of chains: 24 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: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "L" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.81, per 1000 atoms: 0.25 Number of scatterers: 35187 At special positions: 0 Unit cell: (161.7, 150.15, 244.2, 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 156 16.00 O 6885 8.00 N 5802 7.00 C 22344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.04 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 E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 111 " - pdb=" SG CYS F 116 " distance=2.03 Simple disulfide: pdb=" SG CYS F 161 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 116 " distance=2.04 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 217 " 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 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 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 I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8322 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 73 sheets defined 19.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.827A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.851A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.510A 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 783 removed outlier: 3.605A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.558A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.928A 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 919 removed outlier: 3.984A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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: 4.104A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.836A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.833A 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 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.304A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.126A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.808A 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: 4.005A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.209A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.551A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.511A 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 338 through 343 Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.780A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.637A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.823A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 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 removed outlier: 3.544A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.623A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.844A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.693A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 188 through 193 removed outlier: 4.303A pdb=" N LYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.669A pdb=" N THR F 31 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.098A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.156A pdb=" N VAL G 88 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 132 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'H' and resid 65 through 71 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.311A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.969A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.071A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.654A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.826A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.155A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.738A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.634A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 43 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 567 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.828A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.930A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.930A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.183A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.751A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.820A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.391A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 135 through 141 removed outlier: 10.712A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.441A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.362A 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: 3.734A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.679A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.991A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.225A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.014A 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: 6.782A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.483A 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: 5.973A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.792A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.524A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.087A 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: 3.527A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.638A 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: 4.067A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.675A 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: 3.878A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.660A 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 317 removed outlier: 3.656A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.555A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 398 through 403 removed outlier: 3.710A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.182A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 713 through 727 removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 713 through 727 removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'E' and resid 49 through 53 removed outlier: 6.815A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.665A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.705A pdb=" N TRP E 153 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 212 " --> pdb=" O CYS E 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.619A pdb=" N PHE F 84 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 35 through 38 removed outlier: 5.782A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER F 50 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR F 63 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 141 through 148 removed outlier: 3.807A pdb=" N GLY F 160 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 158 " --> pdb=" O PRO F 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER F 201 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 199 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 165 " --> pdb=" O TYR F 197 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR F 197 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 172 through 175 removed outlier: 3.637A pdb=" N THR F 172 " --> pdb=" O ASN F 220 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR F 215 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.719A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 20 through 21 removed outlier: 3.952A pdb=" N ILE L 21 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 49 through 53 removed outlier: 4.080A pdb=" N LEU L 52 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.598A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.542A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 48 through 53 removed outlier: 6.472A pdb=" N LYS G 44 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU G 51 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU G 42 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 39 " --> pdb=" O MET G 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 67 through 70 Processing sheet with id=AG8, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.821A pdb=" N ASN G 143 " --> pdb=" O TYR G 178 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 159 through 160 removed outlier: 4.741A pdb=" N TRP G 153 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS G 212 " --> pdb=" O CYS G 199 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.850A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN H 86 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.588A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 141 through 148 removed outlier: 4.186A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 141 through 148 removed outlier: 4.186A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 172 through 175 removed outlier: 4.942A pdb=" N TYR H 215 " --> pdb=" O VAL H 232 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.801A pdb=" N GLY D 10 " --> pdb=" O ILE D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.528A pdb=" N PHE D 84 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.850A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 141 through 148 removed outlier: 4.084A pdb=" N GLY D 160 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA D 158 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D 165 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR D 197 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 202 " --> pdb=" O HIS D 185 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 173 through 175 removed outlier: 3.565A pdb=" N VAL D 219 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 228 " --> pdb=" O VAL D 219 " (cutoff:3.500A) 1127 hydrogen bonds defined for protein. 3093 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: 9.60 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11196 1.34 - 1.46: 8829 1.46 - 1.58: 15765 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 35985 Sorted by residual: bond pdb=" C ARG A 328 " pdb=" N PHE A 329 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.07e-02 2.33e+03 5.69e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C GLU H 169 " pdb=" N PRO H 170 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 ... (remaining 35980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 48069 1.98 - 3.96: 794 3.96 - 5.95: 91 5.95 - 7.93: 23 7.93 - 9.91: 7 Bond angle restraints: 48984 Sorted by residual: angle pdb=" CA PHE D 167 " pdb=" C PHE D 167 " pdb=" N PRO D 168 " ideal model delta sigma weight residual 120.58 117.63 2.95 7.40e-01 1.83e+00 1.59e+01 angle pdb=" C PRO C 987 " pdb=" N GLU C 988 " pdb=" CA GLU C 988 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ARG A 328 " pdb=" CA ARG A 328 " pdb=" C ARG A 328 " ideal model delta sigma weight residual 109.31 114.61 -5.30 1.42e+00 4.96e-01 1.39e+01 angle pdb=" C ILE C 587 " pdb=" N THR C 588 " pdb=" CA THR C 588 " ideal model delta sigma weight residual 121.80 130.52 -8.72 2.44e+00 1.68e-01 1.28e+01 angle pdb=" C ARG A 273 " pdb=" N THR A 274 " pdb=" CA THR A 274 " ideal model delta sigma weight residual 122.77 118.22 4.55 1.33e+00 5.65e-01 1.17e+01 ... (remaining 48979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 18988 17.54 - 35.09: 1715 35.09 - 52.63: 291 52.63 - 70.18: 61 70.18 - 87.72: 41 Dihedral angle restraints: 21096 sinusoidal: 8160 harmonic: 12936 Sorted by residual: 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 8.40 84.60 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -170.17 84.17 1 1.00e+01 1.00e-02 8.62e+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 -86.00 -166.52 80.52 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5189 0.085 - 0.170: 521 0.170 - 0.255: 7 0.255 - 0.340: 2 0.340 - 0.425: 5 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.51e+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 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 5721 not shown) Planarity restraints: 6297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG A1305 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 205 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO D 206 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 206 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 206 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 330 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.035 5.00e-02 4.00e+02 ... (remaining 6294 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6508 2.78 - 3.31: 30990 3.31 - 3.84: 57877 3.84 - 4.37: 62979 4.37 - 4.90: 110752 Nonbonded interactions: 269106 Sorted by model distance: nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.250 3.040 nonbonded pdb=" O CYS A1032 " pdb=" OG SER A1051 " model vdw 2.255 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.270 3.040 ... (remaining 269101 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = 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' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.510 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 0.070 36096 Z= 0.160 Angle : 0.616 15.624 49260 Z= 0.298 Chirality : 0.047 0.425 5724 Planarity : 0.004 0.070 6255 Dihedral : 13.616 87.722 12603 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.44 % Allowed : 0.34 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4383 helix: 1.21 (0.20), residues: 657 sheet: 1.04 (0.17), residues: 960 loop : -1.31 (0.11), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 106 TYR 0.008 0.001 TYR G 54 PHE 0.013 0.001 PHE A 541 TRP 0.005 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (35985) covalent geometry : angle 0.59517 / 0.29 (48984) SS BOND : bond 0.00165 / 0.12 ( 57) SS BOND : angle 0.58407 / 0.40 ( 114) hydrogen bonds : bond 0.22861 / 14.77 ( 1099) hydrogen bonds : angle 8.56367 / 5.95 ( 3093) link_BETA1-4 : bond 0.00452 / 0.29 ( 12) link_BETA1-4 : angle 0.86916 / 0.61 ( 36) link_NAG-ASN : bond 0.00708 / 0.46 ( 42) link_NAG-ASN : angle 3.19313 / 1.95 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.4652 (mtmm) REVERT: A 302 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 332 ILE cc_start: 0.8102 (pt) cc_final: 0.7630 (tp) REVERT: A 1050 MET cc_start: 0.8700 (pmm) cc_final: 0.8413 (pmm) REVERT: B 1050 MET cc_start: 0.8171 (pmm) cc_final: 0.7705 (pmm) REVERT: C 424 LYS cc_start: 0.8170 (tttt) cc_final: 0.7967 (ttmm) REVERT: E 192 GLU cc_start: 0.0092 (mm-30) cc_final: -0.0483 (pt0) REVERT: F 129 MET cc_start: 0.5922 (tpp) cc_final: 0.4545 (tpp) REVERT: L 170 GLU cc_start: 0.4642 (tp30) cc_final: 0.4157 (tt0) REVERT: G 40 TRP cc_start: 0.5618 (m100) cc_final: 0.5148 (m100) outliers start: 17 outliers final: 3 residues processed: 169 average time/residue: 0.2183 time to fit residues: 62.6079 Evaluate side-chains 100 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 0.2980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 0.0770 overall best weight: 1.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 907 ASN A1101 HIS C 188 ASN E 165 GLN F 33 ASN F 86 GLN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.074380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054336 restraints weight = 269670.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054365 restraints weight = 188052.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.054025 restraints weight = 138552.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054198 restraints weight = 142540.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.054229 restraints weight = 123542.750| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36096 Z= 0.113 Angle : 0.530 13.027 49260 Z= 0.265 Chirality : 0.044 0.396 5724 Planarity : 0.004 0.062 6255 Dihedral : 3.361 19.735 4770 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4383 helix: 1.93 (0.21), residues: 676 sheet: 1.03 (0.16), residues: 1040 loop : -1.17 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.016 0.001 TYR A 266 PHE 0.018 0.001 PHE C 275 TRP 0.012 0.001 TRP A 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (35985) covalent geometry : angle 0.51279 / 0.26 (48984) SS BOND : bond 0.00410 / 0.23 ( 57) SS BOND : angle 0.76967 / 0.55 ( 114) hydrogen bonds : bond 0.03717 / 2.40 ( 1099) hydrogen bonds : angle 6.06625 / 4.25 ( 3093) link_BETA1-4 : bond 0.00251 / 0.15 ( 12) link_BETA1-4 : angle 1.05448 / 0.74 ( 36) link_NAG-ASN : bond 0.00543 / 0.34 ( 42) link_NAG-ASN : angle 2.62214 / 1.68 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.370 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 332 ILE cc_start: 0.7774 (pt) cc_final: 0.7257 (tp) REVERT: A 740 MET cc_start: 0.8327 (tpt) cc_final: 0.7886 (tpt) REVERT: A 1050 MET cc_start: 0.8827 (pmm) cc_final: 0.8483 (pmm) REVERT: B 559 PHE cc_start: 0.2170 (OUTLIER) cc_final: 0.1713 (m-10) REVERT: B 1050 MET cc_start: 0.8257 (pmm) cc_final: 0.7749 (pmm) REVERT: E 154 LYS cc_start: 0.5424 (mppt) cc_final: 0.3784 (ptmm) REVERT: E 192 GLU cc_start: 0.0350 (mm-30) cc_final: -0.0249 (pt0) REVERT: F 33 ASN cc_start: 0.6973 (m-40) cc_final: 0.6188 (m-40) REVERT: F 129 MET cc_start: 0.5989 (tpp) cc_final: 0.4720 (tpp) REVERT: L 94 MET cc_start: -0.1976 (mmt) cc_final: -0.2504 (tpp) REVERT: L 170 GLU cc_start: 0.4820 (tp30) cc_final: 0.4386 (tt0) REVERT: G 94 MET cc_start: -0.0370 (ptp) cc_final: -0.0683 (ptp) REVERT: D 34 MET cc_start: 0.2612 (tpt) cc_final: 0.2388 (mmm) outliers start: 4 outliers final: 1 residues processed: 136 average time/residue: 0.2143 time to fit residues: 50.1068 Evaluate side-chains 92 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 176 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 250 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 297 optimal weight: 7.9990 chunk 362 optimal weight: 4.9990 chunk 382 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 448 ASN A1011 GLN A1058 HIS ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1083 HIS B 314 GLN B 613 GLN B1036 GLN B1071 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN L 203 HIS H 192 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.070077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.050398 restraints weight = 269567.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.048858 restraints weight = 182180.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.049090 restraints weight = 153944.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049208 restraints weight = 127320.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049287 restraints weight = 112265.566| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36096 Z= 0.253 Angle : 0.733 13.023 49260 Z= 0.370 Chirality : 0.048 0.397 5724 Planarity : 0.006 0.246 6255 Dihedral : 4.469 29.368 4770 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4383 helix: 1.27 (0.20), residues: 681 sheet: 0.71 (0.16), residues: 1035 loop : -1.32 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.027 0.002 TYR A 313 PHE 0.033 0.002 PHE C 456 TRP 0.018 0.002 TRP G 40 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (35985) covalent geometry : angle 0.71351 / 0.37 (48984) SS BOND : bond 0.00663 / 0.41 ( 57) SS BOND : angle 1.36531 / 0.99 ( 114) hydrogen bonds : bond 0.04564 / 2.94 ( 1099) hydrogen bonds : angle 5.93382 / 4.13 ( 3093) link_BETA1-4 : bond 0.00681 / 0.36 ( 12) link_BETA1-4 : angle 1.82689 / 1.30 ( 36) link_NAG-ASN : bond 0.00739 / 0.47 ( 42) link_NAG-ASN : angle 3.04652 / 1.92 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 1.274 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 697 MET cc_start: 0.6557 (tpt) cc_final: 0.6356 (tpt) REVERT: A 731 MET cc_start: 0.8650 (ptp) cc_final: 0.8414 (ptm) REVERT: A 740 MET cc_start: 0.8851 (tpt) cc_final: 0.8577 (tpt) REVERT: B 869 MET cc_start: 0.8995 (pmm) cc_final: 0.8704 (pmm) REVERT: B 1050 MET cc_start: 0.8388 (pmm) cc_final: 0.7585 (pmm) REVERT: C 455 LEU cc_start: 0.7923 (tt) cc_final: 0.7607 (tt) REVERT: C 869 MET cc_start: 0.8607 (pmm) cc_final: 0.8006 (pmm) REVERT: E 17 GLU cc_start: 0.4923 (pp20) cc_final: 0.4332 (pm20) REVERT: E 65 ASP cc_start: 0.7662 (m-30) cc_final: 0.7378 (t0) REVERT: E 192 GLU cc_start: 0.0632 (mm-30) cc_final: 0.0245 (pt0) REVERT: F 167 PHE cc_start: 0.3623 (t80) cc_final: 0.3014 (t80) REVERT: G 94 MET cc_start: -0.1183 (ptp) cc_final: -0.1544 (ptp) REVERT: D 34 MET cc_start: 0.3515 (tpt) cc_final: 0.2579 (mmm) outliers start: 4 outliers final: 0 residues processed: 125 average time/residue: 0.2219 time to fit residues: 46.7538 Evaluate side-chains 80 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 438 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 391 optimal weight: 8.9990 chunk 367 optimal weight: 6.9990 chunk 340 optimal weight: 20.0000 chunk 379 optimal weight: 30.0000 chunk 237 optimal weight: 4.9990 chunk 204 optimal weight: 0.3980 chunk 404 optimal weight: 0.1980 chunk 174 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 394 ASN A 954 HIS A1135 ASN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 HIS G 129 GLN H 86 GLN D 126 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.070757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.051931 restraints weight = 280743.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.050659 restraints weight = 231059.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.050435 restraints weight = 190611.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.050537 restraints weight = 169655.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.050599 restraints weight = 148824.641| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36096 Z= 0.157 Angle : 0.585 22.956 49260 Z= 0.289 Chirality : 0.045 0.407 5724 Planarity : 0.004 0.059 6255 Dihedral : 4.086 22.663 4770 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4383 helix: 1.66 (0.20), residues: 675 sheet: 0.69 (0.16), residues: 1081 loop : -1.30 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 905 TYR 0.019 0.001 TYR C 508 PHE 0.026 0.001 PHE A 541 TRP 0.021 0.001 TRP B 353 HIS 0.024 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (35985) covalent geometry : angle 0.56630 / 0.28 (48984) SS BOND : bond 0.00389 / 0.27 ( 57) SS BOND : angle 1.08895 / 0.74 ( 114) hydrogen bonds : bond 0.03607 / 2.30 ( 1099) hydrogen bonds : angle 5.52976 / 3.87 ( 3093) link_BETA1-4 : bond 0.00279 / 0.19 ( 12) link_BETA1-4 : angle 1.10371 / 0.79 ( 36) link_NAG-ASN : bond 0.00511 / 0.32 ( 42) link_NAG-ASN : angle 2.73686 / 1.71 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8840 (tpt) cc_final: 0.8566 (tpt) REVERT: A 1050 MET cc_start: 0.8877 (pmm) cc_final: 0.8634 (pmm) REVERT: B 455 LEU cc_start: 0.7548 (tp) cc_final: 0.7219 (tp) REVERT: B 731 MET cc_start: 0.8628 (pmm) cc_final: 0.8277 (pmm) REVERT: B 1050 MET cc_start: 0.8499 (pmm) cc_final: 0.7376 (pmm) REVERT: C 869 MET cc_start: 0.8290 (pmm) cc_final: 0.7928 (pmm) REVERT: C 900 MET cc_start: 0.8536 (ppp) cc_final: 0.8074 (ppp) REVERT: E 17 GLU cc_start: 0.5132 (pp20) cc_final: 0.4612 (pm20) REVERT: E 192 GLU cc_start: 0.0684 (mm-30) cc_final: 0.0282 (pt0) REVERT: F 129 MET cc_start: 0.6393 (tpp) cc_final: 0.5386 (tpp) REVERT: G 94 MET cc_start: -0.1169 (ptp) cc_final: -0.1505 (ptp) REVERT: H 78 ASP cc_start: 0.6400 (m-30) cc_final: 0.5972 (m-30) REVERT: D 34 MET cc_start: 0.4238 (tpt) cc_final: 0.2925 (tpp) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2080 time to fit residues: 40.7766 Evaluate side-chains 79 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 30 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 144 optimal weight: 0.0870 chunk 200 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 404 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 99 ASN A 607 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 17 ASN C 448 ASN C 450 ASN C 481 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.068959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.050023 restraints weight = 265646.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.048317 restraints weight = 196245.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048286 restraints weight = 182910.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048530 restraints weight = 150114.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.048756 restraints weight = 126280.866| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36096 Z= 0.212 Angle : 0.667 18.984 49260 Z= 0.330 Chirality : 0.046 0.431 5724 Planarity : 0.005 0.079 6255 Dihedral : 4.478 28.462 4770 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4383 helix: 1.33 (0.20), residues: 680 sheet: 0.56 (0.16), residues: 1097 loop : -1.42 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.024 0.002 TYR B 369 PHE 0.027 0.002 PHE A 541 TRP 0.035 0.002 TRP B 353 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (35985) covalent geometry : angle 0.64627 / 0.33 (48984) SS BOND : bond 0.00539 / 0.38 ( 57) SS BOND : angle 1.49065 / 1.02 ( 114) hydrogen bonds : bond 0.03954 / 2.53 ( 1099) hydrogen bonds : angle 5.63101 / 3.93 ( 3093) link_BETA1-4 : bond 0.00247 / 0.13 ( 12) link_BETA1-4 : angle 1.55290 / 1.11 ( 36) link_NAG-ASN : bond 0.00673 / 0.40 ( 42) link_NAG-ASN : angle 2.97881 / 1.88 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8962 (tpt) cc_final: 0.8656 (tpt) REVERT: A 1050 MET cc_start: 0.8927 (pmm) cc_final: 0.8642 (pmm) REVERT: B 1050 MET cc_start: 0.8275 (pmm) cc_final: 0.7044 (pmm) REVERT: C 334 ASN cc_start: 0.7630 (m-40) cc_final: 0.7297 (p0) REVERT: C 869 MET cc_start: 0.8231 (pmm) cc_final: 0.7666 (pmm) REVERT: C 900 MET cc_start: 0.8780 (ppp) cc_final: 0.7962 (ppp) REVERT: E 17 GLU cc_start: 0.4428 (pp20) cc_final: 0.4211 (pm20) REVERT: E 192 GLU cc_start: 0.0492 (mm-30) cc_final: 0.0162 (pt0) REVERT: F 129 MET cc_start: 0.6370 (tpp) cc_final: 0.4972 (tpp) REVERT: L 94 MET cc_start: -0.1277 (mmt) cc_final: -0.1635 (tpp) REVERT: L 121 PHE cc_start: 0.4878 (m-10) cc_final: 0.3840 (t80) REVERT: D 34 MET cc_start: 0.4321 (tpt) cc_final: 0.2236 (mmm) outliers start: 3 outliers final: 1 residues processed: 108 average time/residue: 0.2088 time to fit residues: 38.4142 Evaluate side-chains 81 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 150 optimal weight: 0.0010 chunk 201 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 99 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 239 GLN C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 185 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.069380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.050164 restraints weight = 277707.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.048883 restraints weight = 198452.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.048767 restraints weight = 178803.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.049036 restraints weight = 144945.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.049066 restraints weight = 123920.604| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36096 Z= 0.171 Angle : 0.626 26.890 49260 Z= 0.305 Chirality : 0.045 0.432 5724 Planarity : 0.004 0.058 6255 Dihedral : 4.377 24.872 4770 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4383 helix: 1.54 (0.20), residues: 680 sheet: 0.37 (0.16), residues: 1100 loop : -1.40 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 24 TYR 0.013 0.001 TYR B 873 PHE 0.025 0.001 PHE A 541 TRP 0.013 0.001 TRP G 40 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (35985) covalent geometry : angle 0.60425 / 0.30 (48984) SS BOND : bond 0.00356 / 0.24 ( 57) SS BOND : angle 1.30438 / 0.91 ( 114) hydrogen bonds : bond 0.03652 / 2.35 ( 1099) hydrogen bonds : angle 5.51079 / 3.86 ( 3093) link_BETA1-4 : bond 0.00240 / 0.16 ( 12) link_BETA1-4 : angle 1.18262 / 0.85 ( 36) link_NAG-ASN : bond 0.00546 / 0.34 ( 42) link_NAG-ASN : angle 3.06978 / 1.89 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8398 (ptp) cc_final: 0.8137 (ptp) REVERT: A 740 MET cc_start: 0.8958 (tpt) cc_final: 0.8672 (tpt) REVERT: A 1050 MET cc_start: 0.8945 (pmm) cc_final: 0.8636 (pmm) REVERT: B 1050 MET cc_start: 0.8202 (pmm) cc_final: 0.7224 (pmm) REVERT: C 334 ASN cc_start: 0.7272 (m-40) cc_final: 0.6886 (p0) REVERT: C 869 MET cc_start: 0.8309 (pmm) cc_final: 0.7791 (pmm) REVERT: C 900 MET cc_start: 0.8768 (ppp) cc_final: 0.7874 (ppp) REVERT: E 17 GLU cc_start: 0.4633 (pp20) cc_final: 0.4006 (pm20) REVERT: E 192 GLU cc_start: -0.0104 (mm-30) cc_final: -0.0334 (pt0) REVERT: F 129 MET cc_start: 0.6316 (tpp) cc_final: 0.4996 (tpp) REVERT: L 128 GLU cc_start: 0.3863 (pp20) cc_final: 0.3492 (pp20) REVERT: D 34 MET cc_start: 0.4551 (tpt) cc_final: 0.3655 (tpp) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.2256 time to fit residues: 39.7715 Evaluate side-chains 82 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 71 optimal weight: 4.9990 chunk 427 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 419 optimal weight: 4.9990 chunk 391 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN ** H 192 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 = 0.3803 r_free = 0.3803 target = 0.069106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.049886 restraints weight = 276990.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.048591 restraints weight = 204653.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.048413 restraints weight = 178853.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.048574 restraints weight = 152216.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.048655 restraints weight = 132335.547| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36096 Z= 0.165 Angle : 0.616 20.350 49260 Z= 0.304 Chirality : 0.045 0.435 5724 Planarity : 0.004 0.058 6255 Dihedral : 4.379 24.125 4770 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.80 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4383 helix: 1.60 (0.20), residues: 674 sheet: 0.32 (0.16), residues: 1064 loop : -1.36 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 104 TYR 0.016 0.001 TYR A 453 PHE 0.025 0.001 PHE A 541 TRP 0.018 0.001 TRP G 40 HIS 0.010 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (35985) covalent geometry : angle 0.59430 / 0.30 (48984) SS BOND : bond 0.00377 / 0.26 ( 57) SS BOND : angle 1.32615 / 0.89 ( 114) hydrogen bonds : bond 0.03680 / 2.36 ( 1099) hydrogen bonds : angle 5.47503 / 3.82 ( 3093) link_BETA1-4 : bond 0.00173 / 0.11 ( 12) link_BETA1-4 : angle 1.21066 / 0.89 ( 36) link_NAG-ASN : bond 0.00541 / 0.33 ( 42) link_NAG-ASN : angle 3.00263 / 1.83 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.4990 (tt) cc_final: 0.3772 (mp) REVERT: A 740 MET cc_start: 0.8962 (tpt) cc_final: 0.8616 (tpt) REVERT: A 1050 MET cc_start: 0.8903 (pmm) cc_final: 0.8659 (pmm) REVERT: B 1050 MET cc_start: 0.8347 (pmm) cc_final: 0.7442 (pmm) REVERT: C 334 ASN cc_start: 0.7296 (m-40) cc_final: 0.7028 (p0) REVERT: C 900 MET cc_start: 0.8704 (ppp) cc_final: 0.7996 (ppp) REVERT: C 1029 MET cc_start: 0.8884 (tpp) cc_final: 0.8329 (tpt) REVERT: E 17 GLU cc_start: 0.4988 (pp20) cc_final: 0.4617 (pm20) REVERT: E 148 GLU cc_start: 0.5254 (pm20) cc_final: 0.4994 (pm20) REVERT: F 129 MET cc_start: 0.6312 (tpp) cc_final: 0.4919 (tpp) REVERT: L 94 MET cc_start: 0.1079 (tpp) cc_final: 0.0658 (tpp) REVERT: L 128 GLU cc_start: 0.4057 (pp20) cc_final: 0.3736 (pp20) REVERT: D 34 MET cc_start: 0.4991 (tpt) cc_final: 0.4423 (tpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2157 time to fit residues: 38.6920 Evaluate side-chains 82 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 134 optimal weight: 3.9990 chunk 320 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 371 optimal weight: 30.0000 chunk 406 optimal weight: 10.0000 chunk 378 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS G 27 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** 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 = 0.3758 r_free = 0.3758 target = 0.067629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.047881 restraints weight = 284039.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.047129 restraints weight = 199533.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046874 restraints weight = 178401.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047078 restraints weight = 154560.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.047355 restraints weight = 120848.546| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 36096 Z= 0.261 Angle : 0.749 18.272 49260 Z= 0.373 Chirality : 0.048 0.482 5724 Planarity : 0.005 0.058 6255 Dihedral : 5.095 31.621 4770 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.12 % Favored : 92.84 % Rotamer: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 4383 helix: 0.99 (0.20), residues: 692 sheet: 0.01 (0.16), residues: 1081 loop : -1.58 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 24 TYR 0.023 0.002 TYR G 54 PHE 0.028 0.002 PHE A 541 TRP 0.016 0.002 TRP H 36 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.26 (35985) covalent geometry : angle 0.72648 / 0.37 (48984) SS BOND : bond 0.00544 / 0.35 ( 57) SS BOND : angle 1.64151 / 1.10 ( 114) hydrogen bonds : bond 0.04255 / 2.77 ( 1099) hydrogen bonds : angle 5.93877 / 4.13 ( 3093) link_BETA1-4 : bond 0.00406 / 0.25 ( 12) link_BETA1-4 : angle 1.77978 / 1.30 ( 36) link_NAG-ASN : bond 0.00676 / 0.42 ( 42) link_NAG-ASN : angle 3.31959 / 2.06 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9032 (tpt) cc_final: 0.8782 (tpt) REVERT: A 1050 MET cc_start: 0.8906 (pmm) cc_final: 0.8650 (pmm) REVERT: B 1050 MET cc_start: 0.8339 (pmm) cc_final: 0.7436 (pmm) REVERT: C 900 MET cc_start: 0.8608 (ppp) cc_final: 0.7649 (ppp) REVERT: C 1050 MET cc_start: 0.7866 (ptp) cc_final: 0.7521 (ptp) REVERT: E 17 GLU cc_start: 0.5718 (pp20) cc_final: 0.5448 (pm20) REVERT: E 79 LYS cc_start: 0.7811 (mppt) cc_final: 0.7592 (mmtm) REVERT: E 113 ARG cc_start: 0.7728 (mmp-170) cc_final: 0.6358 (ppt170) REVERT: F 129 MET cc_start: 0.5850 (tpp) cc_final: 0.4783 (tpp) REVERT: F 167 PHE cc_start: 0.3807 (t80) cc_final: 0.3228 (t80) REVERT: L 94 MET cc_start: 0.0903 (tpp) cc_final: 0.0592 (tpp) REVERT: H 149 SER cc_start: 0.4504 (m) cc_final: 0.4256 (t) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.2443 time to fit residues: 43.7640 Evaluate side-chains 86 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 216 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 427 optimal weight: 7.9990 chunk 295 optimal weight: 0.9980 chunk 167 optimal weight: 0.0670 chunk 252 optimal weight: 1.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 165 GLN ** H 192 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 = 0.3785 r_free = 0.3785 target = 0.068495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.048520 restraints weight = 280498.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047920 restraints weight = 192193.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047776 restraints weight = 145920.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.047916 restraints weight = 149893.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047998 restraints weight = 119101.682| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36096 Z= 0.142 Angle : 0.618 14.170 49260 Z= 0.306 Chirality : 0.046 0.451 5724 Planarity : 0.004 0.058 6255 Dihedral : 4.630 27.818 4770 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 4383 helix: 1.44 (0.20), residues: 678 sheet: 0.09 (0.16), residues: 1077 loop : -1.48 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 66 TYR 0.018 0.001 TYR H 64 PHE 0.024 0.001 PHE E 67 TRP 0.014 0.001 TRP A 886 HIS 0.007 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (35985) covalent geometry : angle 0.59619 / 0.30 (48984) SS BOND : bond 0.00526 / 0.36 ( 57) SS BOND : angle 1.48829 / 1.01 ( 114) hydrogen bonds : bond 0.03704 / 2.39 ( 1099) hydrogen bonds : angle 5.55883 / 3.88 ( 3093) link_BETA1-4 : bond 0.00304 / 0.18 ( 12) link_BETA1-4 : angle 1.14088 / 0.84 ( 36) link_NAG-ASN : bond 0.00516 / 0.32 ( 42) link_NAG-ASN : angle 2.96621 / 1.80 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.417 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 552 LEU cc_start: 0.5407 (tt) cc_final: 0.4206 (mp) REVERT: A 731 MET cc_start: 0.8328 (ptp) cc_final: 0.8020 (ptp) REVERT: A 740 MET cc_start: 0.9004 (tpt) cc_final: 0.8741 (tpt) REVERT: A 1050 MET cc_start: 0.8896 (pmm) cc_final: 0.8655 (pmm) REVERT: B 1050 MET cc_start: 0.8404 (pmm) cc_final: 0.7274 (pmm) REVERT: C 740 MET cc_start: 0.8700 (tpp) cc_final: 0.8391 (tpp) REVERT: C 900 MET cc_start: 0.8819 (ppp) cc_final: 0.8515 (ppp) REVERT: C 1029 MET cc_start: 0.8889 (tpp) cc_final: 0.8313 (tpt) REVERT: E 17 GLU cc_start: 0.5662 (pp20) cc_final: 0.5410 (pm20) REVERT: E 113 ARG cc_start: 0.7705 (mmp-170) cc_final: 0.6343 (ptt90) REVERT: E 148 GLU cc_start: 0.5356 (pm20) cc_final: 0.5148 (pm20) REVERT: F 129 MET cc_start: 0.5772 (tpp) cc_final: 0.4551 (tpp) REVERT: F 167 PHE cc_start: 0.3287 (t80) cc_final: 0.2661 (t80) REVERT: L 94 MET cc_start: 0.0921 (tpp) cc_final: 0.0312 (tpp) REVERT: G 40 TRP cc_start: 0.7529 (m100) cc_final: 0.7060 (m100) REVERT: H 149 SER cc_start: 0.4642 (m) cc_final: 0.4369 (t) REVERT: D 34 MET cc_start: 0.5174 (tpt) cc_final: 0.2696 (mmm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2249 time to fit residues: 39.4090 Evaluate side-chains 84 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 126 optimal weight: 1.9990 chunk 373 optimal weight: 6.9990 chunk 322 optimal weight: 0.9990 chunk 208 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 142 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** 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 = 0.3787 r_free = 0.3787 target = 0.068460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.048378 restraints weight = 280003.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.048165 restraints weight = 180321.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.047817 restraints weight = 145925.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047954 restraints weight = 133569.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048257 restraints weight = 110489.453| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.003 0.053 36096 Z= 0.139 Angle : 0.608 12.915 49260 Z= 0.300 Chirality : 0.045 0.443 5724 Planarity : 0.004 0.058 6255 Dihedral : 4.510 27.084 4770 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 4383 helix: 1.50 (0.20), residues: 678 sheet: 0.13 (0.16), residues: 1079 loop : -1.45 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 59 TYR 0.018 0.001 TYR A 38 PHE 0.023 0.001 PHE A 541 TRP 0.012 0.001 TRP F 175 HIS 0.006 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (35985) covalent geometry : angle 0.58768 / 0.30 (48984) SS BOND : bond 0.00336 / 0.24 ( 57) SS BOND : angle 1.36121 / 0.92 ( 114) hydrogen bonds : bond 0.03643 / 2.34 ( 1099) hydrogen bonds : angle 5.45813 / 3.81 ( 3093) link_BETA1-4 : bond 0.00229 / 0.15 ( 12) link_BETA1-4 : angle 1.13468 / 0.84 ( 36) link_NAG-ASN : bond 0.00514 / 0.32 ( 42) link_NAG-ASN : angle 2.89984 / 1.76 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.162 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 392 PHE cc_start: 0.7734 (p90) cc_final: 0.7177 (p90) REVERT: A 552 LEU cc_start: 0.5353 (tt) cc_final: 0.4099 (mp) REVERT: A 740 MET cc_start: 0.9041 (tpt) cc_final: 0.8764 (tpt) REVERT: A 1050 MET cc_start: 0.8934 (pmm) cc_final: 0.8705 (pmm) REVERT: B 1050 MET cc_start: 0.8295 (pmm) cc_final: 0.7433 (pmm) REVERT: C 740 MET cc_start: 0.8770 (tpp) cc_final: 0.8509 (tpp) REVERT: C 900 MET cc_start: 0.8660 (ppp) cc_final: 0.7646 (ppp) REVERT: C 1029 MET cc_start: 0.8921 (tpp) cc_final: 0.8317 (tpt) REVERT: E 79 LYS cc_start: 0.7254 (mppt) cc_final: 0.6920 (mptt) REVERT: E 113 ARG cc_start: 0.7722 (mmp-170) cc_final: 0.6341 (ptt90) REVERT: F 129 MET cc_start: 0.5743 (tpp) cc_final: 0.4276 (tpp) REVERT: F 167 PHE cc_start: 0.3646 (t80) cc_final: 0.2908 (t80) REVERT: L 94 MET cc_start: 0.1232 (tpp) cc_final: 0.0533 (tpp) REVERT: G 6 GLN cc_start: 0.3200 (OUTLIER) cc_final: 0.2447 (pt0) REVERT: G 40 TRP cc_start: 0.6829 (m100) cc_final: 0.6576 (m100) REVERT: H 149 SER cc_start: 0.4751 (m) cc_final: 0.4472 (t) REVERT: D 34 MET cc_start: 0.5538 (tpt) cc_final: 0.2938 (mmm) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2157 time to fit residues: 37.8223 Evaluate side-chains 88 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 50 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 333 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 425 optimal weight: 20.0000 chunk 331 optimal weight: 30.0000 chunk 70 optimal weight: 0.1980 chunk 90 optimal weight: 5.9990 chunk 341 optimal weight: 0.4980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 955 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN ** D 185 HIS ** 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 = 0.3777 r_free = 0.3777 target = 0.068091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048310 restraints weight = 280839.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.047428 restraints weight = 194254.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.047367 restraints weight = 150729.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.047437 restraints weight = 157853.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047535 restraints weight = 121607.258| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36096 Z= 0.157 Angle : 0.617 11.270 49260 Z= 0.306 Chirality : 0.045 0.439 5724 Planarity : 0.004 0.057 6255 Dihedral : 4.520 26.558 4770 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 4383 helix: 1.59 (0.20), residues: 666 sheet: 0.11 (0.16), residues: 1065 loop : -1.42 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1091 TYR 0.018 0.001 TYR C 873 PHE 0.024 0.001 PHE A 541 TRP 0.012 0.001 TRP B 353 HIS 0.006 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (35985) covalent geometry : angle 0.59646 / 0.30 (48984) SS BOND : bond 0.00352 / 0.24 ( 57) SS BOND : angle 1.45267 / 0.95 ( 114) hydrogen bonds : bond 0.03657 / 2.37 ( 1099) hydrogen bonds : angle 5.45586 / 3.81 ( 3093) link_BETA1-4 : bond 0.00182 / 0.12 ( 12) link_BETA1-4 : angle 1.22540 / 0.92 ( 36) link_NAG-ASN : bond 0.00522 / 0.32 ( 42) link_NAG-ASN : angle 2.88565 / 1.76 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5202.60 seconds wall clock time: 91 minutes 36.39 seconds (5496.39 seconds total)