Starting phenix.real_space_refine on Thu Mar 5 14:40:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uhc_26512/03_2026/7uhc_26512.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhc_26512/03_2026/7uhc_26512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uhc_26512/03_2026/7uhc_26512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhc_26512/03_2026/7uhc_26512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uhc_26512/03_2026/7uhc_26512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhc_26512/03_2026/7uhc_26512.map" } resolution = 3.1 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= -0.001 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 14754 2.51 5 N 3927 2.21 5 O 4353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23136 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7058 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 7 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 871 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASN:plan1': 21, 'GLU:plan': 22, 'ASP:plan': 22, 'GLN:plan1': 10, 'PHE:plan': 5, 'ARG:plan': 7, 'TYR:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 390 Chain: "K" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "B" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7058 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 7 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 871 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASN:plan1': 21, 'GLU:plan': 22, 'ASP:plan': 22, 'GLN:plan1': 10, 'PHE:plan': 5, 'ARG:plan': 7, 'TYR:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 390 Chain: "C" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7058 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 7 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 871 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASN:plan1': 21, 'GLU:plan': 22, 'ASP:plan': 22, 'GLN:plan1': 10, 'PHE:plan': 5, 'ARG:plan': 7, 'TYR:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 390 Chain: "E" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.49, per 1000 atoms: 0.24 Number of scatterers: 23136 At special positions: 0 Unit cell: (131.393, 134.402, 197.591, 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 102 16.00 O 4353 8.00 N 3927 7.00 C 14754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.00 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=2.09 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.11 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.07 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=2.02 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=2.08 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.00 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=2.09 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.07 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.08 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.00 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.09 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.11 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.01 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 343 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 234 " " NAG D1304 " - " ASN D 282 " " NAG D1305 " - " ASN D 331 " " NAG D1306 " - " ASN D 603 " " NAG D1307 " - " ASN D 616 " " NAG D1308 " - " ASN D 657 " " NAG D1309 " - " ASN D 709 " " NAG D1310 " - " ASN D1074 " " NAG D1311 " - " ASN D 165 " " NAG D1312 " - " ASN D 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN D 717 " " NAG P 1 " - " ASN D 801 " " NAG Q 1 " - " ASN D1098 " " NAG R 1 " - " ASN D1134 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 42 sheets defined 30.4% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.548A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.855A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.012A 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 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.909A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.638A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.766A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.345A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.031A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 Processing helix chain 'K' and resid 25 through 48 Processing helix chain 'K' and resid 51 through 74 removed outlier: 3.594A pdb=" N GLU K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU K 72 " --> pdb=" O HIS K 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.548A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.855A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.011A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.638A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.766A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.345A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.031A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 25 through 48 Processing helix chain 'C' and resid 51 through 74 removed outlier: 3.593A pdb=" N GLU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.548A pdb=" N ASN D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.856A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.012A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 823 removed outlier: 3.638A pdb=" N PHE D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 919 Processing helix chain 'D' and resid 919 through 940 removed outlier: 3.766A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 944 Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.345A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 5.031A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 Processing helix chain 'E' and resid 25 through 48 Processing helix chain 'E' and resid 51 through 74 removed outlier: 3.593A pdb=" N GLU E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.280A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.011A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.450A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.570A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.255A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.596A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE A 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 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 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.475A pdb=" N ALA A 701 " --> pdb=" O ILE D 788 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LYS D 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN A 703 " --> pdb=" O LYS D 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.280A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.011A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.451A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.892A 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: 3.570A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.255A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.919A pdb=" N ILE B 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.280A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 48 through 55 removed outlier: 7.450A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.570A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.255A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1120 through 1122 1198 hydrogen bonds defined for protein. 3297 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: 5.81 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3976 1.32 - 1.45: 6156 1.45 - 1.58: 13355 1.58 - 1.70: 3 1.70 - 1.83: 126 Bond restraints: 23616 Sorted by residual: bond pdb=" C CYS B 662 " pdb=" O CYS B 662 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.20e-02 6.94e+03 1.49e+01 bond pdb=" C CYS D 662 " pdb=" O CYS D 662 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.20e-02 6.94e+03 1.48e+01 bond pdb=" C CYS A 662 " pdb=" O CYS A 662 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.20e-02 6.94e+03 1.48e+01 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.80e+00 bond pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.70e+00 ... (remaining 23611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.46: 32249 6.46 - 12.91: 106 12.91 - 19.37: 0 19.37 - 25.83: 3 25.83 - 32.28: 3 Bond angle restraints: 32361 Sorted by residual: angle pdb=" C2 NAG G 1 " pdb=" N2 NAG G 1 " pdb=" C7 NAG G 1 " ideal model delta sigma weight residual 124.56 156.84 -32.28 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C2 NAG L 1 " pdb=" N2 NAG L 1 " pdb=" C7 NAG L 1 " ideal model delta sigma weight residual 124.56 156.83 -32.27 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 156.82 -32.26 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C LEU D 861 " pdb=" N PRO D 862 " pdb=" CA PRO D 862 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.01e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.44 -6.78 7.20e-01 1.93e+00 8.88e+01 ... (remaining 32356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 14196 17.61 - 35.23: 387 35.23 - 52.84: 69 52.84 - 70.45: 39 70.45 - 88.07: 21 Dihedral angle restraints: 14712 sinusoidal: 5445 harmonic: 9267 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -152.39 66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS D1082 " pdb=" SG CYS D1082 " pdb=" SG CYS D1126 " pdb=" CB CYS D1126 " ideal model delta sinusoidal sigma weight residual -86.00 -152.38 66.38 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -152.38 66.38 1 1.00e+01 1.00e-02 5.75e+01 ... (remaining 14709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3405 0.101 - 0.203: 456 0.203 - 0.304: 108 0.304 - 0.406: 33 0.406 - 0.507: 3 Chirality restraints: 4005 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.33e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.24e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.24e+01 ... (remaining 4002 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 709 " 0.026 2.00e-02 2.50e+03 2.71e-02 9.15e+00 pdb=" CG ASN D 709 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN D 709 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 709 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG D1309 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.026 2.00e-02 2.50e+03 2.70e-02 9.09e+00 pdb=" CG ASN B 709 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.026 2.00e-02 2.50e+03 2.70e-02 9.08e+00 pdb=" CG ASN A 709 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.033 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 13344 3.02 - 3.49: 21050 3.49 - 3.96: 36074 3.96 - 4.43: 40491 4.43 - 4.90: 65525 Nonbonded interactions: 176484 Sorted by model distance: nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.551 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.551 3.120 nonbonded pdb=" NZ LYS D 811 " pdb=" OD2 ASP D 820 " model vdw 2.552 3.120 nonbonded pdb=" O GLY D 908 " pdb=" NZ LYS D1038 " model vdw 2.571 3.120 nonbonded pdb=" O GLY A 908 " pdb=" NZ LYS A1038 " model vdw 2.572 3.120 ... (remaining 176479 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.720 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.011 0.081 23715 Z= 0.600 Angle : 1.343 32.284 32619 Z= 0.881 Chirality : 0.082 0.507 4005 Planarity : 0.005 0.025 4182 Dihedral : 9.940 88.067 8595 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.13), residues: 3138 helix: 0.58 (0.16), residues: 837 sheet: 0.96 (0.18), residues: 708 loop : -0.30 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.022 0.004 TYR D 489 PHE 0.018 0.003 PHE A 898 TRP 0.012 0.004 TRP D 353 HIS 0.003 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.01031 (23616) covalent geometry : angle 1.33045 (32361) SS BOND : bond 0.03538 ( 39) SS BOND : angle 2.90522 ( 78) hydrogen bonds : bond 0.17945 ( 1162) hydrogen bonds : angle 8.06886 ( 3297) link_BETA1-4 : bond 0.05622 ( 12) link_BETA1-4 : angle 2.47865 ( 36) link_NAG-ASN : bond 0.05782 ( 48) link_NAG-ASN : angle 2.20080 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 303 time to evaluate : 0.736 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 309 average time/residue: 0.1728 time to fit residues: 80.8862 Evaluate side-chains 136 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 616 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A 804 GLN A 935 GLN A1048 HIS A1071 GLN B 784 GLN B 804 GLN B 907 ASN B 913 GLN B 935 GLN B1048 HIS B1071 GLN D 804 GLN D 907 ASN D 913 GLN D 935 GLN D1002 GLN D1048 HIS D1071 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.138854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090419 restraints weight = 39989.144| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.12 r_work: 0.3138 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23715 Z= 0.139 Angle : 0.566 7.220 32619 Z= 0.302 Chirality : 0.045 0.172 4005 Planarity : 0.004 0.037 4182 Dihedral : 5.962 59.821 4608 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.51 % Allowed : 5.68 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.14), residues: 3138 helix: 2.42 (0.18), residues: 837 sheet: 1.25 (0.19), residues: 684 loop : -0.19 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.020 0.001 TYR A1067 PHE 0.016 0.001 PHE B 400 TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (23616) covalent geometry : angle 0.55001 (32361) SS BOND : bond 0.00178 ( 39) SS BOND : angle 1.15437 ( 78) hydrogen bonds : bond 0.05714 ( 1162) hydrogen bonds : angle 5.86296 ( 3297) link_BETA1-4 : bond 0.00583 ( 12) link_BETA1-4 : angle 1.73022 ( 36) link_NAG-ASN : bond 0.00845 ( 48) link_NAG-ASN : angle 1.78074 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8564 (m-30) cc_final: 0.8362 (m-30) REVERT: A 780 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8318 (tt0) REVERT: B 320 VAL cc_start: 0.8514 (t) cc_final: 0.8167 (p) REVERT: B 353 TRP cc_start: 0.8392 (p-90) cc_final: 0.8149 (p-90) REVERT: B 365 TYR cc_start: 0.7738 (m-80) cc_final: 0.7128 (m-80) REVERT: D 41 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7875 (mtpp) REVERT: D 353 TRP cc_start: 0.8417 (p-90) cc_final: 0.8194 (p-90) REVERT: D 697 MET cc_start: 0.9218 (ptm) cc_final: 0.8958 (ptp) outliers start: 29 outliers final: 9 residues processed: 179 average time/residue: 0.1357 time to fit residues: 40.6905 Evaluate side-chains 138 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 309 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 755 GLN A1002 GLN A1135 ASN B 655 HIS B 755 GLN D 655 HIS D 703 ASN D 755 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081312 restraints weight = 39948.523| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.04 r_work: 0.2942 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 23715 Z= 0.366 Angle : 0.683 8.541 32619 Z= 0.355 Chirality : 0.050 0.183 4005 Planarity : 0.005 0.048 4182 Dihedral : 5.878 58.462 4608 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.56 % Allowed : 6.88 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.14), residues: 3138 helix: 2.17 (0.17), residues: 846 sheet: 0.93 (0.19), residues: 675 loop : -0.38 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 905 TYR 0.024 0.002 TYR A1067 PHE 0.025 0.002 PHE A 92 TRP 0.016 0.003 TRP A 353 HIS 0.009 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00890 (23616) covalent geometry : angle 0.66857 (32361) SS BOND : bond 0.00576 ( 39) SS BOND : angle 0.91662 ( 78) hydrogen bonds : bond 0.05754 ( 1162) hydrogen bonds : angle 5.60046 ( 3297) link_BETA1-4 : bond 0.00470 ( 12) link_BETA1-4 : angle 1.17922 ( 36) link_NAG-ASN : bond 0.00664 ( 48) link_NAG-ASN : angle 2.07177 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 VAL cc_start: 0.9098 (t) cc_final: 0.8854 (p) REVERT: A 586 ASP cc_start: 0.8546 (m-30) cc_final: 0.8296 (m-30) REVERT: B 353 TRP cc_start: 0.8345 (p-90) cc_final: 0.8102 (p-90) REVERT: B 534 VAL cc_start: 0.9193 (t) cc_final: 0.8953 (p) REVERT: D 41 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8068 (mtpp) REVERT: D 353 TRP cc_start: 0.8336 (p-90) cc_final: 0.8065 (p-90) REVERT: D 1002 GLN cc_start: 0.8692 (tp40) cc_final: 0.8395 (tp40) outliers start: 30 outliers final: 17 residues processed: 163 average time/residue: 0.1249 time to fit residues: 34.3775 Evaluate side-chains 139 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 973 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 66 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 257 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 163 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 248 optimal weight: 0.0010 chunk 77 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.133072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084901 restraints weight = 39583.445| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.67 r_work: 0.2971 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23715 Z= 0.113 Angle : 0.496 7.152 32619 Z= 0.259 Chirality : 0.044 0.175 4005 Planarity : 0.004 0.042 4182 Dihedral : 5.455 58.976 4608 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.20 % Allowed : 7.40 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.14), residues: 3138 helix: 2.69 (0.18), residues: 825 sheet: 1.06 (0.20), residues: 642 loop : -0.30 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.020 0.001 TYR B1067 PHE 0.011 0.001 PHE D 238 TRP 0.016 0.001 TRP A 353 HIS 0.002 0.000 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00237 (23616) covalent geometry : angle 0.48201 (32361) SS BOND : bond 0.00194 ( 39) SS BOND : angle 0.64176 ( 78) hydrogen bonds : bond 0.04357 ( 1162) hydrogen bonds : angle 5.13098 ( 3297) link_BETA1-4 : bond 0.00446 ( 12) link_BETA1-4 : angle 0.97840 ( 36) link_NAG-ASN : bond 0.00416 ( 48) link_NAG-ASN : angle 1.76221 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6609 (m-80) cc_final: 0.6256 (m-80) REVERT: A 534 VAL cc_start: 0.9057 (t) cc_final: 0.8833 (p) REVERT: A 586 ASP cc_start: 0.8417 (m-30) cc_final: 0.8148 (m-30) REVERT: A 725 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: D 41 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7868 (mtpp) REVERT: D 353 TRP cc_start: 0.8090 (p-90) cc_final: 0.7869 (p-90) REVERT: D 973 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.9018 (pt) outliers start: 23 outliers final: 11 residues processed: 139 average time/residue: 0.1356 time to fit residues: 31.5804 Evaluate side-chains 127 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 186 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 202 optimal weight: 0.0050 chunk 139 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.131982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083838 restraints weight = 39610.935| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.63 r_work: 0.2948 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23715 Z= 0.161 Angle : 0.507 8.300 32619 Z= 0.261 Chirality : 0.044 0.173 4005 Planarity : 0.004 0.038 4182 Dihedral : 5.356 58.955 4608 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 7.66 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.15), residues: 3138 helix: 2.69 (0.18), residues: 834 sheet: 0.97 (0.20), residues: 663 loop : -0.37 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.021 0.001 TYR A1067 PHE 0.013 0.001 PHE D 238 TRP 0.024 0.002 TRP A 353 HIS 0.003 0.001 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00377 (23616) covalent geometry : angle 0.49257 (32361) SS BOND : bond 0.00289 ( 39) SS BOND : angle 0.55278 ( 78) hydrogen bonds : bond 0.04327 ( 1162) hydrogen bonds : angle 5.04329 ( 3297) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 0.93403 ( 36) link_NAG-ASN : bond 0.00416 ( 48) link_NAG-ASN : angle 1.80558 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6696 (m-80) cc_final: 0.6372 (m-80) REVERT: A 534 VAL cc_start: 0.9091 (t) cc_final: 0.8875 (p) REVERT: A 586 ASP cc_start: 0.8442 (m-30) cc_final: 0.8159 (m-30) REVERT: A 901 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8524 (pt0) REVERT: D 41 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7962 (mtpp) REVERT: D 353 TRP cc_start: 0.8082 (p-90) cc_final: 0.7853 (p-90) outliers start: 28 outliers final: 10 residues processed: 142 average time/residue: 0.1225 time to fit residues: 29.5727 Evaluate side-chains 123 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 172 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 301 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.133171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085303 restraints weight = 39602.270| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.64 r_work: 0.2973 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23715 Z= 0.109 Angle : 0.468 6.597 32619 Z= 0.243 Chirality : 0.043 0.171 4005 Planarity : 0.004 0.038 4182 Dihedral : 5.096 58.495 4608 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.30 % Allowed : 8.39 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.15), residues: 3138 helix: 2.67 (0.18), residues: 855 sheet: 1.02 (0.20), residues: 663 loop : -0.34 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.020 0.001 TYR A1067 PHE 0.011 0.001 PHE D 238 TRP 0.026 0.001 TRP A 353 HIS 0.002 0.000 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00240 (23616) covalent geometry : angle 0.45540 (32361) SS BOND : bond 0.00209 ( 39) SS BOND : angle 0.48694 ( 78) hydrogen bonds : bond 0.03877 ( 1162) hydrogen bonds : angle 4.85367 ( 3297) link_BETA1-4 : bond 0.00419 ( 12) link_BETA1-4 : angle 0.88331 ( 36) link_NAG-ASN : bond 0.00361 ( 48) link_NAG-ASN : angle 1.63834 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6576 (m-80) cc_final: 0.6276 (m-80) REVERT: A 534 VAL cc_start: 0.9081 (t) cc_final: 0.8874 (p) REVERT: A 586 ASP cc_start: 0.8470 (m-30) cc_final: 0.8137 (m-30) REVERT: B 365 TYR cc_start: 0.8180 (m-80) cc_final: 0.7634 (m-80) REVERT: B 1041 ASP cc_start: 0.8688 (m-30) cc_final: 0.8393 (t0) REVERT: D 41 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7893 (mtpp) REVERT: D 269 TYR cc_start: 0.7888 (m-10) cc_final: 0.7465 (m-10) REVERT: D 534 VAL cc_start: 0.9131 (t) cc_final: 0.8924 (p) outliers start: 25 outliers final: 15 residues processed: 150 average time/residue: 0.1202 time to fit residues: 31.5011 Evaluate side-chains 130 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 260 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 180 optimal weight: 0.0030 chunk 284 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.133438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087153 restraints weight = 38743.845| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.42 r_work: 0.3000 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23715 Z= 0.097 Angle : 0.459 6.457 32619 Z= 0.237 Chirality : 0.043 0.170 4005 Planarity : 0.004 0.036 4182 Dihedral : 4.865 57.953 4608 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.15 % Allowed : 8.91 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.15), residues: 3138 helix: 2.78 (0.18), residues: 855 sheet: 1.03 (0.20), residues: 678 loop : -0.31 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.020 0.001 TYR A1067 PHE 0.010 0.001 PHE D 238 TRP 0.028 0.002 TRP B 353 HIS 0.001 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00206 (23616) covalent geometry : angle 0.44743 (32361) SS BOND : bond 0.00156 ( 39) SS BOND : angle 0.45698 ( 78) hydrogen bonds : bond 0.03631 ( 1162) hydrogen bonds : angle 4.73192 ( 3297) link_BETA1-4 : bond 0.00430 ( 12) link_BETA1-4 : angle 0.88900 ( 36) link_NAG-ASN : bond 0.00411 ( 48) link_NAG-ASN : angle 1.57171 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6511 (m-80) cc_final: 0.6218 (m-80) REVERT: A 586 ASP cc_start: 0.8491 (m-30) cc_final: 0.8199 (m-30) REVERT: A 725 GLU cc_start: 0.8652 (tt0) cc_final: 0.8249 (tt0) REVERT: A 858 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8746 (pp) REVERT: B 365 TYR cc_start: 0.8284 (m-80) cc_final: 0.7759 (m-80) REVERT: B 858 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8829 (pp) REVERT: B 1094 VAL cc_start: 0.8858 (m) cc_final: 0.8542 (p) REVERT: D 41 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7909 (mtpp) REVERT: D 269 TYR cc_start: 0.7958 (m-10) cc_final: 0.7464 (m-10) REVERT: D 858 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8841 (pp) outliers start: 22 outliers final: 13 residues processed: 149 average time/residue: 0.1197 time to fit residues: 31.0040 Evaluate side-chains 134 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 35 optimal weight: 40.0000 chunk 185 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 238 optimal weight: 0.0980 chunk 227 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 100 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.085544 restraints weight = 39294.620| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.65 r_work: 0.2979 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23715 Z= 0.106 Angle : 0.460 6.078 32619 Z= 0.238 Chirality : 0.043 0.168 4005 Planarity : 0.004 0.037 4182 Dihedral : 4.670 58.695 4608 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.99 % Allowed : 9.32 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.15), residues: 3138 helix: 2.79 (0.18), residues: 855 sheet: 0.97 (0.20), residues: 678 loop : -0.29 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 995 TYR 0.019 0.001 TYR A1067 PHE 0.011 0.001 PHE D 238 TRP 0.030 0.002 TRP B 353 HIS 0.001 0.000 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00235 (23616) covalent geometry : angle 0.44959 (32361) SS BOND : bond 0.00185 ( 39) SS BOND : angle 0.45591 ( 78) hydrogen bonds : bond 0.03598 ( 1162) hydrogen bonds : angle 4.67786 ( 3297) link_BETA1-4 : bond 0.00404 ( 12) link_BETA1-4 : angle 0.86201 ( 36) link_NAG-ASN : bond 0.00309 ( 48) link_NAG-ASN : angle 1.50559 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6495 (m-80) cc_final: 0.6213 (m-80) REVERT: A 586 ASP cc_start: 0.8454 (m-30) cc_final: 0.8173 (m-30) REVERT: A 725 GLU cc_start: 0.8647 (tt0) cc_final: 0.8263 (tt0) REVERT: A 858 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8755 (pp) REVERT: B 168 PHE cc_start: 0.7753 (t80) cc_final: 0.7532 (t80) REVERT: B 365 TYR cc_start: 0.8272 (m-80) cc_final: 0.7793 (m-80) REVERT: B 858 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8834 (pp) REVERT: B 1094 VAL cc_start: 0.8888 (m) cc_final: 0.8559 (p) REVERT: D 269 TYR cc_start: 0.7925 (m-10) cc_final: 0.7384 (m-10) REVERT: D 858 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8830 (pp) outliers start: 19 outliers final: 15 residues processed: 136 average time/residue: 0.1190 time to fit residues: 28.8916 Evaluate side-chains 133 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 202 optimal weight: 2.9990 chunk 244 optimal weight: 0.0020 chunk 221 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 chunk 304 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.083339 restraints weight = 39835.160| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.67 r_work: 0.2933 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23715 Z= 0.175 Angle : 0.506 5.953 32619 Z= 0.260 Chirality : 0.045 0.171 4005 Planarity : 0.004 0.035 4182 Dihedral : 4.804 56.652 4608 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.25 % Allowed : 9.53 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.15), residues: 3138 helix: 2.60 (0.17), residues: 873 sheet: 0.82 (0.20), residues: 702 loop : -0.33 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.021 0.001 TYR A1067 PHE 0.015 0.001 PHE A 898 TRP 0.031 0.002 TRP B 353 HIS 0.003 0.001 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00416 (23616) covalent geometry : angle 0.49471 (32361) SS BOND : bond 0.00321 ( 39) SS BOND : angle 0.53461 ( 78) hydrogen bonds : bond 0.04186 ( 1162) hydrogen bonds : angle 4.84676 ( 3297) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 0.84211 ( 36) link_NAG-ASN : bond 0.00313 ( 48) link_NAG-ASN : angle 1.61947 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6661 (m-80) cc_final: 0.6364 (m-80) REVERT: A 586 ASP cc_start: 0.8503 (m-30) cc_final: 0.8199 (m-30) REVERT: A 725 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: A 858 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8821 (pp) REVERT: B 168 PHE cc_start: 0.7832 (t80) cc_final: 0.7538 (t80) REVERT: B 365 TYR cc_start: 0.8277 (m-80) cc_final: 0.7838 (m-80) REVERT: B 858 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8927 (pp) REVERT: B 1002 GLN cc_start: 0.8213 (tp40) cc_final: 0.7967 (tp40) REVERT: D 269 TYR cc_start: 0.7927 (m-10) cc_final: 0.7289 (m-10) REVERT: D 858 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8874 (pp) outliers start: 24 outliers final: 18 residues processed: 139 average time/residue: 0.1292 time to fit residues: 31.5528 Evaluate side-chains 136 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 243 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 292 optimal weight: 0.0060 chunk 1 optimal weight: 3.9990 chunk 162 optimal weight: 0.0370 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 overall best weight: 0.5474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085293 restraints weight = 39565.668| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.64 r_work: 0.2975 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23715 Z= 0.097 Angle : 0.462 7.645 32619 Z= 0.239 Chirality : 0.043 0.168 4005 Planarity : 0.004 0.038 4182 Dihedral : 4.690 58.584 4608 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 10.00 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.15), residues: 3138 helix: 2.68 (0.17), residues: 873 sheet: 0.93 (0.20), residues: 678 loop : -0.21 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.020 0.001 TYR A1067 PHE 0.010 0.001 PHE D 238 TRP 0.033 0.002 TRP B 353 HIS 0.001 0.000 HIS D1064 Details of bonding type rmsd covalent geometry : bond 0.00203 (23616) covalent geometry : angle 0.45152 (32361) SS BOND : bond 0.00162 ( 39) SS BOND : angle 0.47927 ( 78) hydrogen bonds : bond 0.03617 ( 1162) hydrogen bonds : angle 4.64418 ( 3297) link_BETA1-4 : bond 0.00400 ( 12) link_BETA1-4 : angle 0.81397 ( 36) link_NAG-ASN : bond 0.00467 ( 48) link_NAG-ASN : angle 1.52892 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6549 (m-80) cc_final: 0.6260 (m-80) REVERT: A 586 ASP cc_start: 0.8446 (m-30) cc_final: 0.8165 (m-30) REVERT: A 725 GLU cc_start: 0.8608 (tt0) cc_final: 0.8244 (tt0) REVERT: B 168 PHE cc_start: 0.7743 (t80) cc_final: 0.7530 (t80) REVERT: B 365 TYR cc_start: 0.8269 (m-80) cc_final: 0.7823 (m-80) REVERT: B 858 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8869 (pp) REVERT: B 1002 GLN cc_start: 0.7993 (tp40) cc_final: 0.7740 (tp40) REVERT: B 1045 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8565 (ttpp) REVERT: B 1094 VAL cc_start: 0.8875 (m) cc_final: 0.8531 (p) REVERT: D 269 TYR cc_start: 0.7865 (m-10) cc_final: 0.7214 (m-10) REVERT: D 858 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8841 (pp) REVERT: D 1045 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8492 (ttpp) outliers start: 15 outliers final: 13 residues processed: 138 average time/residue: 0.1234 time to fit residues: 29.7589 Evaluate side-chains 134 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 73 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 41 optimal weight: 40.0000 chunk 63 optimal weight: 0.8980 chunk 253 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 160 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.084793 restraints weight = 39637.121| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.66 r_work: 0.2967 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23715 Z= 0.109 Angle : 0.462 6.634 32619 Z= 0.237 Chirality : 0.043 0.166 4005 Planarity : 0.004 0.036 4182 Dihedral : 4.604 58.179 4608 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.04 % Allowed : 9.84 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.15), residues: 3138 helix: 2.73 (0.17), residues: 873 sheet: 0.91 (0.20), residues: 678 loop : -0.21 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 355 TYR 0.020 0.001 TYR A1067 PHE 0.011 0.001 PHE D 238 TRP 0.032 0.002 TRP B 353 HIS 0.002 0.000 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00246 (23616) covalent geometry : angle 0.45017 (32361) SS BOND : bond 0.00214 ( 39) SS BOND : angle 0.44458 ( 78) hydrogen bonds : bond 0.03620 ( 1162) hydrogen bonds : angle 4.60887 ( 3297) link_BETA1-4 : bond 0.00401 ( 12) link_BETA1-4 : angle 0.82187 ( 36) link_NAG-ASN : bond 0.00312 ( 48) link_NAG-ASN : angle 1.58010 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5503.94 seconds wall clock time: 94 minutes 35.71 seconds (5675.71 seconds total)