Starting phenix.real_space_refine on Sat Jul 4 21:59:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.map" model { file = "/net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdg_22821/07_2026/7kdg_22821.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 15090 2.51 5 N 3852 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23700 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "B" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 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 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 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 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.02, per 1000 atoms: 0.25 Number of scatterers: 23700 At special positions: 0 Unit cell: (136.32, 127.8, 171.465, 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 99 16.00 O 4659 8.00 N 3852 7.00 C 15090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 928.2 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 27.2% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.953A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.177A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.559A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.171A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.854A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.640A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.529A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.152A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.305A 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 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.074A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.544A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.072A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.859A 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 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.634A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.501A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.546A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.229A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.941A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.604A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.211A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.055A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.823A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.618A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.523A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.109A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.169A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.675A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.675A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.662A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.588A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.293A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.293A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.886A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.577A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.691A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.623A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.208A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.441A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.238A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.754A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.176A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.689A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.525A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.627A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.604A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.585A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.694A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.463A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.754A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.126A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.624A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.596A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.323A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.016A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.810A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.604A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.514A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.185A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.468A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.755A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 2892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.10 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6182 1.33 - 1.46: 4733 1.46 - 1.58: 13160 1.58 - 1.71: 0 1.71 - 1.83: 123 Bond restraints: 24198 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 29034 2.76 - 5.52: 3780 5.52 - 8.28: 83 8.28 - 11.04: 4 11.04 - 13.80: 3 Bond angle restraints: 32904 Sorted by residual: angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.07 119.91 -10.84 1.52e+00 4.33e-01 5.09e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 109.07 119.48 -10.41 1.52e+00 4.33e-01 4.69e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 109.07 119.39 -10.32 1.52e+00 4.33e-01 4.61e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.00e+00 1.00e+00 3.64e+01 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 118.62 -6.02 1.00e+00 1.00e+00 3.63e+01 ... (remaining 32899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 12975 18.03 - 36.06: 758 36.06 - 54.09: 105 54.09 - 72.12: 32 72.12 - 90.15: 32 Dihedral angle restraints: 13902 sinusoidal: 5412 harmonic: 8490 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 -162.66 76.66 1 1.00e+01 1.00e-02 7.38e+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 -162.12 76.12 1 1.00e+01 1.00e-02 7.30e+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 -162.06 76.06 1 1.00e+01 1.00e-02 7.29e+01 ... (remaining 13899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2802 0.105 - 0.210: 1023 0.210 - 0.316: 109 0.316 - 0.421: 14 0.421 - 0.526: 3 Chirality restraints: 3951 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.92e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.55e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.34e+01 ... (remaining 3948 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.161 2.00e-02 2.50e+03 1.71e-01 3.67e+02 pdb=" CG ASN C 331 " -0.110 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.261 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.155 2.00e-02 2.50e+03 1.68e-01 3.52e+02 pdb=" CG ASN A 657 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.262 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.147 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" CG ASN C 657 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.245 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.190 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11492 2.99 - 3.47: 22373 3.47 - 3.95: 39655 3.95 - 4.42: 43974 4.42 - 4.90: 74954 Nonbonded interactions: 192448 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.515 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.515 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.517 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.529 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.553 3.040 ... (remaining 192443 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 24.440 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.014 0.076 24297 Z= 0.786 Angle : 1.790 13.796 33165 Z= 1.183 Chirality : 0.098 0.526 3951 Planarity : 0.013 0.176 4158 Dihedral : 12.773 90.155 8310 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.22 % Favored : 93.46 % Rotamer: Outliers : 0.31 % Allowed : 1.06 % Favored : 98.63 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 2844 helix: -0.39 (0.18), residues: 627 sheet: 0.22 (0.20), residues: 552 loop : -0.98 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1019 TYR 0.142 0.020 TYR A 269 PHE 0.104 0.012 PHE B 718 TRP 0.090 0.022 TRP B 64 HIS 0.009 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.01383 / 0.79 (24198) covalent geometry : angle 1.75833 / 1.18 (32904) SS BOND : bond 0.01278 / 0.81 ( 36) SS BOND : angle 2.54501 / 1.77 ( 72) hydrogen bonds : bond 0.14984 / 9.41 ( 1035) hydrogen bonds : angle 8.25076 / 5.78 ( 2892) link_BETA1-4 : bond 0.02604 / 1.49 ( 15) link_BETA1-4 : angle 4.84308 / 3.21 ( 45) link_NAG-ASN : bond 0.01136 / 0.73 ( 48) link_NAG-ASN : angle 4.57825 / 3.13 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 376 time to evaluate : 0.907 Fit side-chains REVERT: A 421 TYR cc_start: 0.7435 (m-80) cc_final: 0.6644 (m-80) REVERT: A 643 PHE cc_start: 0.7983 (t80) cc_final: 0.7716 (t80) REVERT: B 421 TYR cc_start: 0.7030 (m-80) cc_final: 0.5822 (m-80) REVERT: B 508 TYR cc_start: 0.7754 (m-80) cc_final: 0.7359 (m-80) REVERT: B 731 MET cc_start: 0.9143 (ptt) cc_final: 0.8842 (ptt) REVERT: B 855 PHE cc_start: 0.7609 (m-80) cc_final: 0.7334 (m-80) outliers start: 8 outliers final: 1 residues processed: 383 average time/residue: 0.1752 time to fit residues: 103.7935 Evaluate side-chains 200 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1004 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 314 GLN A 955 ASN C 196 ASN C 207 HIS C 314 GLN C 422 ASN C 804 GLN C1113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.169099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111482 restraints weight = 30261.491| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.52 r_work: 0.3247 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24297 Z= 0.150 Angle : 0.714 13.520 33165 Z= 0.356 Chirality : 0.047 0.208 3951 Planarity : 0.004 0.044 4158 Dihedral : 5.959 57.350 3101 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.29 % Allowed : 5.36 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 2844 helix: 1.34 (0.20), residues: 678 sheet: 0.21 (0.18), residues: 678 loop : -0.73 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 408 TYR 0.020 0.002 TYR B 170 PHE 0.025 0.002 PHE B 400 TRP 0.020 0.002 TRP B 64 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (24198) covalent geometry : angle 0.67426 / 0.35 (32904) SS BOND : bond 0.00524 / 0.35 ( 36) SS BOND : angle 1.69118 / 1.07 ( 72) hydrogen bonds : bond 0.04459 / 2.90 ( 1035) hydrogen bonds : angle 6.21102 / 4.36 ( 2892) link_BETA1-4 : bond 0.00395 / 0.24 ( 15) link_BETA1-4 : angle 1.73524 / 1.15 ( 45) link_NAG-ASN : bond 0.00369 / 0.22 ( 48) link_NAG-ASN : angle 3.32176 / 2.19 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7128 (t80) cc_final: 0.6674 (t80) REVERT: A 428 ASP cc_start: 0.8060 (p0) cc_final: 0.7857 (t0) REVERT: A 508 TYR cc_start: 0.8476 (m-80) cc_final: 0.8148 (m-80) REVERT: A 592 PHE cc_start: 0.7768 (p90) cc_final: 0.7527 (p90) REVERT: A 745 ASP cc_start: 0.8323 (p0) cc_final: 0.8047 (p0) REVERT: A 776 LYS cc_start: 0.8440 (tttt) cc_final: 0.8094 (ttpp) REVERT: A 814 LYS cc_start: 0.8298 (mttt) cc_final: 0.7914 (mttp) REVERT: B 97 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6532 (mttp) REVERT: B 205 SER cc_start: 0.8543 (p) cc_final: 0.7889 (t) REVERT: B 309 GLU cc_start: 0.8021 (tp30) cc_final: 0.7672 (tp30) REVERT: B 421 TYR cc_start: 0.6685 (m-80) cc_final: 0.6242 (m-10) REVERT: B 452 LEU cc_start: 0.7208 (mm) cc_final: 0.6921 (mm) REVERT: B 776 LYS cc_start: 0.8424 (tttt) cc_final: 0.7999 (ttpp) REVERT: B 855 PHE cc_start: 0.7867 (m-80) cc_final: 0.7615 (m-80) REVERT: B 964 LYS cc_start: 0.8562 (mttt) cc_final: 0.8154 (mtpt) REVERT: C 205 SER cc_start: 0.8427 (p) cc_final: 0.7984 (t) REVERT: C 314 GLN cc_start: 0.8768 (tt0) cc_final: 0.8100 (tp-100) REVERT: C 403 ARG cc_start: 0.6597 (ttt180) cc_final: 0.6060 (ttt90) REVERT: C 510 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.7208 (m) REVERT: C 592 PHE cc_start: 0.8046 (p90) cc_final: 0.7694 (p90) REVERT: C 643 PHE cc_start: 0.8264 (t80) cc_final: 0.8061 (t80) REVERT: C 902 MET cc_start: 0.8590 (tpt) cc_final: 0.8294 (mmm) REVERT: C 964 LYS cc_start: 0.8658 (mttt) cc_final: 0.8268 (mtpt) outliers start: 33 outliers final: 14 residues processed: 242 average time/residue: 0.1605 time to fit residues: 61.7611 Evaluate side-chains 196 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 178 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 244 optimal weight: 0.1980 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 24 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 935 GLN C 804 GLN C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.169707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112357 restraints weight = 30329.611| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.51 r_work: 0.3275 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24297 Z= 0.118 Angle : 0.594 20.222 33165 Z= 0.300 Chirality : 0.045 0.488 3951 Planarity : 0.004 0.043 4158 Dihedral : 5.169 54.067 3101 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.45 % Allowed : 6.69 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2844 helix: 2.03 (0.20), residues: 663 sheet: 0.32 (0.18), residues: 645 loop : -0.58 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.024 0.001 TYR C 508 PHE 0.020 0.001 PHE B 400 TRP 0.012 0.001 TRP B 64 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (24198) covalent geometry : angle 0.55603 / 0.29 (32904) SS BOND : bond 0.00349 / 0.23 ( 36) SS BOND : angle 1.54683 / 0.99 ( 72) hydrogen bonds : bond 0.03838 / 2.48 ( 1035) hydrogen bonds : angle 5.64359 / 3.96 ( 2892) link_BETA1-4 : bond 0.00416 / 0.23 ( 15) link_BETA1-4 : angle 1.35578 / 0.92 ( 45) link_NAG-ASN : bond 0.00326 / 0.21 ( 48) link_NAG-ASN : angle 2.98818 / 2.35 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8389 (p) cc_final: 0.8054 (t) REVERT: A 574 ASP cc_start: 0.7204 (t0) cc_final: 0.6852 (t0) REVERT: A 592 PHE cc_start: 0.7817 (p90) cc_final: 0.7499 (p90) REVERT: A 776 LYS cc_start: 0.8492 (tttt) cc_final: 0.8113 (ttpp) REVERT: A 814 LYS cc_start: 0.8248 (mttt) cc_final: 0.7782 (mtpp) REVERT: B 97 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6560 (mttp) REVERT: B 198 ASP cc_start: 0.7548 (m-30) cc_final: 0.7310 (p0) REVERT: B 205 SER cc_start: 0.8678 (p) cc_final: 0.8146 (t) REVERT: B 237 ARG cc_start: 0.6314 (ttp-110) cc_final: 0.6049 (ttp-110) REVERT: B 309 GLU cc_start: 0.8027 (tp30) cc_final: 0.7683 (tp30) REVERT: B 334 ASN cc_start: 0.7526 (m110) cc_final: 0.7169 (m110) REVERT: B 776 LYS cc_start: 0.8471 (tttt) cc_final: 0.8178 (ttpp) REVERT: B 855 PHE cc_start: 0.7943 (m-80) cc_final: 0.7715 (m-80) REVERT: B 964 LYS cc_start: 0.8568 (mttt) cc_final: 0.8159 (mtpt) REVERT: C 33 THR cc_start: 0.6905 (p) cc_final: 0.6703 (p) REVERT: C 205 SER cc_start: 0.8566 (p) cc_final: 0.8149 (t) REVERT: C 403 ARG cc_start: 0.6664 (ttt180) cc_final: 0.6228 (ttt90) REVERT: C 452 LEU cc_start: 0.7886 (mt) cc_final: 0.7536 (mm) REVERT: C 592 PHE cc_start: 0.8118 (p90) cc_final: 0.7779 (p90) REVERT: C 900 MET cc_start: 0.8279 (mtp) cc_final: 0.8026 (mtp) REVERT: C 964 LYS cc_start: 0.8618 (mttt) cc_final: 0.8261 (mtpt) outliers start: 37 outliers final: 18 residues processed: 233 average time/residue: 0.1509 time to fit residues: 56.5735 Evaluate side-chains 203 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 285 optimal weight: 0.5980 chunk 132 optimal weight: 40.0000 chunk 91 optimal weight: 0.2980 chunk 35 optimal weight: 30.0000 chunk 101 optimal weight: 0.0000 chunk 220 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 872 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.169244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111783 restraints weight = 30318.094| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.49 r_work: 0.3267 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 24297 Z= 0.120 Angle : 0.549 8.774 33165 Z= 0.280 Chirality : 0.044 0.204 3951 Planarity : 0.004 0.042 4158 Dihedral : 4.874 53.475 3101 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.49 % Allowed : 7.67 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2844 helix: 2.06 (0.20), residues: 666 sheet: 0.36 (0.18), residues: 645 loop : -0.57 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.022 0.001 TYR A 170 PHE 0.017 0.001 PHE B 400 TRP 0.014 0.001 TRP C 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24198) covalent geometry : angle 0.52412 / 0.27 (32904) SS BOND : bond 0.00399 / 0.26 ( 36) SS BOND : angle 1.51310 / 0.95 ( 72) hydrogen bonds : bond 0.03586 / 2.32 ( 1035) hydrogen bonds : angle 5.47086 / 3.82 ( 2892) link_BETA1-4 : bond 0.00336 / 0.18 ( 15) link_BETA1-4 : angle 1.26438 / 0.87 ( 45) link_NAG-ASN : bond 0.00278 / 0.18 ( 48) link_NAG-ASN : angle 2.25108 / 1.47 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8532 (p) cc_final: 0.8129 (t) REVERT: A 574 ASP cc_start: 0.7162 (t0) cc_final: 0.6890 (t0) REVERT: A 592 PHE cc_start: 0.7833 (p90) cc_final: 0.7481 (p90) REVERT: A 776 LYS cc_start: 0.8530 (tttt) cc_final: 0.8102 (ttpp) REVERT: A 804 GLN cc_start: 0.8632 (mm110) cc_final: 0.8267 (mm-40) REVERT: A 814 LYS cc_start: 0.8256 (mttt) cc_final: 0.7788 (mtpp) REVERT: B 97 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6559 (mttm) REVERT: B 205 SER cc_start: 0.8673 (p) cc_final: 0.8398 (t) REVERT: B 309 GLU cc_start: 0.8013 (tp30) cc_final: 0.7659 (tp30) REVERT: B 554 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8118 (mp0) REVERT: B 776 LYS cc_start: 0.8498 (tttt) cc_final: 0.8226 (ttpp) REVERT: B 964 LYS cc_start: 0.8630 (mttt) cc_final: 0.8265 (mtpt) REVERT: B 1144 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 192 PHE cc_start: 0.7772 (m-80) cc_final: 0.7468 (m-10) REVERT: C 205 SER cc_start: 0.8512 (p) cc_final: 0.8140 (t) REVERT: C 403 ARG cc_start: 0.6598 (ttt180) cc_final: 0.6268 (ttt90) REVERT: C 452 LEU cc_start: 0.7884 (mt) cc_final: 0.7598 (mm) REVERT: C 592 PHE cc_start: 0.8031 (p90) cc_final: 0.7657 (p90) REVERT: C 661 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: C 964 LYS cc_start: 0.8687 (mttt) cc_final: 0.8310 (mtpt) outliers start: 38 outliers final: 21 residues processed: 241 average time/residue: 0.1473 time to fit residues: 56.9093 Evaluate side-chains 207 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 117 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 506 GLN A 675 GLN B 804 GLN C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109558 restraints weight = 30225.350| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.48 r_work: 0.3244 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24297 Z= 0.162 Angle : 0.584 18.077 33165 Z= 0.292 Chirality : 0.048 1.167 3951 Planarity : 0.004 0.040 4158 Dihedral : 4.871 54.136 3101 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.60 % Allowed : 8.18 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 2844 helix: 1.97 (0.20), residues: 666 sheet: 0.37 (0.18), residues: 660 loop : -0.64 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.017 0.002 PHE B1121 TRP 0.011 0.002 TRP C 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (24198) covalent geometry : angle 0.54685 / 0.28 (32904) SS BOND : bond 0.00366 / 0.22 ( 36) SS BOND : angle 1.62970 / 1.02 ( 72) hydrogen bonds : bond 0.03765 / 2.43 ( 1035) hydrogen bonds : angle 5.47785 / 3.83 ( 2892) link_BETA1-4 : bond 0.00371 / 0.20 ( 15) link_BETA1-4 : angle 1.31437 / 0.90 ( 45) link_NAG-ASN : bond 0.00593 / 0.42 ( 48) link_NAG-ASN : angle 2.90299 / 1.75 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 506 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: A 574 ASP cc_start: 0.7168 (t0) cc_final: 0.6844 (t0) REVERT: A 578 ASP cc_start: 0.7975 (t0) cc_final: 0.7661 (t0) REVERT: A 776 LYS cc_start: 0.8468 (tttt) cc_final: 0.8209 (tttm) REVERT: A 814 LYS cc_start: 0.8230 (mttt) cc_final: 0.7808 (mtpp) REVERT: B 97 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6604 (mttm) REVERT: B 190 ARG cc_start: 0.5877 (ttm170) cc_final: 0.5358 (tpp-160) REVERT: B 205 SER cc_start: 0.8653 (p) cc_final: 0.8346 (m) REVERT: B 309 GLU cc_start: 0.7997 (tp30) cc_final: 0.7638 (tp30) REVERT: B 554 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8222 (mp0) REVERT: B 574 ASP cc_start: 0.7212 (t0) cc_final: 0.6955 (t0) REVERT: B 776 LYS cc_start: 0.8523 (tttt) cc_final: 0.8249 (ttpp) REVERT: B 964 LYS cc_start: 0.8637 (mttt) cc_final: 0.8288 (mtpt) REVERT: B 1144 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: C 205 SER cc_start: 0.8514 (p) cc_final: 0.8204 (t) REVERT: C 403 ARG cc_start: 0.6625 (ttt180) cc_final: 0.6306 (ttt90) REVERT: C 452 LEU cc_start: 0.7952 (mt) cc_final: 0.7652 (mm) REVERT: C 506 GLN cc_start: 0.8095 (mt0) cc_final: 0.7644 (mp10) REVERT: C 592 PHE cc_start: 0.8040 (p90) cc_final: 0.7685 (p90) REVERT: C 661 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: C 964 LYS cc_start: 0.8701 (mttt) cc_final: 0.8315 (mtpt) outliers start: 41 outliers final: 23 residues processed: 224 average time/residue: 0.1462 time to fit residues: 52.4466 Evaluate side-chains 207 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 208 optimal weight: 10.0000 chunk 193 optimal weight: 0.0370 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 675 GLN C 675 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.166139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106228 restraints weight = 30634.090| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.43 r_work: 0.3223 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 24297 Z= 0.248 Angle : 0.628 13.494 33165 Z= 0.317 Chirality : 0.047 0.543 3951 Planarity : 0.004 0.040 4158 Dihedral : 5.034 55.404 3101 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.56 % Allowed : 8.84 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 2844 helix: 1.69 (0.20), residues: 666 sheet: 0.25 (0.18), residues: 657 loop : -0.79 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 237 TYR 0.022 0.002 TYR A 265 PHE 0.026 0.002 PHE B1121 TRP 0.016 0.002 TRP C 353 HIS 0.007 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (24198) covalent geometry : angle 0.59848 / 0.31 (32904) SS BOND : bond 0.00415 / 0.22 ( 36) SS BOND : angle 1.79887 / 1.14 ( 72) hydrogen bonds : bond 0.04188 / 2.70 ( 1035) hydrogen bonds : angle 5.67988 / 3.97 ( 2892) link_BETA1-4 : bond 0.00256 / 0.13 ( 15) link_BETA1-4 : angle 1.48875 / 1.01 ( 45) link_NAG-ASN : bond 0.00419 / 0.28 ( 48) link_NAG-ASN : angle 2.57303 / 1.62 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7177 (t0) cc_final: 0.6849 (t0) REVERT: A 578 ASP cc_start: 0.8015 (t0) cc_final: 0.7682 (t0) REVERT: A 776 LYS cc_start: 0.8539 (tttt) cc_final: 0.8253 (tttm) REVERT: A 814 LYS cc_start: 0.8223 (mttt) cc_final: 0.7840 (mtpp) REVERT: A 1144 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 190 ARG cc_start: 0.5756 (ttm170) cc_final: 0.5035 (tpp-160) REVERT: B 205 SER cc_start: 0.8664 (p) cc_final: 0.8431 (m) REVERT: B 207 HIS cc_start: 0.5877 (t70) cc_final: 0.5670 (t70) REVERT: B 309 GLU cc_start: 0.7953 (tp30) cc_final: 0.7591 (tp30) REVERT: B 403 ARG cc_start: 0.5887 (ttm-80) cc_final: 0.5518 (ttt90) REVERT: B 554 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8241 (mp0) REVERT: B 565 PHE cc_start: 0.7540 (m-80) cc_final: 0.7279 (m-80) REVERT: B 574 ASP cc_start: 0.7254 (t0) cc_final: 0.6945 (t0) REVERT: B 776 LYS cc_start: 0.8571 (tttt) cc_final: 0.8306 (ttpp) REVERT: B 964 LYS cc_start: 0.8675 (mttt) cc_final: 0.8328 (mtpt) REVERT: B 1144 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 192 PHE cc_start: 0.7896 (m-80) cc_final: 0.7626 (m-10) REVERT: C 205 SER cc_start: 0.8528 (p) cc_final: 0.8202 (t) REVERT: C 403 ARG cc_start: 0.6709 (ttt180) cc_final: 0.6371 (ttt90) REVERT: C 452 LEU cc_start: 0.7967 (mt) cc_final: 0.7657 (mm) REVERT: C 506 GLN cc_start: 0.8136 (mt0) cc_final: 0.7667 (mp10) REVERT: C 574 ASP cc_start: 0.7175 (t0) cc_final: 0.6748 (t0) REVERT: C 592 PHE cc_start: 0.8065 (p90) cc_final: 0.7721 (p90) REVERT: C 643 PHE cc_start: 0.8276 (t80) cc_final: 0.7816 (t80) REVERT: C 776 LYS cc_start: 0.8543 (tttt) cc_final: 0.8216 (ttpp) REVERT: C 804 GLN cc_start: 0.8309 (mt0) cc_final: 0.8060 (mt0) REVERT: C 964 LYS cc_start: 0.8734 (mttt) cc_final: 0.8339 (mtpt) outliers start: 40 outliers final: 30 residues processed: 223 average time/residue: 0.1630 time to fit residues: 58.3936 Evaluate side-chains 216 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 147 optimal weight: 0.0060 chunk 172 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.167238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109768 restraints weight = 30259.283| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.48 r_work: 0.3268 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 24297 Z= 0.110 Angle : 0.528 11.723 33165 Z= 0.266 Chirality : 0.044 0.458 3951 Planarity : 0.004 0.040 4158 Dihedral : 4.713 53.848 3101 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.37 % Allowed : 9.39 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2844 helix: 2.12 (0.20), residues: 663 sheet: 0.20 (0.18), residues: 675 loop : -0.55 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.018 0.001 TYR C1067 PHE 0.020 0.001 PHE A 65 TRP 0.015 0.001 TRP C 353 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24198) covalent geometry : angle 0.50209 / 0.26 (32904) SS BOND : bond 0.00325 / 0.20 ( 36) SS BOND : angle 1.49345 / 0.94 ( 72) hydrogen bonds : bond 0.03457 / 2.24 ( 1035) hydrogen bonds : angle 5.36091 / 3.75 ( 2892) link_BETA1-4 : bond 0.00370 / 0.21 ( 15) link_BETA1-4 : angle 1.13046 / 0.78 ( 45) link_NAG-ASN : bond 0.00296 / 0.20 ( 48) link_NAG-ASN : angle 2.25647 / 1.42 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6430 (ttt180) cc_final: 0.6142 (ttt180) REVERT: A 532 ASN cc_start: 0.8674 (t0) cc_final: 0.8398 (t0) REVERT: A 574 ASP cc_start: 0.7033 (t0) cc_final: 0.6761 (t0) REVERT: A 578 ASP cc_start: 0.7949 (t0) cc_final: 0.7661 (t0) REVERT: A 776 LYS cc_start: 0.8409 (tttt) cc_final: 0.8151 (tttm) REVERT: A 814 LYS cc_start: 0.8174 (mttt) cc_final: 0.7798 (mtpp) REVERT: A 988 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8164 (mm-30) REVERT: B 97 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6516 (mttm) REVERT: B 190 ARG cc_start: 0.5772 (ttm170) cc_final: 0.5008 (tpp-160) REVERT: B 554 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8157 (mp0) REVERT: B 565 PHE cc_start: 0.7442 (m-80) cc_final: 0.7171 (m-80) REVERT: B 574 ASP cc_start: 0.7145 (t0) cc_final: 0.6758 (t0) REVERT: B 776 LYS cc_start: 0.8498 (tttt) cc_final: 0.8282 (ttpp) REVERT: B 780 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8111 (pt0) REVERT: B 964 LYS cc_start: 0.8632 (mttt) cc_final: 0.8276 (mtpt) REVERT: B 1144 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 192 PHE cc_start: 0.7802 (m-80) cc_final: 0.7496 (m-10) REVERT: C 205 SER cc_start: 0.8483 (p) cc_final: 0.8145 (t) REVERT: C 403 ARG cc_start: 0.6573 (ttt180) cc_final: 0.6298 (ttt90) REVERT: C 452 LEU cc_start: 0.7966 (mt) cc_final: 0.7661 (mm) REVERT: C 506 GLN cc_start: 0.8156 (mt0) cc_final: 0.7691 (mp10) REVERT: C 574 ASP cc_start: 0.7087 (t0) cc_final: 0.6656 (t0) REVERT: C 592 PHE cc_start: 0.8011 (p90) cc_final: 0.7634 (p90) REVERT: C 643 PHE cc_start: 0.8135 (t80) cc_final: 0.7790 (t80) REVERT: C 804 GLN cc_start: 0.8295 (mt0) cc_final: 0.8028 (mt0) REVERT: C 964 LYS cc_start: 0.8669 (mttt) cc_final: 0.8286 (mtpt) outliers start: 35 outliers final: 25 residues processed: 228 average time/residue: 0.1625 time to fit residues: 59.5798 Evaluate side-chains 212 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 249 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 266 optimal weight: 0.4980 chunk 226 optimal weight: 0.0970 chunk 256 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 213 optimal weight: 0.0370 chunk 102 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.8858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.166845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109192 restraints weight = 30224.933| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.50 r_work: 0.3251 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24297 Z= 0.126 Angle : 0.526 10.952 33165 Z= 0.267 Chirality : 0.044 0.404 3951 Planarity : 0.004 0.039 4158 Dihedral : 4.607 54.000 3101 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.21 % Allowed : 9.55 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2844 helix: 2.17 (0.20), residues: 663 sheet: 0.21 (0.18), residues: 675 loop : -0.56 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 237 TYR 0.018 0.001 TYR C1067 PHE 0.025 0.001 PHE B 106 TRP 0.019 0.001 TRP C 353 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (24198) covalent geometry : angle 0.50055 / 0.26 (32904) SS BOND : bond 0.00318 / 0.20 ( 36) SS BOND : angle 1.71542 / 1.03 ( 72) hydrogen bonds : bond 0.03467 / 2.23 ( 1035) hydrogen bonds : angle 5.29224 / 3.70 ( 2892) link_BETA1-4 : bond 0.00341 / 0.19 ( 15) link_BETA1-4 : angle 1.16246 / 0.80 ( 45) link_NAG-ASN : bond 0.00293 / 0.20 ( 48) link_NAG-ASN : angle 2.14922 / 1.37 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.6227 (ttm-80) cc_final: 0.6018 (ttt180) REVERT: A 506 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: A 532 ASN cc_start: 0.8690 (t0) cc_final: 0.8414 (t0) REVERT: A 574 ASP cc_start: 0.7017 (t0) cc_final: 0.6764 (t0) REVERT: A 578 ASP cc_start: 0.7912 (t0) cc_final: 0.7586 (t0) REVERT: A 776 LYS cc_start: 0.8488 (tttt) cc_final: 0.8228 (tttm) REVERT: A 814 LYS cc_start: 0.8130 (mttt) cc_final: 0.7760 (mtpp) REVERT: A 1100 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 106 PHE cc_start: 0.6761 (m-80) cc_final: 0.6447 (m-80) REVERT: B 190 ARG cc_start: 0.5742 (ttm170) cc_final: 0.5005 (tpp-160) REVERT: B 554 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8148 (mp0) REVERT: B 565 PHE cc_start: 0.7486 (m-80) cc_final: 0.7224 (m-80) REVERT: B 574 ASP cc_start: 0.7276 (t0) cc_final: 0.6842 (t0) REVERT: B 776 LYS cc_start: 0.8554 (tttt) cc_final: 0.8340 (ttpp) REVERT: B 964 LYS cc_start: 0.8656 (mttt) cc_final: 0.8306 (mtpt) REVERT: B 1144 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: C 192 PHE cc_start: 0.7769 (m-80) cc_final: 0.7415 (m-10) REVERT: C 205 SER cc_start: 0.8511 (p) cc_final: 0.8194 (t) REVERT: C 403 ARG cc_start: 0.6468 (ttt180) cc_final: 0.6258 (ttt90) REVERT: C 452 LEU cc_start: 0.8006 (mt) cc_final: 0.7697 (mm) REVERT: C 506 GLN cc_start: 0.8128 (mt0) cc_final: 0.7699 (mp10) REVERT: C 574 ASP cc_start: 0.7118 (t0) cc_final: 0.6645 (t0) REVERT: C 592 PHE cc_start: 0.8033 (p90) cc_final: 0.7684 (p90) REVERT: C 643 PHE cc_start: 0.8223 (t80) cc_final: 0.7903 (t80) REVERT: C 964 LYS cc_start: 0.8735 (mttt) cc_final: 0.8360 (mtpt) outliers start: 31 outliers final: 22 residues processed: 223 average time/residue: 0.1544 time to fit residues: 55.5656 Evaluate side-chains 213 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 145 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.0060 chunk 279 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 804 GLN B 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.167259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110191 restraints weight = 30271.709| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.59 r_work: 0.3240 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 24297 Z= 0.128 Angle : 0.527 12.750 33165 Z= 0.267 Chirality : 0.044 0.390 3951 Planarity : 0.004 0.039 4158 Dihedral : 4.568 54.454 3101 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.29 % Allowed : 9.98 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2844 helix: 2.19 (0.20), residues: 663 sheet: 0.20 (0.18), residues: 675 loop : -0.56 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.023 0.001 PHE B 168 TRP 0.020 0.001 TRP C 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24198) covalent geometry : angle 0.49985 / 0.26 (32904) SS BOND : bond 0.00323 / 0.21 ( 36) SS BOND : angle 2.02274 / 1.26 ( 72) hydrogen bonds : bond 0.03437 / 2.21 ( 1035) hydrogen bonds : angle 5.27189 / 3.68 ( 2892) link_BETA1-4 : bond 0.00337 / 0.19 ( 15) link_BETA1-4 : angle 1.12961 / 0.77 ( 45) link_NAG-ASN : bond 0.00276 / 0.19 ( 48) link_NAG-ASN : angle 2.09368 / 1.34 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.6272 (ttm-80) cc_final: 0.6057 (ttt180) REVERT: A 532 ASN cc_start: 0.8698 (t0) cc_final: 0.8409 (t0) REVERT: A 574 ASP cc_start: 0.7039 (t0) cc_final: 0.6795 (t0) REVERT: A 578 ASP cc_start: 0.7923 (t0) cc_final: 0.7590 (t0) REVERT: A 776 LYS cc_start: 0.8483 (tttt) cc_final: 0.8225 (tttm) REVERT: A 814 LYS cc_start: 0.8149 (mttt) cc_final: 0.7746 (mtpp) REVERT: A 914 ASN cc_start: 0.9060 (p0) cc_final: 0.8648 (p0) REVERT: A 1100 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8206 (p) REVERT: B 97 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6523 (mttm) REVERT: B 190 ARG cc_start: 0.5750 (ttm170) cc_final: 0.5008 (tpp-160) REVERT: B 554 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8141 (mp0) REVERT: B 565 PHE cc_start: 0.7494 (m-80) cc_final: 0.7245 (m-80) REVERT: B 571 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7536 (t0) REVERT: B 574 ASP cc_start: 0.7316 (t0) cc_final: 0.6883 (t0) REVERT: B 776 LYS cc_start: 0.8635 (tttt) cc_final: 0.8404 (ttpp) REVERT: B 964 LYS cc_start: 0.8686 (mttt) cc_final: 0.8327 (mtpt) REVERT: B 1144 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: C 192 PHE cc_start: 0.7788 (m-80) cc_final: 0.7443 (m-10) REVERT: C 205 SER cc_start: 0.8525 (p) cc_final: 0.8209 (t) REVERT: C 403 ARG cc_start: 0.6484 (ttt180) cc_final: 0.6279 (ttt90) REVERT: C 452 LEU cc_start: 0.7998 (mt) cc_final: 0.7678 (mm) REVERT: C 506 GLN cc_start: 0.8161 (mt0) cc_final: 0.7709 (mp10) REVERT: C 574 ASP cc_start: 0.7152 (t0) cc_final: 0.6675 (t0) REVERT: C 592 PHE cc_start: 0.8038 (p90) cc_final: 0.7678 (p90) REVERT: C 643 PHE cc_start: 0.8187 (t80) cc_final: 0.7864 (t80) REVERT: C 964 LYS cc_start: 0.8743 (mttt) cc_final: 0.8364 (mtpt) outliers start: 33 outliers final: 23 residues processed: 210 average time/residue: 0.1518 time to fit residues: 51.3687 Evaluate side-chains 209 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 93 optimal weight: 0.0470 chunk 144 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.166082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108256 restraints weight = 30259.701| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.50 r_work: 0.3248 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 24297 Z= 0.147 Angle : 0.537 12.058 33165 Z= 0.272 Chirality : 0.044 0.366 3951 Planarity : 0.004 0.040 4158 Dihedral : 4.591 55.585 3101 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.21 % Allowed : 10.17 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2844 helix: 2.22 (0.21), residues: 651 sheet: 0.17 (0.18), residues: 675 loop : -0.59 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 237 TYR 0.019 0.001 TYR C1067 PHE 0.020 0.001 PHE A 65 TRP 0.023 0.002 TRP C 353 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (24198) covalent geometry : angle 0.51120 / 0.27 (32904) SS BOND : bond 0.00408 / 0.26 ( 36) SS BOND : angle 1.96159 / 1.22 ( 72) hydrogen bonds : bond 0.03565 / 2.29 ( 1035) hydrogen bonds : angle 5.30486 / 3.71 ( 2892) link_BETA1-4 : bond 0.00328 / 0.17 ( 15) link_BETA1-4 : angle 1.16976 / 0.80 ( 45) link_NAG-ASN : bond 0.00285 / 0.19 ( 48) link_NAG-ASN : angle 2.06737 / 1.32 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6953 (t80) cc_final: 0.6670 (t80) REVERT: A 532 ASN cc_start: 0.8704 (t0) cc_final: 0.8415 (t0) REVERT: A 574 ASP cc_start: 0.7027 (t0) cc_final: 0.6777 (t0) REVERT: A 578 ASP cc_start: 0.7884 (t0) cc_final: 0.7546 (t0) REVERT: A 776 LYS cc_start: 0.8475 (tttt) cc_final: 0.8186 (tttm) REVERT: A 814 LYS cc_start: 0.8186 (mttt) cc_final: 0.7791 (mtpp) REVERT: A 1100 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 1144 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: B 97 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6467 (mttm) REVERT: B 106 PHE cc_start: 0.6679 (m-80) cc_final: 0.6375 (m-80) REVERT: B 190 ARG cc_start: 0.5721 (ttm170) cc_final: 0.4960 (tpp-160) REVERT: B 554 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8136 (mp0) REVERT: B 565 PHE cc_start: 0.7433 (m-80) cc_final: 0.7188 (m-80) REVERT: B 571 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7549 (t0) REVERT: B 574 ASP cc_start: 0.7273 (t0) cc_final: 0.6830 (t0) REVERT: B 776 LYS cc_start: 0.8619 (tttt) cc_final: 0.8362 (ttpp) REVERT: B 804 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8137 (mt0) REVERT: B 964 LYS cc_start: 0.8646 (mttt) cc_final: 0.8286 (mtpt) REVERT: B 1144 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: C 192 PHE cc_start: 0.7741 (m-80) cc_final: 0.7352 (m-10) REVERT: C 205 SER cc_start: 0.8503 (p) cc_final: 0.8195 (t) REVERT: C 403 ARG cc_start: 0.6392 (ttt180) cc_final: 0.6187 (ttt90) REVERT: C 452 LEU cc_start: 0.7954 (mt) cc_final: 0.7638 (mm) REVERT: C 574 ASP cc_start: 0.7106 (t0) cc_final: 0.6615 (t0) REVERT: C 592 PHE cc_start: 0.8045 (p90) cc_final: 0.7715 (p90) REVERT: C 643 PHE cc_start: 0.8182 (t80) cc_final: 0.7834 (t80) REVERT: C 964 LYS cc_start: 0.8738 (mttt) cc_final: 0.8344 (mtpt) outliers start: 31 outliers final: 20 residues processed: 212 average time/residue: 0.1569 time to fit residues: 53.3447 Evaluate side-chains 205 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 228 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 260 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 229 optimal weight: 30.0000 chunk 267 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN B 914 ASN B 935 GLN C 613 GLN C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.169187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106599 restraints weight = 31068.822| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.42 r_work: 0.3283 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 24297 Z= 0.340 Angle : 0.683 14.025 33165 Z= 0.346 Chirality : 0.049 0.329 3951 Planarity : 0.005 0.051 4158 Dihedral : 5.057 58.009 3101 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.10 % Allowed : 10.25 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 2844 helix: 1.64 (0.20), residues: 648 sheet: -0.11 (0.17), residues: 702 loop : -0.89 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 237 TYR 0.046 0.002 TYR B 904 PHE 0.035 0.003 PHE B1121 TRP 0.027 0.003 TRP C 353 HIS 0.010 0.002 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.34 (24198) covalent geometry : angle 0.65608 / 0.34 (32904) SS BOND : bond 0.00422 / 0.27 ( 36) SS BOND : angle 2.33627 / 1.47 ( 72) hydrogen bonds : bond 0.04564 / 2.92 ( 1035) hydrogen bonds : angle 5.80370 / 4.05 ( 2892) link_BETA1-4 : bond 0.00270 / 0.14 ( 15) link_BETA1-4 : angle 1.61530 / 1.07 ( 45) link_NAG-ASN : bond 0.00443 / 0.27 ( 48) link_NAG-ASN : angle 2.35008 / 1.52 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7100.32 seconds wall clock time: 121 minutes 56.22 seconds (7316.22 seconds total)