Starting phenix.real_space_refine on Thu Mar 5 20:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tl9_25984/03_2026/7tl9_25984_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tl9_25984/03_2026/7tl9_25984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tl9_25984/03_2026/7tl9_25984_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tl9_25984/03_2026/7tl9_25984_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tl9_25984/03_2026/7tl9_25984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tl9_25984/03_2026/7tl9_25984.map" } resolution = 3.5 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= -0.003 sd= 0.156 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 107 5.16 5 C 15968 2.51 5 N 4071 2.21 5 O 4870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 25016 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8227 Classifications: {'peptide': 1050} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 998} Chain breaks: 5 Chain: "B" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8070 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 7888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7888 Classifications: {'peptide': 1005} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 955} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.46, per 1000 atoms: 0.22 Number of scatterers: 25016 At special positions: 0 Unit cell: (136.08, 131.76, 203.04, 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 107 16.00 O 4870 8.00 N 4071 7.00 C 15968 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 ALPHA1-4 " NAG S 2 " - " MAN S 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1201 " - " ASN A 331 " " NAG A1202 " - " ASN A 343 " " NAG A1203 " - " ASN A 616 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 61 " " NAG A1206 " - " ASN A 165 " " NAG A1207 " - " ASN A 709 " " NAG A1208 " - " ASN A 122 " " NAG A1209 " - " ASN A 234 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 657 " " NAG B1204 " - " ASN B 709 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 165 " " NAG C1203 " - " ASN C 331 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 122 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 709 " " NAG C1208 " - " ASN C1134 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN B 331 " " NAG H 1 " - " ASN C1098 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG N 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1074 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5792 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 44 sheets defined 26.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.852A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.961A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.890A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 633 through 639 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.725A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.665A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.564A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.552A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.200A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.553A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.037A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.423A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.764A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.829A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.817A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.836A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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: 4.626A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.899A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.809A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.915A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.806A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.546A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.523A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.824A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.529A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.011A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.260A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.646A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.869A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.269A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.575A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.692A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.134A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.134A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.525A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.870A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.949A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.229A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.102A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.272A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.828A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.585A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.731A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.857A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.622A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.918A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.343A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.930A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.503A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.549A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.588A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.583A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.866A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.928A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.542A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.635A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1096 1005 hydrogen bonds defined for protein. 2775 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: 6.47 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7848 1.34 - 1.47: 6449 1.47 - 1.59: 11143 1.59 - 1.72: 0 1.72 - 1.85: 131 Bond restraints: 25571 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" CB ASN C1098 " pdb=" CG ASN C1098 " ideal model delta sigma weight residual 1.516 1.586 -0.070 2.50e-02 1.60e+03 7.93e+00 bond pdb=" C1 NAG C1207 " pdb=" O5 NAG C1207 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.42e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 ... (remaining 25566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 34028 2.31 - 4.61: 672 4.61 - 6.92: 51 6.92 - 9.22: 20 9.22 - 11.53: 5 Bond angle restraints: 34776 Sorted by residual: angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 124.32 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" C SER C1097 " pdb=" N ASN C1098 " pdb=" CA ASN C1098 " ideal model delta sigma weight residual 125.66 133.21 -7.55 1.85e+00 2.92e-01 1.67e+01 angle pdb=" C ASN C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" CA ASN C1098 " pdb=" CB ASN C1098 " pdb=" CG ASN C1098 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" CB MET A1050 " pdb=" CG MET A1050 " pdb=" SD MET A1050 " ideal model delta sigma weight residual 112.70 101.17 11.53 3.00e+00 1.11e-01 1.48e+01 ... (remaining 34771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 15061 22.57 - 45.15: 796 45.15 - 67.72: 105 67.72 - 90.29: 40 90.29 - 112.86: 23 Dihedral angle restraints: 16025 sinusoidal: 7033 harmonic: 8992 Sorted by residual: 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 -168.85 82.85 1 1.00e+01 1.00e-02 8.41e+01 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 -166.61 80.61 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.02 78.02 1 1.00e+01 1.00e-02 7.61e+01 ... (remaining 16022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4108 0.199 - 0.399: 16 0.399 - 0.598: 0 0.598 - 0.797: 1 0.797 - 0.996: 1 Chirality restraints: 4126 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" C1 NAG A1207 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1207 " pdb=" O5 NAG A1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C2 NAG U 2 " pdb=" C1 NAG U 2 " pdb=" C3 NAG U 2 " pdb=" N2 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 4123 not shown) Planarity restraints: 4442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 214A" 0.048 5.00e-02 4.00e+02 7.13e-02 8.12e+00 pdb=" N PRO C 214B" -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 214B" 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 214B" 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 295 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 353 " 0.021 2.00e-02 2.50e+03 1.68e-02 7.03e+00 pdb=" CG TRP A 353 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 353 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 353 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 353 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 353 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 353 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 353 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 353 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 353 " 0.010 2.00e-02 2.50e+03 ... (remaining 4439 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5379 2.79 - 3.32: 21064 3.32 - 3.84: 40834 3.84 - 4.37: 46740 4.37 - 4.90: 82386 Nonbonded interactions: 196403 Sorted by model distance: nonbonded pdb=" O PHE A 592 " pdb=" OH TYR B 837 " model vdw 2.260 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.302 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.312 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.312 3.040 ... (remaining 196398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 142 or resid 168 through 342 or resid 350 throu \ gh 515 or resid 527 through 620 or resid 640 through 677 or resid 689 through 82 \ 7 or resid 854 through 1204)) selection = (chain 'B' and (resid 27 through 620 or resid 640 through 827 or resid 854 throu \ gh 1204)) selection = (chain 'C' and (resid 27 through 142 or resid 168 through 342 or resid 350 throu \ gh 515 or resid 527 through 677 or resid 689 through 1204)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'b' selection = chain 'd' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.840 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.004 0.071 25669 Z= 0.226 Angle : 0.802 15.962 35031 Z= 0.405 Chirality : 0.057 0.996 4126 Planarity : 0.006 0.071 4404 Dihedral : 14.379 112.864 10116 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: -0.78 (0.14), residues: 3039 helix: 0.01 (0.18), residues: 696 sheet: 0.36 (0.20), residues: 625 loop : -1.09 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.021 0.002 TYR A1067 PHE 0.021 0.002 PHE A 906 TRP 0.041 0.002 TRP A 353 HIS 0.007 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00441 (25571) covalent geometry : angle 0.74419 (34776) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.52887 ( 78) hydrogen bonds : bond 0.08265 ( 996) hydrogen bonds : angle 6.11773 ( 2775) link_ALPHA1-4 : bond 0.01472 ( 1) link_ALPHA1-4 : angle 4.01290 ( 3) link_BETA1-4 : bond 0.01569 ( 20) link_BETA1-4 : angle 5.07903 ( 60) link_NAG-ASN : bond 0.00758 ( 38) link_NAG-ASN : angle 3.63844 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 900 MET cc_start: 0.8617 (mtp) cc_final: 0.8371 (mtm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1609 time to fit residues: 17.4758 Evaluate side-chains 44 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 804 GLN B 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.100710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.070352 restraints weight = 75153.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069828 restraints weight = 55325.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069703 restraints weight = 47356.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069844 restraints weight = 45602.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069841 restraints weight = 41785.259| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25669 Z= 0.122 Angle : 0.561 13.870 35031 Z= 0.272 Chirality : 0.046 0.461 4126 Planarity : 0.004 0.058 4404 Dihedral : 9.121 105.950 4562 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.19 % Allowed : 2.71 % Favored : 97.11 % 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: -0.14 (0.15), residues: 3039 helix: 1.22 (0.20), residues: 717 sheet: 0.29 (0.20), residues: 630 loop : -0.82 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.014 0.001 TYR A1067 PHE 0.017 0.001 PHE C 375 TRP 0.025 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00273 (25571) covalent geometry : angle 0.52312 (34776) SS BOND : bond 0.00257 ( 39) SS BOND : angle 0.76367 ( 78) hydrogen bonds : bond 0.03902 ( 996) hydrogen bonds : angle 5.11733 ( 2775) link_ALPHA1-4 : bond 0.00782 ( 1) link_ALPHA1-4 : angle 1.95051 ( 3) link_BETA1-4 : bond 0.01123 ( 20) link_BETA1-4 : angle 3.21869 ( 60) link_NAG-ASN : bond 0.00403 ( 38) link_NAG-ASN : angle 2.67806 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8648 (ptm) cc_final: 0.8371 (ptm) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.1728 time to fit residues: 14.5031 Evaluate side-chains 45 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 886 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 143 optimal weight: 8.9990 chunk 287 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 804 GLN B 907 ASN B 935 GLN C 644 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.097782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067130 restraints weight = 77134.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066829 restraints weight = 58494.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066697 restraints weight = 51469.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066890 restraints weight = 48183.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066889 restraints weight = 43988.188| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25669 Z= 0.213 Angle : 0.607 13.364 35031 Z= 0.299 Chirality : 0.047 0.509 4126 Planarity : 0.004 0.048 4404 Dihedral : 7.877 103.107 4562 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.37 % Allowed : 5.34 % Favored : 94.29 % 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: -0.10 (0.15), residues: 3039 helix: 1.38 (0.20), residues: 723 sheet: 0.28 (0.20), residues: 634 loop : -0.85 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 634 TYR 0.015 0.001 TYR A1067 PHE 0.028 0.002 PHE B 906 TRP 0.054 0.002 TRP B 436 HIS 0.009 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00502 (25571) covalent geometry : angle 0.57126 (34776) SS BOND : bond 0.00355 ( 39) SS BOND : angle 0.78699 ( 78) hydrogen bonds : bond 0.04686 ( 996) hydrogen bonds : angle 5.17714 ( 2775) link_ALPHA1-4 : bond 0.00925 ( 1) link_ALPHA1-4 : angle 2.39791 ( 3) link_BETA1-4 : bond 0.01066 ( 20) link_BETA1-4 : angle 3.30439 ( 60) link_NAG-ASN : bond 0.00460 ( 38) link_NAG-ASN : angle 2.72196 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8664 (mm) cc_final: 0.8403 (pt) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.1409 time to fit residues: 13.1080 Evaluate side-chains 47 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 231 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 212 optimal weight: 20.0000 chunk 285 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 112 optimal weight: 0.9980 chunk 237 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.099943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069517 restraints weight = 73530.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068583 restraints weight = 56787.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068404 restraints weight = 47721.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068515 restraints weight = 49783.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068605 restraints weight = 42131.211| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25669 Z= 0.153 Angle : 0.544 13.000 35031 Z= 0.266 Chirality : 0.045 0.469 4126 Planarity : 0.003 0.045 4404 Dihedral : 7.478 98.068 4562 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.56 % Allowed : 6.82 % Favored : 92.62 % 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: 0.02 (0.15), residues: 3039 helix: 1.68 (0.20), residues: 721 sheet: 0.22 (0.20), residues: 624 loop : -0.81 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.014 0.001 TYR A1067 PHE 0.030 0.001 PHE C 375 TRP 0.012 0.001 TRP C 353 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00355 (25571) covalent geometry : angle 0.50862 (34776) SS BOND : bond 0.00277 ( 39) SS BOND : angle 0.61410 ( 78) hydrogen bonds : bond 0.04058 ( 996) hydrogen bonds : angle 4.97977 ( 2775) link_ALPHA1-4 : bond 0.00930 ( 1) link_ALPHA1-4 : angle 2.02752 ( 3) link_BETA1-4 : bond 0.01028 ( 20) link_BETA1-4 : angle 3.14619 ( 60) link_NAG-ASN : bond 0.00394 ( 38) link_NAG-ASN : angle 2.54726 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8691 (ptm) cc_final: 0.8431 (ptm) outliers start: 15 outliers final: 10 residues processed: 54 average time/residue: 0.1292 time to fit residues: 13.0045 Evaluate side-chains 48 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 199 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 901 GLN B 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.097305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066239 restraints weight = 75763.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066107 restraints weight = 56891.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065947 restraints weight = 46256.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066169 restraints weight = 46699.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066244 restraints weight = 40832.997| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25669 Z= 0.239 Angle : 0.613 12.831 35031 Z= 0.301 Chirality : 0.047 0.511 4126 Planarity : 0.004 0.045 4404 Dihedral : 7.525 101.875 4562 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.78 % Allowed : 7.82 % Favored : 91.40 % 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: -0.08 (0.15), residues: 3039 helix: 1.59 (0.20), residues: 716 sheet: 0.14 (0.20), residues: 631 loop : -0.85 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.015 0.001 TYR B1067 PHE 0.028 0.002 PHE C 375 TRP 0.030 0.002 TRP B 436 HIS 0.009 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00569 (25571) covalent geometry : angle 0.57917 (34776) SS BOND : bond 0.00388 ( 39) SS BOND : angle 0.73753 ( 78) hydrogen bonds : bond 0.04750 ( 996) hydrogen bonds : angle 5.15586 ( 2775) link_ALPHA1-4 : bond 0.00990 ( 1) link_ALPHA1-4 : angle 2.28343 ( 3) link_BETA1-4 : bond 0.01030 ( 20) link_BETA1-4 : angle 3.25695 ( 60) link_NAG-ASN : bond 0.00452 ( 38) link_NAG-ASN : angle 2.66967 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 878 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8808 (tt) REVERT: B 1142 GLN cc_start: 0.8128 (tp40) cc_final: 0.7820 (tp-100) outliers start: 21 outliers final: 14 residues processed: 60 average time/residue: 0.1331 time to fit residues: 14.3998 Evaluate side-chains 56 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 201 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 275 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069534 restraints weight = 73952.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069187 restraints weight = 52732.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068983 restraints weight = 48383.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069039 restraints weight = 47912.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069147 restraints weight = 40885.385| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25669 Z= 0.096 Angle : 0.515 12.836 35031 Z= 0.251 Chirality : 0.045 0.442 4126 Planarity : 0.003 0.043 4404 Dihedral : 7.171 96.596 4562 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.56 % Allowed : 8.23 % Favored : 91.21 % 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: 0.22 (0.15), residues: 3039 helix: 2.09 (0.20), residues: 704 sheet: 0.18 (0.20), residues: 607 loop : -0.70 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.015 0.001 TYR C 265 PHE 0.027 0.001 PHE C 375 TRP 0.046 0.001 TRP B 436 HIS 0.003 0.000 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00202 (25571) covalent geometry : angle 0.48103 (34776) SS BOND : bond 0.00215 ( 39) SS BOND : angle 0.49961 ( 78) hydrogen bonds : bond 0.03645 ( 996) hydrogen bonds : angle 4.83210 ( 2775) link_ALPHA1-4 : bond 0.00831 ( 1) link_ALPHA1-4 : angle 1.98715 ( 3) link_BETA1-4 : bond 0.01041 ( 20) link_BETA1-4 : angle 3.00065 ( 60) link_NAG-ASN : bond 0.00443 ( 38) link_NAG-ASN : angle 2.44887 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8648 (ptm) cc_final: 0.8365 (ptm) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.1285 time to fit residues: 13.2606 Evaluate side-chains 51 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 142 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 274 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069736 restraints weight = 74100.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069031 restraints weight = 54925.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069017 restraints weight = 48303.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069093 restraints weight = 47007.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069189 restraints weight = 41471.415| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25669 Z= 0.095 Angle : 0.508 12.690 35031 Z= 0.246 Chirality : 0.044 0.442 4126 Planarity : 0.003 0.043 4404 Dihedral : 6.985 94.899 4562 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.63 % Allowed : 8.53 % Favored : 90.84 % 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: 0.32 (0.15), residues: 3039 helix: 2.24 (0.20), residues: 698 sheet: 0.27 (0.20), residues: 601 loop : -0.66 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.014 0.001 TYR B1067 PHE 0.026 0.001 PHE C 375 TRP 0.078 0.002 TRP B 436 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00208 (25571) covalent geometry : angle 0.47358 (34776) SS BOND : bond 0.00202 ( 39) SS BOND : angle 0.49117 ( 78) hydrogen bonds : bond 0.03510 ( 996) hydrogen bonds : angle 4.74737 ( 2775) link_ALPHA1-4 : bond 0.00849 ( 1) link_ALPHA1-4 : angle 2.05096 ( 3) link_BETA1-4 : bond 0.01020 ( 20) link_BETA1-4 : angle 2.98086 ( 60) link_NAG-ASN : bond 0.00410 ( 38) link_NAG-ASN : angle 2.44060 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8841 (mm) cc_final: 0.8320 (tt) REVERT: A 697 MET cc_start: 0.8633 (ptm) cc_final: 0.8360 (ptm) REVERT: A 878 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8839 (tt) outliers start: 17 outliers final: 11 residues processed: 58 average time/residue: 0.1368 time to fit residues: 14.4569 Evaluate side-chains 53 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 198 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 187 optimal weight: 0.4980 chunk 141 optimal weight: 30.0000 chunk 233 optimal weight: 3.9990 chunk 116 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.099745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069114 restraints weight = 73613.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068714 restraints weight = 53103.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068539 restraints weight = 47335.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068579 restraints weight = 46328.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068739 restraints weight = 40459.484| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25669 Z= 0.130 Angle : 0.524 12.601 35031 Z= 0.254 Chirality : 0.045 0.453 4126 Planarity : 0.003 0.042 4404 Dihedral : 6.929 94.660 4562 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.44 % Allowed : 9.05 % Favored : 90.51 % 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: 0.31 (0.15), residues: 3039 helix: 2.15 (0.20), residues: 710 sheet: 0.27 (0.20), residues: 601 loop : -0.65 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.014 0.001 TYR B1067 PHE 0.025 0.001 PHE C 375 TRP 0.068 0.002 TRP B 436 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00299 (25571) covalent geometry : angle 0.48983 (34776) SS BOND : bond 0.00234 ( 39) SS BOND : angle 0.55580 ( 78) hydrogen bonds : bond 0.03757 ( 996) hydrogen bonds : angle 4.80287 ( 2775) link_ALPHA1-4 : bond 0.00911 ( 1) link_ALPHA1-4 : angle 2.07901 ( 3) link_BETA1-4 : bond 0.01024 ( 20) link_BETA1-4 : angle 3.01094 ( 60) link_NAG-ASN : bond 0.00402 ( 38) link_NAG-ASN : angle 2.46138 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.5385 (t80) cc_final: 0.5147 (t80) REVERT: A 449 TYR cc_start: 0.6806 (m-10) cc_final: 0.6458 (m-80) REVERT: A 624 ILE cc_start: 0.8852 (mm) cc_final: 0.8333 (tt) REVERT: A 697 MET cc_start: 0.8647 (ptm) cc_final: 0.8365 (ptm) REVERT: A 878 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8816 (tt) outliers start: 12 outliers final: 11 residues processed: 54 average time/residue: 0.1428 time to fit residues: 13.9331 Evaluate side-chains 53 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 179 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 178 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 288 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 305 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.099015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.068344 restraints weight = 73059.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066662 restraints weight = 59881.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066600 restraints weight = 54324.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066684 restraints weight = 49640.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066978 restraints weight = 43997.143| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 25669 Z= 0.267 Angle : 0.637 12.512 35031 Z= 0.313 Chirality : 0.047 0.498 4126 Planarity : 0.004 0.042 4404 Dihedral : 7.310 99.619 4562 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.56 % Allowed : 9.31 % Favored : 90.14 % 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: -0.03 (0.15), residues: 3039 helix: 1.71 (0.20), residues: 715 sheet: 0.07 (0.20), residues: 616 loop : -0.82 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.017 0.002 TYR A 279 PHE 0.025 0.002 PHE C 375 TRP 0.064 0.003 TRP B 436 HIS 0.009 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00629 (25571) covalent geometry : angle 0.60495 (34776) SS BOND : bond 0.00409 ( 39) SS BOND : angle 0.81015 ( 78) hydrogen bonds : bond 0.04918 ( 996) hydrogen bonds : angle 5.19863 ( 2775) link_ALPHA1-4 : bond 0.01052 ( 1) link_ALPHA1-4 : angle 2.29163 ( 3) link_BETA1-4 : bond 0.01033 ( 20) link_BETA1-4 : angle 3.24885 ( 60) link_NAG-ASN : bond 0.00494 ( 38) link_NAG-ASN : angle 2.64443 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.6981 (m-10) cc_final: 0.6580 (m-80) REVERT: A 624 ILE cc_start: 0.8935 (mm) cc_final: 0.8382 (tt) REVERT: A 697 MET cc_start: 0.8715 (ptm) cc_final: 0.8455 (ptm) REVERT: A 878 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 1142 GLN cc_start: 0.8087 (tp40) cc_final: 0.7803 (tp-100) outliers start: 15 outliers final: 12 residues processed: 56 average time/residue: 0.1378 time to fit residues: 13.8660 Evaluate side-chains 56 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 255 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 chunk 275 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 279 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.098250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067685 restraints weight = 76075.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067235 restraints weight = 60465.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067414 restraints weight = 45482.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067455 restraints weight = 44157.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067565 restraints weight = 40443.936| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25669 Z= 0.096 Angle : 0.515 12.774 35031 Z= 0.250 Chirality : 0.045 0.428 4126 Planarity : 0.003 0.042 4404 Dihedral : 6.946 93.943 4562 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.41 % Allowed : 9.64 % 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: 0.26 (0.15), residues: 3039 helix: 2.17 (0.20), residues: 705 sheet: 0.17 (0.20), residues: 612 loop : -0.68 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.015 0.001 TYR B1067 PHE 0.026 0.001 PHE C 375 TRP 0.058 0.001 TRP B 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00208 (25571) covalent geometry : angle 0.48075 (34776) SS BOND : bond 0.00228 ( 39) SS BOND : angle 0.51202 ( 78) hydrogen bonds : bond 0.03628 ( 996) hydrogen bonds : angle 4.81858 ( 2775) link_ALPHA1-4 : bond 0.00849 ( 1) link_ALPHA1-4 : angle 1.99283 ( 3) link_BETA1-4 : bond 0.01083 ( 20) link_BETA1-4 : angle 2.97819 ( 60) link_NAG-ASN : bond 0.00441 ( 38) link_NAG-ASN : angle 2.43382 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.5708 (t80) cc_final: 0.5337 (t80) REVERT: A 449 TYR cc_start: 0.6744 (m-10) cc_final: 0.6419 (m-80) REVERT: A 624 ILE cc_start: 0.8842 (mm) cc_final: 0.8365 (tt) REVERT: A 697 MET cc_start: 0.8688 (ptm) cc_final: 0.8419 (ptm) REVERT: A 878 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8832 (tt) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.1486 time to fit residues: 14.0061 Evaluate side-chains 50 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 211 optimal weight: 0.4980 chunk 290 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 255 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.099900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069283 restraints weight = 73427.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068593 restraints weight = 54959.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068359 restraints weight = 48132.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068577 restraints weight = 45073.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068649 restraints weight = 41258.841| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25669 Z= 0.106 Angle : 0.511 12.526 35031 Z= 0.247 Chirality : 0.044 0.445 4126 Planarity : 0.003 0.042 4404 Dihedral : 6.781 92.017 4562 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.41 % Allowed : 9.68 % Favored : 89.91 % 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: 0.31 (0.15), residues: 3039 helix: 2.18 (0.20), residues: 710 sheet: 0.23 (0.20), residues: 619 loop : -0.66 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.014 0.001 TYR B1067 PHE 0.024 0.001 PHE C 375 TRP 0.057 0.001 TRP B 436 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00238 (25571) covalent geometry : angle 0.47689 (34776) SS BOND : bond 0.00216 ( 39) SS BOND : angle 0.52071 ( 78) hydrogen bonds : bond 0.03603 ( 996) hydrogen bonds : angle 4.73966 ( 2775) link_ALPHA1-4 : bond 0.00872 ( 1) link_ALPHA1-4 : angle 2.06153 ( 3) link_BETA1-4 : bond 0.01014 ( 20) link_BETA1-4 : angle 2.99119 ( 60) link_NAG-ASN : bond 0.00405 ( 38) link_NAG-ASN : angle 2.44082 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3509.23 seconds wall clock time: 61 minutes 44.39 seconds (3704.39 seconds total)