Starting phenix.real_space_refine on Sat Jun 21 22:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tl9_25984/06_2025/7tl9_25984_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tl9_25984/06_2025/7tl9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tl9_25984/06_2025/7tl9_25984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tl9_25984/06_2025/7tl9_25984.map" model { file = "/net/cci-nas-00/data/ceres_data/7tl9_25984/06_2025/7tl9_25984_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tl9_25984/06_2025/7tl9_25984_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.44, per 1000 atoms: 0.66 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: 8.48 Conformation dependent library (CDL) restraints added in 4.4 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: 4.09 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: 13.71 Time building geometry restraints manager: 8.84 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 1147 or resid 1201 through 1204)) selection = (chain 'B' and (resid 27 through 620 or resid 640 through 827 or resid 854 throu \ gh 1147 or resid 1201 through 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 1147 or resid 1201 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: 199.580 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: 2.920 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 69.270 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 278.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (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 TRP 0.041 0.002 TRP A 353 HIS 0.007 0.001 HIS A 625 PHE 0.021 0.002 PHE A 906 TYR 0.021 0.002 TYR A1067 ARG 0.006 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 38) link_NAG-ASN : angle 3.63844 ( 114) 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) hydrogen bonds : bond 0.08265 ( 996) hydrogen bonds : angle 6.11773 ( 2775) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.52887 ( 78) covalent geometry : bond 0.00441 (25571) covalent geometry : angle 0.74419 (34776) *********************** 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 : 2.343 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: 0.4733 time to fit residues: 52.5649 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 : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 146 optimal weight: 30.0000 chunk 179 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.098690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068719 restraints weight = 77351.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067733 restraints weight = 58406.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067873 restraints weight = 49277.027| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25669 Z= 0.146 Angle : 0.577 13.866 35031 Z= 0.281 Chirality : 0.046 0.470 4126 Planarity : 0.004 0.057 4404 Dihedral : 9.090 106.299 4562 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.19 % Allowed : 2.93 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3039 helix: 1.16 (0.20), residues: 723 sheet: 0.27 (0.20), residues: 630 loop : -0.84 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 436 HIS 0.005 0.001 HIS B1058 PHE 0.018 0.001 PHE B 906 TYR 0.014 0.001 TYR A1067 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 38) link_NAG-ASN : angle 2.69631 ( 114) link_ALPHA1-4 : bond 0.00638 ( 1) link_ALPHA1-4 : angle 1.93780 ( 3) link_BETA1-4 : bond 0.00946 ( 20) link_BETA1-4 : angle 3.24539 ( 60) hydrogen bonds : bond 0.04095 ( 996) hydrogen bonds : angle 5.14163 ( 2775) SS BOND : bond 0.00289 ( 39) SS BOND : angle 0.80338 ( 78) covalent geometry : bond 0.00336 (25571) covalent geometry : angle 0.54043 (34776) *********************** 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 52 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8654 (ptm) cc_final: 0.8396 (ptm) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.5040 time to fit residues: 46.5880 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 : 2.592 ------------------------------------------------------------------------------- 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 209 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 214 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 258 optimal weight: 0.3980 chunk 243 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 141 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 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 = 0.3942 r_free = 0.3942 target = 0.100763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070337 restraints weight = 74211.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070184 restraints weight = 53214.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.069889 restraints weight = 47381.909| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1018 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 13.346 35031 Z= 0.250 Chirality : 0.044 0.443 4126 Planarity : 0.003 0.050 4404 Dihedral : 7.592 99.186 4562 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.26 % Allowed : 4.52 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3039 helix: 1.81 (0.20), residues: 704 sheet: 0.29 (0.20), residues: 611 loop : -0.70 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 436 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.001 PHE C 375 TYR 0.015 0.001 TYR C 265 ARG 0.003 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 38) link_NAG-ASN : angle 2.54383 ( 114) link_ALPHA1-4 : bond 0.00852 ( 1) link_ALPHA1-4 : angle 2.13219 ( 3) link_BETA1-4 : bond 0.01129 ( 20) link_BETA1-4 : angle 3.14154 ( 60) hydrogen bonds : bond 0.03547 ( 996) hydrogen bonds : angle 4.86689 ( 2775) SS BOND : bond 0.00202 ( 39) SS BOND : angle 0.54879 ( 78) covalent geometry : bond 0.00203 (25571) covalent geometry : angle 0.47711 (34776) *********************** 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 52 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 2.516 Fit side-chains revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8703 (mm) cc_final: 0.8406 (pt) REVERT: A 697 MET cc_start: 0.8650 (ptm) cc_final: 0.8325 (ptm) REVERT: A 900 MET cc_start: 0.8580 (mtp) cc_final: 0.8307 (mtm) REVERT: B 436 TRP cc_start: 0.6199 (t60) cc_final: 0.5993 (p-90) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.3205 time to fit residues: 28.9131 Evaluate side-chains 44 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 7.9990 chunk 288 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 145 optimal weight: 40.0000 chunk 15 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 644 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.098553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068535 restraints weight = 77388.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068119 restraints weight = 56400.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067966 restraints weight = 48828.572| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25669 Z= 0.125 Angle : 0.525 13.149 35031 Z= 0.255 Chirality : 0.045 0.451 4126 Planarity : 0.003 0.045 4404 Dihedral : 7.261 96.003 4562 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.52 % Allowed : 5.82 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3039 helix: 1.86 (0.20), residues: 717 sheet: 0.29 (0.20), residues: 601 loop : -0.66 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 436 HIS 0.005 0.001 HIS B1058 PHE 0.018 0.001 PHE C 400 TYR 0.013 0.001 TYR B1067 ARG 0.005 0.000 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 38) link_NAG-ASN : angle 2.54334 ( 114) link_ALPHA1-4 : bond 0.00911 ( 1) link_ALPHA1-4 : angle 2.08711 ( 3) link_BETA1-4 : bond 0.01032 ( 20) link_BETA1-4 : angle 3.11887 ( 60) hydrogen bonds : bond 0.03745 ( 996) hydrogen bonds : angle 4.81250 ( 2775) SS BOND : bond 0.00227 ( 39) SS BOND : angle 0.55032 ( 78) covalent geometry : bond 0.00286 (25571) covalent geometry : angle 0.48809 (34776) *********************** 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 56 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8634 (ptm) cc_final: 0.8354 (ptm) REVERT: A 900 MET cc_start: 0.8718 (mtp) cc_final: 0.8424 (mtm) outliers start: 14 outliers final: 7 residues processed: 54 average time/residue: 0.3334 time to fit residues: 33.4162 Evaluate side-chains 46 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 69 optimal weight: 0.2980 chunk 9 optimal weight: 0.0770 chunk 183 optimal weight: 0.6980 chunk 140 optimal weight: 20.0000 chunk 146 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.8142 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.099168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069871 restraints weight = 77701.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069142 restraints weight = 58961.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069276 restraints weight = 46879.341| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25669 Z= 0.090 Angle : 0.495 13.050 35031 Z= 0.240 Chirality : 0.044 0.426 4126 Planarity : 0.003 0.045 4404 Dihedral : 6.980 93.949 4562 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.33 % Allowed : 6.67 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3039 helix: 2.17 (0.20), residues: 707 sheet: 0.36 (0.21), residues: 591 loop : -0.57 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.002 0.000 HIS A1088 PHE 0.028 0.001 PHE C 375 TYR 0.014 0.001 TYR C 265 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 38) link_NAG-ASN : angle 2.44540 ( 114) link_ALPHA1-4 : bond 0.00850 ( 1) link_ALPHA1-4 : angle 2.03131 ( 3) link_BETA1-4 : bond 0.01053 ( 20) link_BETA1-4 : angle 2.98115 ( 60) hydrogen bonds : bond 0.03322 ( 996) hydrogen bonds : angle 4.65876 ( 2775) SS BOND : bond 0.00175 ( 39) SS BOND : angle 0.46477 ( 78) covalent geometry : bond 0.00192 (25571) covalent geometry : angle 0.45983 (34776) *********************** 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 53 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.5406 (t80) cc_final: 0.4984 (t80) REVERT: A 697 MET cc_start: 0.8597 (ptm) cc_final: 0.8308 (ptm) REVERT: A 900 MET cc_start: 0.8656 (mtp) cc_final: 0.8345 (mtm) REVERT: C 902 MET cc_start: 0.8717 (tpp) cc_final: 0.8472 (mmt) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.3292 time to fit residues: 31.0857 Evaluate side-chains 46 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain C residue 375 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 46 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 84 optimal weight: 0.0570 chunk 106 optimal weight: 8.9990 chunk 256 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 245 optimal weight: 20.0000 chunk 131 optimal weight: 30.0000 chunk 164 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 overall best weight: 1.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.098205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068455 restraints weight = 76750.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067815 restraints weight = 55474.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067757 restraints weight = 48877.232| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1457 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 : 0.520 12.892 35031 Z= 0.252 Chirality : 0.045 0.448 4126 Planarity : 0.003 0.044 4404 Dihedral : 6.917 94.520 4562 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.33 % Allowed : 7.16 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3039 helix: 2.07 (0.20), residues: 718 sheet: 0.43 (0.20), residues: 617 loop : -0.61 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 436 HIS 0.005 0.001 HIS B1058 PHE 0.027 0.001 PHE C 375 TYR 0.014 0.001 TYR B1067 ARG 0.002 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 38) link_NAG-ASN : angle 2.48642 ( 114) link_ALPHA1-4 : bond 0.00914 ( 1) link_ALPHA1-4 : angle 2.10822 ( 3) link_BETA1-4 : bond 0.01011 ( 20) link_BETA1-4 : angle 3.01720 ( 60) hydrogen bonds : bond 0.03721 ( 996) hydrogen bonds : angle 4.72794 ( 2775) SS BOND : bond 0.00225 ( 39) SS BOND : angle 0.53377 ( 78) covalent geometry : bond 0.00300 (25571) covalent geometry : angle 0.48509 (34776) *********************** 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 50 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.5452 (t80) cc_final: 0.5143 (t80) REVERT: A 449 TYR cc_start: 0.6752 (m-80) cc_final: 0.6222 (m-80) REVERT: A 697 MET cc_start: 0.8647 (ptm) cc_final: 0.8369 (ptm) REVERT: A 900 MET cc_start: 0.8759 (mtp) cc_final: 0.8480 (mtm) REVERT: B 436 TRP cc_start: 0.6318 (t60) cc_final: 0.6095 (p-90) outliers start: 9 outliers final: 8 residues processed: 49 average time/residue: 0.3357 time to fit residues: 30.4847 Evaluate side-chains 47 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL 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 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 6 optimal weight: 5.9990 chunk 130 optimal weight: 50.0000 chunk 52 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 275 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 762 GLN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.097513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067055 restraints weight = 76500.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066618 restraints weight = 62053.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066735 restraints weight = 47842.767| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25669 Z= 0.211 Angle : 0.590 12.724 35031 Z= 0.289 Chirality : 0.046 0.486 4126 Planarity : 0.004 0.043 4404 Dihedral : 7.134 98.302 4562 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.59 % Allowed : 7.49 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3039 helix: 1.83 (0.20), residues: 716 sheet: 0.22 (0.20), residues: 621 loop : -0.68 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 436 HIS 0.008 0.001 HIS B1058 PHE 0.025 0.001 PHE C 375 TYR 0.015 0.001 TYR B1067 ARG 0.002 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 38) link_NAG-ASN : angle 2.59017 ( 114) link_ALPHA1-4 : bond 0.00966 ( 1) link_ALPHA1-4 : angle 2.22893 ( 3) link_BETA1-4 : bond 0.01020 ( 20) link_BETA1-4 : angle 3.13421 ( 60) hydrogen bonds : bond 0.04547 ( 996) hydrogen bonds : angle 5.00759 ( 2775) SS BOND : bond 0.00336 ( 39) SS BOND : angle 0.70159 ( 78) covalent geometry : bond 0.00494 (25571) covalent geometry : angle 0.55677 (34776) *********************** 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 61 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.6547 (m-80) cc_final: 0.6062 (m-80) REVERT: A 697 MET cc_start: 0.8682 (ptm) cc_final: 0.8430 (ptm) REVERT: A 878 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8783 (tt) REVERT: B 371 LEU cc_start: 0.3244 (OUTLIER) cc_final: 0.2900 (tp) REVERT: B 1142 GLN cc_start: 0.8156 (tp40) cc_final: 0.7831 (tp-100) REVERT: C 902 MET cc_start: 0.8933 (tpp) cc_final: 0.8693 (mmt) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.3248 time to fit residues: 35.4604 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 : 2.893 ------------------------------------------------------------------------------- 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 371 LEU Chi-restraints excluded: chain B residue 987 VAL 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 194 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 44 optimal weight: 0.0670 chunk 298 optimal weight: 0.1980 chunk 297 optimal weight: 4.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.098413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068523 restraints weight = 76480.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067964 restraints weight = 59348.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067862 restraints weight = 50871.981| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1677 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= 0.094 Angle : 0.508 12.963 35031 Z= 0.247 Chirality : 0.044 0.430 4126 Planarity : 0.003 0.042 4404 Dihedral : 6.852 93.095 4562 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.44 % Allowed : 7.90 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3039 helix: 2.24 (0.20), residues: 699 sheet: 0.27 (0.20), residues: 616 loop : -0.58 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.003 0.000 HIS A1088 PHE 0.025 0.001 PHE C 375 TYR 0.014 0.001 TYR A1067 ARG 0.002 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 38) link_NAG-ASN : angle 2.43451 ( 114) link_ALPHA1-4 : bond 0.00826 ( 1) link_ALPHA1-4 : angle 2.01209 ( 3) link_BETA1-4 : bond 0.01050 ( 20) link_BETA1-4 : angle 2.96150 ( 60) hydrogen bonds : bond 0.03557 ( 996) hydrogen bonds : angle 4.72383 ( 2775) SS BOND : bond 0.00213 ( 39) SS BOND : angle 0.49962 ( 78) covalent geometry : bond 0.00199 (25571) covalent geometry : angle 0.47387 (34776) *********************** 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 : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.6920 (m-80) cc_final: 0.6422 (m-80) REVERT: A 624 ILE cc_start: 0.8801 (mm) cc_final: 0.8270 (tt) REVERT: A 697 MET cc_start: 0.8634 (ptm) cc_final: 0.8359 (ptm) REVERT: B 371 LEU cc_start: 0.3338 (OUTLIER) cc_final: 0.2911 (tp) REVERT: C 902 MET cc_start: 0.8801 (tpp) cc_final: 0.8586 (tpt) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.3529 time to fit residues: 34.3382 Evaluate side-chains 50 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 987 VAL 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 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 118 optimal weight: 7.9990 chunk 187 optimal weight: 0.0370 chunk 169 optimal weight: 4.9990 chunk 285 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.098036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067752 restraints weight = 77427.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067494 restraints weight = 59366.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067386 restraints weight = 50140.261| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25669 Z= 0.118 Angle : 0.512 12.781 35031 Z= 0.248 Chirality : 0.044 0.442 4126 Planarity : 0.003 0.041 4404 Dihedral : 6.778 92.565 4562 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.41 % Allowed : 8.05 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3039 helix: 2.21 (0.20), residues: 705 sheet: 0.34 (0.20), residues: 609 loop : -0.59 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS B1058 PHE 0.024 0.001 PHE C 375 TYR 0.024 0.001 TYR A 423 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 38) link_NAG-ASN : angle 2.45646 ( 114) link_ALPHA1-4 : bond 0.00881 ( 1) link_ALPHA1-4 : angle 2.07492 ( 3) link_BETA1-4 : bond 0.01010 ( 20) link_BETA1-4 : angle 2.98073 ( 60) hydrogen bonds : bond 0.03652 ( 996) hydrogen bonds : angle 4.71184 ( 2775) SS BOND : bond 0.00217 ( 39) SS BOND : angle 0.51587 ( 78) covalent geometry : bond 0.00269 (25571) covalent geometry : angle 0.47759 (34776) *********************** 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 54 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 5.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.6891 (m-80) cc_final: 0.6396 (m-80) REVERT: A 624 ILE cc_start: 0.8832 (mm) cc_final: 0.8301 (tt) REVERT: A 697 MET cc_start: 0.8619 (ptm) cc_final: 0.8353 (ptm) REVERT: B 371 LEU cc_start: 0.3198 (OUTLIER) cc_final: 0.2855 (tp) REVERT: B 902 MET cc_start: 0.9054 (mmm) cc_final: 0.8843 (mmt) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.5530 time to fit residues: 54.7794 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 : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 987 VAL 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 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 249 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 271 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.098095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067779 restraints weight = 76622.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067495 restraints weight = 59183.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067381 restraints weight = 50658.036| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25669 Z= 0.132 Angle : 0.521 12.681 35031 Z= 0.253 Chirality : 0.045 0.445 4126 Planarity : 0.003 0.042 4404 Dihedral : 6.755 92.130 4562 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.56 % Allowed : 7.90 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3039 helix: 2.19 (0.20), residues: 705 sheet: 0.32 (0.20), residues: 609 loop : -0.59 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 436 HIS 0.004 0.001 HIS B1058 PHE 0.024 0.001 PHE C 375 TYR 0.018 0.001 TYR A 423 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 38) link_NAG-ASN : angle 2.46552 ( 114) link_ALPHA1-4 : bond 0.00914 ( 1) link_ALPHA1-4 : angle 2.07986 ( 3) link_BETA1-4 : bond 0.01020 ( 20) link_BETA1-4 : angle 3.00272 ( 60) hydrogen bonds : bond 0.03783 ( 996) hydrogen bonds : angle 4.73541 ( 2775) SS BOND : bond 0.00233 ( 39) SS BOND : angle 0.54337 ( 78) covalent geometry : bond 0.00304 (25571) covalent geometry : angle 0.48688 (34776) ********************** 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 59 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 4.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.6896 (m-80) cc_final: 0.6420 (m-80) REVERT: A 624 ILE cc_start: 0.8848 (mm) cc_final: 0.8315 (tt) REVERT: A 697 MET cc_start: 0.8630 (ptm) cc_final: 0.8349 (ptm) REVERT: A 878 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8783 (tt) REVERT: B 371 LEU cc_start: 0.3029 (OUTLIER) cc_final: 0.2607 (tp) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.4545 time to fit residues: 49.5820 Evaluate side-chains 55 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 3.502 ------------------------------------------------------------------------------- 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 1094 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 987 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 48 optimal weight: 0.0000 chunk 267 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 246 optimal weight: 7.9990 chunk 233 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 0.0010 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.098049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067691 restraints weight = 76255.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.067310 restraints weight = 60824.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067227 restraints weight = 51194.616| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25669 Z= 0.135 Angle : 0.524 12.725 35031 Z= 0.254 Chirality : 0.045 0.443 4126 Planarity : 0.003 0.041 4404 Dihedral : 6.752 91.675 4562 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.52 % Allowed : 8.16 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3039 helix: 2.16 (0.20), residues: 710 sheet: 0.30 (0.20), residues: 610 loop : -0.61 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 436 HIS 0.004 0.001 HIS B1058 PHE 0.024 0.001 PHE C 375 TYR 0.014 0.001 TYR B1067 ARG 0.002 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 38) link_NAG-ASN : angle 2.48007 ( 114) link_ALPHA1-4 : bond 0.00913 ( 1) link_ALPHA1-4 : angle 2.07990 ( 3) link_BETA1-4 : bond 0.01016 ( 20) link_BETA1-4 : angle 3.00599 ( 60) hydrogen bonds : bond 0.03790 ( 996) hydrogen bonds : angle 4.74033 ( 2775) SS BOND : bond 0.00235 ( 39) SS BOND : angle 0.54259 ( 78) covalent geometry : bond 0.00312 (25571) covalent geometry : angle 0.48952 (34776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7528.26 seconds wall clock time: 138 minutes 16.90 seconds (8296.90 seconds total)