Starting phenix.real_space_refine on Sat Jul 4 21:54:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.map" model { file = "/net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ke7_22833/07_2026/7ke7_22833.cif" } resolution = 3.32 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= -0.002 sd= 0.045 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 15084 2.51 5 N 3852 2.21 5 O 4653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.03s 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: 23688 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "B" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 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: 4.86, per 1000 atoms: 0.21 Number of scatterers: 23688 At special positions: 0 Unit cell: (135.424, 128.018, 168.222, 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 4653 8.00 N 3852 7.00 C 15084 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 657 " " 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 B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 996.4 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: 5478 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 49 sheets defined 27.8% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.994A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.551A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.745A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.117A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.543A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.040A 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 918 removed outlier: 3.620A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) 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: 3.645A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.674A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (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 1143 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.598A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.585A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.609A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.998A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 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 966 removed outlier: 3.615A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.768A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.067A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 4.016A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.795A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.534A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.784A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.627A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.432A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.181A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 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 966 removed outlier: 3.770A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.649A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.701A 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: 8.143A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.334A 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: 6.659A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.772A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.148A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.452A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.263A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.632A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.744A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 656 removed outlier: 4.477A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.929A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.204A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.232A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.555A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.348A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.968A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.231A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.177A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.615A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.889A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.276A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.697A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 65 through 66 removed outlier: 4.478A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.380A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.410A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.923A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.923A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.507A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.375A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.667A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 1024 hydrogen bonds defined for protein. 2787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 2.58 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: 6042 1.33 - 1.45: 4770 1.45 - 1.58: 13251 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 24186 Sorted by residual: bond pdb=" CA ALA A 520 " pdb=" C ALA A 520 " ideal model delta sigma weight residual 1.518 1.556 -0.038 9.60e-03 1.09e+04 1.60e+01 bond pdb=" C5 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 26266 2.20 - 4.41: 6173 4.41 - 6.61: 429 6.61 - 8.81: 12 8.81 - 11.02: 6 Bond angle restraints: 32886 Sorted by residual: angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 112.24 122.06 -9.82 1.28e+00 6.10e-01 5.89e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 119.98 -11.02 1.49e+00 4.50e-01 5.47e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 118.32 -9.36 1.49e+00 4.50e-01 3.94e+01 angle pdb=" OD1 ASN C 331 " pdb=" CG ASN C 331 " pdb=" ND2 ASN C 331 " ideal model delta sigma weight residual 122.60 116.64 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" CA PHE A 186 " pdb=" CB PHE A 186 " pdb=" CG PHE A 186 " ideal model delta sigma weight residual 113.80 119.59 -5.79 1.00e+00 1.00e+00 3.35e+01 ... (remaining 32881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12871 17.93 - 35.85: 832 35.85 - 53.78: 111 53.78 - 71.71: 46 71.71 - 89.64: 30 Dihedral angle restraints: 13890 sinusoidal: 5406 harmonic: 8484 Sorted by residual: dihedral pdb=" C ASN A 99 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" CB ASN A 99 " ideal model delta harmonic sigma weight residual -122.60 -150.66 28.06 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CA ASN A 99 " pdb=" CB ASN A 99 " ideal model delta harmonic sigma weight residual 122.80 147.77 -24.97 0 2.50e+00 1.60e-01 9.97e+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 93.00 -178.81 -88.19 1 1.00e+01 1.00e-02 9.30e+01 ... (remaining 13887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 3865 0.226 - 0.452: 80 0.452 - 0.679: 2 0.679 - 0.905: 0 0.905 - 1.131: 1 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.16e+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 -2.58 0.18 2.00e-02 2.50e+03 8.43e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.89e+01 ... (remaining 3945 not shown) Planarity restraints: 4203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.228 2.00e-02 2.50e+03 2.70e-01 9.14e+02 pdb=" CG ASN B 331 " -0.147 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.429 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " 0.214 2.00e-02 2.50e+03 2.55e-01 8.14e+02 pdb=" CG ASN C 603 " -0.135 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " -0.410 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.304 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " 0.209 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" CG ASN C 165 " -0.132 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " -0.358 2.00e-02 2.50e+03 pdb=" C1 NAG C1309 " 0.279 2.00e-02 2.50e+03 ... (remaining 4200 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 11764 2.98 - 3.46: 23722 3.46 - 3.94: 39565 3.94 - 4.42: 44948 4.42 - 4.90: 74448 Nonbonded interactions: 194447 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.502 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.514 3.040 nonbonded pdb=" OE2 GLU C 132 " pdb=" OG1 THR C 167 " model vdw 2.518 3.040 nonbonded pdb=" O LYS C 964 " pdb=" OG SER C 967 " model vdw 2.530 3.040 nonbonded pdb=" OE2 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.548 3.040 ... (remaining 194442 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: 0.02 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.550 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 0.078 24285 Z= 0.772 Angle : 1.771 11.018 33147 Z= 1.158 Chirality : 0.100 1.131 3948 Planarity : 0.015 0.276 4155 Dihedral : 13.159 89.635 8304 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.49 % Favored : 92.23 % Rotamer: Outliers : 0.08 % Allowed : 1.02 % Favored : 98.90 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 2844 helix: -0.68 (0.17), residues: 653 sheet: -0.37 (0.24), residues: 408 loop : -1.11 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 408 TYR 0.141 0.023 TYR C 741 PHE 0.073 0.013 PHE B 802 TRP 0.152 0.026 TRP C 886 HIS 0.016 0.004 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01369 / 0.77 (24186) covalent geometry : angle 1.74059 / 1.16 (32886) SS BOND : bond 0.01209 / 0.77 ( 36) SS BOND : angle 2.12911 / 1.38 ( 72) hydrogen bonds : bond 0.15083 / 9.94 ( 1018) hydrogen bonds : angle 8.65685 / 6.05 ( 2787) link_BETA1-4 : bond 0.02609 / 1.52 ( 15) link_BETA1-4 : angle 4.74582 / 3.15 ( 45) link_NAG-ASN : bond 0.01018 / 0.64 ( 48) link_NAG-ASN : angle 4.59295 / 3.14 ( 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 274 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.1702 time to fit residues: 73.3066 Evaluate side-chains 136 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN A 957 GLN A1088 HIS B 394 ASN B1088 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 762 GLN C 856 ASN C 955 ASN C1058 HIS C1088 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.094801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.065268 restraints weight = 61961.120| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.79 r_work: 0.3105 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24285 Z= 0.161 Angle : 0.786 16.707 33147 Z= 0.397 Chirality : 0.049 0.399 3948 Planarity : 0.004 0.045 4155 Dihedral : 6.458 43.311 3101 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.33 % Allowed : 5.33 % Favored : 93.34 % Cbeta Deviations : 0.00 % 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: -0.59 (0.15), residues: 2844 helix: 0.72 (0.19), residues: 661 sheet: -0.54 (0.20), residues: 570 loop : -0.78 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 357 TYR 0.020 0.002 TYR B 505 PHE 0.020 0.002 PHE C 392 TRP 0.027 0.002 TRP A 436 HIS 0.013 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (24186) covalent geometry : angle 0.71412 / 0.38 (32886) SS BOND : bond 0.00609 / 0.41 ( 36) SS BOND : angle 2.71587 / 1.50 ( 72) hydrogen bonds : bond 0.05443 / 3.57 ( 1018) hydrogen bonds : angle 6.73216 / 4.71 ( 2787) link_BETA1-4 : bond 0.00472 / 0.32 ( 15) link_BETA1-4 : angle 1.94287 / 1.34 ( 45) link_NAG-ASN : bond 0.00395 / 0.25 ( 48) link_NAG-ASN : angle 4.57263 / 2.93 ( 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 201 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8272 (m-30) cc_final: 0.8018 (t0) REVERT: A 351 TYR cc_start: 0.9397 (p90) cc_final: 0.9048 (p90) REVERT: B 360 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8451 (t0) REVERT: B 855 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.5875 (m-80) REVERT: B 979 ASP cc_start: 0.8673 (t0) cc_final: 0.8446 (t0) REVERT: C 969 ASN cc_start: 0.8741 (m-40) cc_final: 0.8412 (t0) REVERT: C 1107 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.7867 (mpt-90) outliers start: 34 outliers final: 17 residues processed: 189 average time/residue: 0.1612 time to fit residues: 49.1894 Evaluate side-chains 139 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 734 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 334 ASN B 675 GLN B 901 GLN B 914 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 901 GLN C 926 GLN C1011 GLN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061204 restraints weight = 64106.357| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.96 r_work: 0.2987 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 24285 Z= 0.315 Angle : 0.787 16.401 33147 Z= 0.401 Chirality : 0.049 0.341 3948 Planarity : 0.005 0.051 4155 Dihedral : 6.032 37.029 3101 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.39 % Allowed : 6.82 % Favored : 90.80 % 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: -0.73 (0.15), residues: 2844 helix: 0.52 (0.19), residues: 663 sheet: -0.75 (0.19), residues: 604 loop : -0.76 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.032 0.002 TYR B1067 PHE 0.034 0.003 PHE C1089 TRP 0.027 0.002 TRP A 436 HIS 0.010 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.31 (24186) covalent geometry : angle 0.74931 / 0.39 (32886) SS BOND : bond 0.00832 / 0.52 ( 36) SS BOND : angle 2.54357 / 1.55 ( 72) hydrogen bonds : bond 0.05358 / 3.55 ( 1018) hydrogen bonds : angle 6.68925 / 4.66 ( 2787) link_BETA1-4 : bond 0.00315 / 0.20 ( 15) link_BETA1-4 : angle 1.67840 / 1.17 ( 45) link_NAG-ASN : bond 0.00392 / 0.24 ( 48) link_NAG-ASN : angle 3.22355 / 2.05 ( 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 188 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8258 (m-30) cc_final: 0.7904 (t0) REVERT: A 351 TYR cc_start: 0.9496 (p90) cc_final: 0.9023 (p90) REVERT: A 377 PHE cc_start: 0.7584 (t80) cc_final: 0.7369 (t80) REVERT: A 979 ASP cc_start: 0.9325 (m-30) cc_final: 0.9028 (m-30) REVERT: A 990 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8506 (pt0) REVERT: B 360 ASN cc_start: 0.9261 (t0) cc_final: 0.8485 (t0) REVERT: B 389 ASP cc_start: 0.8646 (t0) cc_final: 0.8391 (t0) REVERT: B 855 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.5872 (m-80) REVERT: C 169 GLU cc_start: 0.8820 (tt0) cc_final: 0.8550 (tm-30) REVERT: C 969 ASN cc_start: 0.8863 (m-40) cc_final: 0.8606 (t0) outliers start: 61 outliers final: 37 residues processed: 173 average time/residue: 0.1537 time to fit residues: 43.6092 Evaluate side-chains 148 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1011 GLN B1058 HIS ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 926 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.092533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063158 restraints weight = 63195.827| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.97 r_work: 0.3044 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24285 Z= 0.191 Angle : 0.673 12.132 33147 Z= 0.344 Chirality : 0.046 0.344 3948 Planarity : 0.004 0.051 4155 Dihedral : 5.604 37.868 3101 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.47 % Allowed : 8.23 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 2844 helix: 0.77 (0.19), residues: 669 sheet: -0.78 (0.19), residues: 624 loop : -0.71 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.027 0.002 TYR A 495 PHE 0.032 0.002 PHE A 392 TRP 0.014 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (24186) covalent geometry : angle 0.63914 / 0.34 (32886) SS BOND : bond 0.00865 / 0.52 ( 36) SS BOND : angle 2.69022 / 1.60 ( 72) hydrogen bonds : bond 0.04626 / 3.06 ( 1018) hydrogen bonds : angle 6.38835 / 4.45 ( 2787) link_BETA1-4 : bond 0.00331 / 0.22 ( 15) link_BETA1-4 : angle 1.33847 / 0.95 ( 45) link_NAG-ASN : bond 0.00306 / 0.20 ( 48) link_NAG-ASN : angle 2.59553 / 1.64 ( 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 194 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 131 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8273 (m-30) cc_final: 0.7954 (t0) REVERT: A 351 TYR cc_start: 0.9532 (p90) cc_final: 0.9041 (p90) REVERT: A 731 MET cc_start: 0.9231 (ptt) cc_final: 0.9016 (ptt) REVERT: A 979 ASP cc_start: 0.9337 (m-30) cc_final: 0.8967 (m-30) REVERT: A 990 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8469 (pt0) REVERT: A 1029 MET cc_start: 0.7446 (tpp) cc_final: 0.7177 (mmt) REVERT: A 1050 MET cc_start: 0.7862 (ptm) cc_final: 0.7657 (ptt) REVERT: B 360 ASN cc_start: 0.9248 (t0) cc_final: 0.8533 (t0) REVERT: B 389 ASP cc_start: 0.8592 (t0) cc_final: 0.8353 (t0) REVERT: B 394 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7868 (m-40) REVERT: B 466 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8074 (mtp85) REVERT: B 514 SER cc_start: 0.9330 (t) cc_final: 0.8837 (p) REVERT: B 731 MET cc_start: 0.8900 (ptm) cc_final: 0.8646 (ptm) REVERT: B 855 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: C 1107 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.7602 (mmt90) outliers start: 63 outliers final: 34 residues processed: 179 average time/residue: 0.1556 time to fit residues: 46.0341 Evaluate side-chains 145 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 55 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 901 GLN C 926 GLN C 949 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.089438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059974 restraints weight = 64314.678| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.93 r_work: 0.2960 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 24285 Z= 0.370 Angle : 0.790 13.028 33147 Z= 0.405 Chirality : 0.049 0.339 3948 Planarity : 0.005 0.055 4155 Dihedral : 5.789 35.139 3101 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.13 % Allowed : 9.32 % Favored : 87.54 % Cbeta Deviations : 0.00 % 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: -0.85 (0.15), residues: 2844 helix: 0.55 (0.19), residues: 652 sheet: -0.80 (0.20), residues: 623 loop : -0.90 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 408 TYR 0.030 0.002 TYR B1067 PHE 0.047 0.003 PHE A 392 TRP 0.012 0.002 TRP C 886 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.37 (24186) covalent geometry : angle 0.75878 / 0.40 (32886) SS BOND : bond 0.00896 / 0.55 ( 36) SS BOND : angle 3.02589 / 1.80 ( 72) hydrogen bonds : bond 0.05310 / 3.53 ( 1018) hydrogen bonds : angle 6.70154 / 4.68 ( 2787) link_BETA1-4 : bond 0.00258 / 0.17 ( 15) link_BETA1-4 : angle 1.46496 / 1.01 ( 45) link_NAG-ASN : bond 0.00449 / 0.27 ( 48) link_NAG-ASN : angle 2.62755 / 1.67 ( 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 191 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 111 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8234 (m-30) cc_final: 0.8030 (t0) REVERT: A 351 TYR cc_start: 0.9543 (p90) cc_final: 0.9061 (p90) REVERT: A 731 MET cc_start: 0.9288 (ptt) cc_final: 0.9044 (ptt) REVERT: A 979 ASP cc_start: 0.9420 (m-30) cc_final: 0.9095 (m-30) REVERT: B 360 ASN cc_start: 0.9097 (t0) cc_final: 0.8394 (t0) REVERT: B 389 ASP cc_start: 0.8666 (t0) cc_final: 0.8454 (t0) REVERT: B 394 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: B 514 SER cc_start: 0.9326 (t) cc_final: 0.8850 (p) REVERT: C 90 VAL cc_start: 0.7831 (t) cc_final: 0.7589 (p) REVERT: C 169 GLU cc_start: 0.8934 (tt0) cc_final: 0.8725 (tm-30) REVERT: C 1107 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.7599 (mmt90) outliers start: 80 outliers final: 59 residues processed: 177 average time/residue: 0.1484 time to fit residues: 44.2989 Evaluate side-chains 162 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 102 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 36 optimal weight: 30.0000 chunk 65 optimal weight: 0.9990 chunk 282 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 926 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.093198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064162 restraints weight = 63089.217| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.97 r_work: 0.3070 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24285 Z= 0.139 Angle : 0.633 13.033 33147 Z= 0.325 Chirality : 0.045 0.283 3948 Planarity : 0.004 0.059 4155 Dihedral : 5.300 39.798 3101 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.04 % Allowed : 10.81 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.56 (0.15), residues: 2844 helix: 0.86 (0.20), residues: 668 sheet: -0.65 (0.20), residues: 605 loop : -0.75 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.017 0.001 TYR B 505 PHE 0.025 0.001 PHE A 392 TRP 0.017 0.001 TRP C 104 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (24186) covalent geometry : angle 0.60592 / 0.32 (32886) SS BOND : bond 0.00758 / 0.44 ( 36) SS BOND : angle 2.56373 / 1.52 ( 72) hydrogen bonds : bond 0.04343 / 2.86 ( 1018) hydrogen bonds : angle 6.24844 / 4.36 ( 2787) link_BETA1-4 : bond 0.00389 / 0.25 ( 15) link_BETA1-4 : angle 1.15100 / 0.84 ( 45) link_NAG-ASN : bond 0.00303 / 0.19 ( 48) link_NAG-ASN : angle 2.18033 / 1.37 ( 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 179 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8851 (t80) cc_final: 0.8646 (t80) REVERT: A 351 TYR cc_start: 0.9545 (p90) cc_final: 0.9029 (p90) REVERT: A 731 MET cc_start: 0.9247 (ptt) cc_final: 0.9021 (ptt) REVERT: A 979 ASP cc_start: 0.9351 (m-30) cc_final: 0.9009 (m-30) REVERT: A 1029 MET cc_start: 0.7435 (tpp) cc_final: 0.7171 (mmt) REVERT: B 360 ASN cc_start: 0.9076 (t0) cc_final: 0.8461 (t0) REVERT: B 389 ASP cc_start: 0.8582 (t0) cc_final: 0.8347 (t0) REVERT: B 394 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.7992 (m-40) REVERT: B 514 SER cc_start: 0.9402 (t) cc_final: 0.8902 (p) REVERT: B 855 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6018 (m-80) REVERT: C 740 MET cc_start: 0.8296 (tpt) cc_final: 0.8024 (tpt) REVERT: C 1107 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.8036 (mtt90) outliers start: 52 outliers final: 30 residues processed: 165 average time/residue: 0.1573 time to fit residues: 43.0355 Evaluate side-chains 141 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 729 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 137 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 260 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.091278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062150 restraints weight = 63851.454| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.95 r_work: 0.3020 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 24285 Z= 0.238 Angle : 0.679 13.015 33147 Z= 0.348 Chirality : 0.046 0.277 3948 Planarity : 0.004 0.060 4155 Dihedral : 5.321 38.930 3101 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.35 % Allowed : 10.61 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.61 (0.15), residues: 2844 helix: 0.83 (0.20), residues: 665 sheet: -0.69 (0.20), residues: 634 loop : -0.78 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.020 0.002 TYR B1067 PHE 0.028 0.002 PHE C 186 TRP 0.015 0.002 TRP A 886 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (24186) covalent geometry : angle 0.64949 / 0.34 (32886) SS BOND : bond 0.00765 / 0.47 ( 36) SS BOND : angle 2.96254 / 1.65 ( 72) hydrogen bonds : bond 0.04687 / 3.11 ( 1018) hydrogen bonds : angle 6.36765 / 4.44 ( 2787) link_BETA1-4 : bond 0.00279 / 0.19 ( 15) link_BETA1-4 : angle 1.23015 / 0.87 ( 45) link_NAG-ASN : bond 0.00304 / 0.19 ( 48) link_NAG-ASN : angle 2.21149 / 1.40 ( 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 169 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 109 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 351 TYR cc_start: 0.9544 (p90) cc_final: 0.9031 (p90) REVERT: A 731 MET cc_start: 0.9263 (ptt) cc_final: 0.9010 (ptt) REVERT: A 979 ASP cc_start: 0.9373 (m-30) cc_final: 0.9022 (m-30) REVERT: A 1029 MET cc_start: 0.7480 (tpp) cc_final: 0.7195 (mmt) REVERT: B 360 ASN cc_start: 0.9074 (t0) cc_final: 0.8427 (t0) REVERT: B 394 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7951 (m-40) REVERT: B 428 ASP cc_start: 0.9020 (p0) cc_final: 0.8775 (m-30) REVERT: B 514 SER cc_start: 0.9370 (t) cc_final: 0.8948 (p) REVERT: B 855 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: C 90 VAL cc_start: 0.7711 (t) cc_final: 0.7450 (p) REVERT: C 1107 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8197 (mtt-85) outliers start: 60 outliers final: 51 residues processed: 153 average time/residue: 0.1450 time to fit residues: 37.6086 Evaluate side-chains 159 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 222 optimal weight: 0.0970 chunk 290 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN B 901 GLN B 914 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.093967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.065138 restraints weight = 62943.621| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.97 r_work: 0.3093 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24285 Z= 0.123 Angle : 0.595 12.823 33147 Z= 0.305 Chirality : 0.044 0.272 3948 Planarity : 0.004 0.059 4155 Dihedral : 4.993 42.554 3101 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.08 % Allowed : 11.12 % Favored : 86.80 % 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: -0.45 (0.15), residues: 2844 helix: 1.00 (0.20), residues: 673 sheet: -0.60 (0.20), residues: 609 loop : -0.70 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.015 0.001 TYR B 505 PHE 0.023 0.001 PHE A 392 TRP 0.019 0.001 TRP A 886 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24186) covalent geometry : angle 0.57213 / 0.30 (32886) SS BOND : bond 0.00650 / 0.38 ( 36) SS BOND : angle 2.28640 / 1.30 ( 72) hydrogen bonds : bond 0.04105 / 2.69 ( 1018) hydrogen bonds : angle 6.06001 / 4.23 ( 2787) link_BETA1-4 : bond 0.00362 / 0.23 ( 15) link_BETA1-4 : angle 1.06574 / 0.77 ( 45) link_NAG-ASN : bond 0.00277 / 0.18 ( 48) link_NAG-ASN : angle 1.93202 / 1.22 ( 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 183 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8091 (mm) REVERT: A 351 TYR cc_start: 0.9543 (p90) cc_final: 0.9016 (p90) REVERT: A 408 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8647 (tmm-80) REVERT: A 731 MET cc_start: 0.9238 (ptt) cc_final: 0.9016 (ptt) REVERT: A 979 ASP cc_start: 0.9321 (m-30) cc_final: 0.8970 (m-30) REVERT: A 1127 ASP cc_start: 0.9175 (m-30) cc_final: 0.8818 (p0) REVERT: B 334 ASN cc_start: 0.9283 (m110) cc_final: 0.9072 (m110) REVERT: B 346 ARG cc_start: 0.8334 (tpp80) cc_final: 0.8085 (tpp80) REVERT: B 360 ASN cc_start: 0.9034 (t0) cc_final: 0.8424 (t0) REVERT: B 394 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8008 (m-40) REVERT: B 428 ASP cc_start: 0.9036 (p0) cc_final: 0.8808 (m-30) REVERT: B 514 SER cc_start: 0.9392 (t) cc_final: 0.8926 (p) REVERT: B 855 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: C 1107 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8060 (mtt90) outliers start: 53 outliers final: 34 residues processed: 169 average time/residue: 0.1516 time to fit residues: 42.8692 Evaluate side-chains 155 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 729 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 170 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 223 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 196 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN B 901 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.092702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063631 restraints weight = 63812.011| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.98 r_work: 0.3059 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24285 Z= 0.175 Angle : 0.619 13.867 33147 Z= 0.316 Chirality : 0.045 0.264 3948 Planarity : 0.004 0.058 4155 Dihedral : 5.019 42.532 3101 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.19 % Allowed : 11.24 % Favored : 86.56 % Cbeta Deviations : 0.00 % 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: -0.47 (0.15), residues: 2844 helix: 0.96 (0.20), residues: 673 sheet: -0.59 (0.19), residues: 623 loop : -0.71 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.016 0.001 TYR B1067 PHE 0.034 0.001 PHE A 392 TRP 0.018 0.001 TRP A 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (24186) covalent geometry : angle 0.59650 / 0.31 (32886) SS BOND : bond 0.00702 / 0.44 ( 36) SS BOND : angle 2.34229 / 1.35 ( 72) hydrogen bonds : bond 0.04286 / 2.82 ( 1018) hydrogen bonds : angle 6.10037 / 4.26 ( 2787) link_BETA1-4 : bond 0.00290 / 0.18 ( 15) link_BETA1-4 : angle 1.13768 / 0.81 ( 45) link_NAG-ASN : bond 0.00254 / 0.17 ( 48) link_NAG-ASN : angle 1.95238 / 1.23 ( 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 175 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 351 TYR cc_start: 0.9549 (p90) cc_final: 0.9014 (p90) REVERT: A 365 TYR cc_start: 0.8977 (m-80) cc_final: 0.8361 (m-80) REVERT: A 565 PHE cc_start: 0.8250 (m-80) cc_final: 0.7771 (m-80) REVERT: A 731 MET cc_start: 0.9241 (ptt) cc_final: 0.8989 (ptt) REVERT: A 979 ASP cc_start: 0.9324 (m-30) cc_final: 0.8979 (m-30) REVERT: A 1127 ASP cc_start: 0.9179 (m-30) cc_final: 0.8830 (p0) REVERT: B 346 ARG cc_start: 0.8394 (tpp80) cc_final: 0.8163 (tpp80) REVERT: B 360 ASN cc_start: 0.9055 (t0) cc_final: 0.8464 (t0) REVERT: B 394 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7995 (m-40) REVERT: B 428 ASP cc_start: 0.9058 (p0) cc_final: 0.8851 (m-30) REVERT: B 514 SER cc_start: 0.9361 (t) cc_final: 0.8965 (p) REVERT: B 855 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: C 90 VAL cc_start: 0.7707 (t) cc_final: 0.7421 (p) REVERT: C 406 GLU cc_start: 0.8481 (mp0) cc_final: 0.8079 (mp0) REVERT: C 1107 ARG cc_start: 0.8493 (mtt-85) cc_final: 0.8211 (mtt-85) outliers start: 56 outliers final: 44 residues processed: 162 average time/residue: 0.1348 time to fit residues: 37.1630 Evaluate side-chains 162 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 729 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 253 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 287 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.093170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064175 restraints weight = 63367.911| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.98 r_work: 0.3071 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24285 Z= 0.155 Angle : 0.601 13.664 33147 Z= 0.308 Chirality : 0.044 0.258 3948 Planarity : 0.004 0.059 4155 Dihedral : 4.952 43.473 3101 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.04 % Allowed : 11.44 % Favored : 86.53 % Cbeta Deviations : 0.00 % 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: -0.47 (0.15), residues: 2844 helix: 0.98 (0.20), residues: 670 sheet: -0.68 (0.19), residues: 636 loop : -0.68 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.017 0.001 TYR C 365 PHE 0.030 0.001 PHE A 392 TRP 0.019 0.001 TRP A 886 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (24186) covalent geometry : angle 0.58018 / 0.30 (32886) SS BOND : bond 0.00649 / 0.40 ( 36) SS BOND : angle 2.21664 / 1.26 ( 72) hydrogen bonds : bond 0.04166 / 2.74 ( 1018) hydrogen bonds : angle 6.01950 / 4.20 ( 2787) link_BETA1-4 : bond 0.00305 / 0.19 ( 15) link_BETA1-4 : angle 1.08114 / 0.78 ( 45) link_NAG-ASN : bond 0.00221 / 0.14 ( 48) link_NAG-ASN : angle 1.87365 / 1.18 ( 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 175 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8096 (mm) REVERT: A 351 TYR cc_start: 0.9555 (p90) cc_final: 0.8996 (p90) REVERT: A 365 TYR cc_start: 0.8976 (m-80) cc_final: 0.8361 (m-80) REVERT: A 408 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8693 (tmm-80) REVERT: A 565 PHE cc_start: 0.8237 (m-80) cc_final: 0.7741 (m-80) REVERT: A 731 MET cc_start: 0.9219 (ptt) cc_final: 0.8972 (ptt) REVERT: A 979 ASP cc_start: 0.9308 (m-30) cc_final: 0.8843 (t0) REVERT: A 1029 MET cc_start: 0.7167 (tpp) cc_final: 0.6773 (mmt) REVERT: A 1127 ASP cc_start: 0.9167 (m-30) cc_final: 0.8846 (p0) REVERT: B 334 ASN cc_start: 0.9277 (m110) cc_final: 0.9021 (p0) REVERT: B 346 ARG cc_start: 0.8432 (tpp80) cc_final: 0.8170 (tpp80) REVERT: B 360 ASN cc_start: 0.9015 (t0) cc_final: 0.8326 (t0) REVERT: B 394 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8002 (m-40) REVERT: B 514 SER cc_start: 0.9358 (t) cc_final: 0.8975 (p) REVERT: B 855 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: C 90 VAL cc_start: 0.7681 (t) cc_final: 0.7391 (p) REVERT: C 406 GLU cc_start: 0.8462 (mp0) cc_final: 0.8048 (mp0) REVERT: C 1050 MET cc_start: 0.8374 (ptm) cc_final: 0.7980 (ptt) REVERT: C 1107 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8003 (mpt-90) outliers start: 52 outliers final: 46 residues processed: 163 average time/residue: 0.1499 time to fit residues: 41.1993 Evaluate side-chains 168 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 729 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 218 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.065274 restraints weight = 63294.124| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.91 r_work: 0.3102 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24285 Z= 0.129 Angle : 0.580 13.546 33147 Z= 0.298 Chirality : 0.044 0.257 3948 Planarity : 0.004 0.058 4155 Dihedral : 4.813 44.323 3101 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.84 % Allowed : 11.79 % Favored : 86.37 % Cbeta Deviations : 0.00 % 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: -0.37 (0.15), residues: 2844 helix: 1.09 (0.20), residues: 670 sheet: -0.61 (0.20), residues: 608 loop : -0.64 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.017 0.001 TYR C 741 PHE 0.026 0.001 PHE A 392 TRP 0.018 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (24186) covalent geometry : angle 0.56125 / 0.29 (32886) SS BOND : bond 0.00602 / 0.37 ( 36) SS BOND : angle 2.02960 / 1.17 ( 72) hydrogen bonds : bond 0.04009 / 2.64 ( 1018) hydrogen bonds : angle 5.89628 / 4.13 ( 2787) link_BETA1-4 : bond 0.00323 / 0.22 ( 15) link_BETA1-4 : angle 1.03366 / 0.74 ( 45) link_NAG-ASN : bond 0.00216 / 0.14 ( 48) link_NAG-ASN : angle 1.76387 / 1.10 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6480.09 seconds wall clock time: 111 minutes 59.91 seconds (6719.91 seconds total)