Starting phenix.real_space_refine on Sun Jul 5 04:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxr_25503/07_2026/7sxr_25503.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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 111 5.16 5 C 16059 2.51 5 N 4128 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25236 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.15, per 1000 atoms: 0.24 Number of scatterers: 25236 At special positions: 0 Unit cell: (141, 147, 196, 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 111 16.00 O 4938 8.00 N 4128 7.00 C 16059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 41 sheets defined 24.7% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.086A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.627A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.456A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.090A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.626A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (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 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.902A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.071A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.553A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.051A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.854A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.612A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.021A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.584A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.546A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.891A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.007A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.518A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.852A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.692A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.870A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.600A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.936A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.676A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.950A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.590A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.288A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 5.535A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.620A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.204A 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: 4.031A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 11.408A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.066A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 154 through 172 current: chain 'A' and resid 259 through 260 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.686A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.201A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.520A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.101A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.829A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.919A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.802A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.039A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.181A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 6.846A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.596A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 354 through 358 current: chain 'B' and resid 508 through 516 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.674A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.939A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.354A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 6.496A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.161A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.927A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.483A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.294A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 354 through 358 current: chain 'C' and resid 508 through 516 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.263A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.932A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.333A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 852 hydrogen bonds defined for protein. 2373 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: 5.72 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7762 1.34 - 1.46: 6538 1.46 - 1.59: 11365 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 25803 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 ... (remaining 25798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 33605 1.82 - 3.64: 1367 3.64 - 5.46: 107 5.46 - 7.28: 34 7.28 - 9.10: 11 Bond angle restraints: 35124 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.21 -5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.19 -5.49 1.22e+00 6.72e-01 2.03e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.06 -5.36 1.22e+00 6.72e-01 1.93e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.43 -4.50 1.20e+00 6.94e-01 1.40e+01 ... (remaining 35119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13754 17.93 - 35.86: 958 35.86 - 53.79: 119 53.79 - 71.72: 51 71.72 - 89.65: 28 Dihedral angle restraints: 14910 sinusoidal: 5832 harmonic: 9078 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -57.51 -28.49 1 1.00e+01 1.00e-02 1.16e+01 ... (remaining 14907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3227 0.063 - 0.125: 800 0.125 - 0.188: 114 0.188 - 0.251: 13 0.251 - 0.314: 4 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C MET C 902 " 0.051 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C GLN C 920 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 551 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C VAL C 551 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL C 551 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 552 " 0.014 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6869 2.81 - 3.33: 21263 3.33 - 3.85: 43118 3.85 - 4.38: 49692 4.38 - 4.90: 84644 Nonbonded interactions: 205586 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.310 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.313 3.040 ... (remaining 205581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.660 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 40.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.005 0.067 25905 Z= 0.226 Angle : 0.822 15.070 35388 Z= 0.436 Chirality : 0.055 0.314 4158 Planarity : 0.006 0.055 4476 Dihedral : 12.984 89.650 8940 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3072 helix: 0.71 (0.18), residues: 670 sheet: 0.42 (0.19), residues: 686 loop : -0.78 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.025 0.002 TYR C1067 PHE 0.033 0.002 PHE B 135 TRP 0.018 0.002 TRP A 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (25803) covalent geometry : angle 0.79415 / 0.43 (35124) SS BOND : bond 0.00274 / 0.18 ( 42) SS BOND : angle 1.34706 / 0.89 ( 84) hydrogen bonds : bond 0.12917 / 8.44 ( 852) hydrogen bonds : angle 7.05191 / 4.83 ( 2373) link_BETA1-4 : bond 0.00685 / 0.45 ( 18) link_BETA1-4 : angle 1.42996 / 0.97 ( 54) link_NAG-ASN : bond 0.00734 / 0.37 ( 42) link_NAG-ASN : angle 3.46825 / 2.92 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.937 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: A 85 PRO cc_start: 0.9410 (Cg_exo) cc_final: 0.9190 (Cg_endo) REVERT: A 153 MET cc_start: 0.4599 (ptt) cc_final: 0.3915 (tpt) REVERT: A 436 TRP cc_start: 0.6779 (p90) cc_final: 0.6474 (p-90) REVERT: A 755 GLN cc_start: 0.8430 (mm110) cc_final: 0.8091 (mm110) REVERT: A 1002 GLN cc_start: 0.8596 (tt0) cc_final: 0.8262 (tm-30) REVERT: B 135 PHE cc_start: 0.7695 (m-10) cc_final: 0.7485 (m-80) REVERT: B 421 TYR cc_start: 0.8528 (m-10) cc_final: 0.7974 (m-10) REVERT: B 512 VAL cc_start: 0.9252 (t) cc_final: 0.8695 (p) REVERT: B 985 ASP cc_start: 0.8136 (p0) cc_final: 0.7160 (p0) REVERT: C 378 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8950 (ttpp) REVERT: C 456 PHE cc_start: 0.8351 (m-10) cc_final: 0.8033 (m-10) REVERT: C 497 PHE cc_start: 0.4573 (m-10) cc_final: 0.4339 (m-10) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.6820 time to fit residues: 132.2034 Evaluate side-chains 78 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 613 GLN A 926 GLN B 901 GLN C1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.075527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047581 restraints weight = 98304.519| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.58 r_work: 0.2868 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25905 Z= 0.150 Angle : 0.548 10.645 35388 Z= 0.277 Chirality : 0.043 0.225 4158 Planarity : 0.004 0.046 4476 Dihedral : 4.205 21.078 3342 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.80 % Allowed : 5.45 % Favored : 93.74 % 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: 0.30 (0.14), residues: 3072 helix: 1.77 (0.20), residues: 687 sheet: 0.48 (0.19), residues: 713 loop : -0.58 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 567 TYR 0.016 0.001 TYR C 489 PHE 0.019 0.001 PHE A 347 TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (25803) covalent geometry : angle 0.52472 / 0.27 (35124) SS BOND : bond 0.00179 / 0.12 ( 42) SS BOND : angle 0.71583 / 0.49 ( 84) hydrogen bonds : bond 0.04103 / 2.75 ( 852) hydrogen bonds : angle 5.66034 / 3.81 ( 2373) link_BETA1-4 : bond 0.00199 / 0.14 ( 18) link_BETA1-4 : angle 1.07390 / 0.73 ( 54) link_NAG-ASN : bond 0.00516 / 0.27 ( 42) link_NAG-ASN : angle 2.60739 / 2.14 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4732 (ptt) cc_final: 0.3973 (tpt) REVERT: A 755 GLN cc_start: 0.8943 (mm110) cc_final: 0.8481 (mm110) REVERT: A 1002 GLN cc_start: 0.9197 (tt0) cc_final: 0.8711 (tm-30) REVERT: A 1145 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8274 (tm) REVERT: B 135 PHE cc_start: 0.7789 (m-10) cc_final: 0.7496 (m-80) REVERT: B 512 VAL cc_start: 0.9099 (t) cc_final: 0.8624 (p) REVERT: B 985 ASP cc_start: 0.8336 (p0) cc_final: 0.7970 (p0) REVERT: C 456 PHE cc_start: 0.8524 (m-10) cc_final: 0.8219 (m-10) REVERT: C 1010 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8746 (mp10) outliers start: 22 outliers final: 3 residues processed: 100 average time/residue: 0.6146 time to fit residues: 72.3625 Evaluate side-chains 78 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 164 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 234 optimal weight: 0.0370 chunk 273 optimal weight: 6.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 824 ASN B 872 GLN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.073233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045304 restraints weight = 98410.787| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.52 r_work: 0.2793 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 25905 Z= 0.292 Angle : 0.627 10.192 35388 Z= 0.312 Chirality : 0.045 0.230 4158 Planarity : 0.004 0.043 4476 Dihedral : 4.392 21.284 3342 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.02 % Allowed : 6.51 % Favored : 92.46 % 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: 0.24 (0.15), residues: 3072 helix: 1.86 (0.20), residues: 695 sheet: 0.23 (0.20), residues: 666 loop : -0.57 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.021 0.002 TYR C 756 PHE 0.027 0.002 PHE B 157 TRP 0.015 0.002 TRP A 886 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.29 (25803) covalent geometry : angle 0.60649 / 0.31 (35124) SS BOND : bond 0.00216 / 0.14 ( 42) SS BOND : angle 0.79591 / 0.52 ( 84) hydrogen bonds : bond 0.04695 / 3.15 ( 852) hydrogen bonds : angle 5.57552 / 3.78 ( 2373) link_BETA1-4 : bond 0.00192 / 0.13 ( 18) link_BETA1-4 : angle 1.22230 / 0.83 ( 54) link_NAG-ASN : bond 0.00593 / 0.35 ( 42) link_NAG-ASN : angle 2.60657 / 2.15 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4830 (ptt) cc_final: 0.3834 (tpt) REVERT: A 1002 GLN cc_start: 0.9215 (tt0) cc_final: 0.8755 (tm-30) REVERT: A 1010 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: A 1145 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8315 (tm) REVERT: B 104 TRP cc_start: 0.7799 (m-90) cc_final: 0.7474 (m-90) REVERT: B 200 TYR cc_start: 0.9002 (m-80) cc_final: 0.8747 (m-80) REVERT: B 985 ASP cc_start: 0.8200 (p0) cc_final: 0.7921 (p0) REVERT: B 1145 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8594 (tm) REVERT: C 402 ILE cc_start: 0.8709 (pp) cc_final: 0.8425 (pp) REVERT: C 456 PHE cc_start: 0.8611 (m-10) cc_final: 0.8309 (m-10) REVERT: C 858 LEU cc_start: 0.9204 (mp) cc_final: 0.8911 (pp) outliers start: 28 outliers final: 6 residues processed: 96 average time/residue: 0.5849 time to fit residues: 66.3358 Evaluate side-chains 79 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 907 ASN B 69 HIS C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.074291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.046549 restraints weight = 96996.156| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.45 r_work: 0.2824 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25905 Z= 0.134 Angle : 0.517 10.286 35388 Z= 0.258 Chirality : 0.043 0.241 4158 Planarity : 0.003 0.042 4476 Dihedral : 4.115 20.901 3342 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.80 % Allowed : 7.65 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.42 (0.15), residues: 3072 helix: 2.12 (0.20), residues: 694 sheet: 0.26 (0.20), residues: 669 loop : -0.47 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.014 0.001 TYR B1067 PHE 0.017 0.001 PHE B 392 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (25803) covalent geometry : angle 0.49723 / 0.25 (35124) SS BOND : bond 0.00152 / 0.10 ( 42) SS BOND : angle 0.56137 / 0.38 ( 84) hydrogen bonds : bond 0.03988 / 2.68 ( 852) hydrogen bonds : angle 5.25611 / 3.56 ( 2373) link_BETA1-4 : bond 0.00272 / 0.18 ( 18) link_BETA1-4 : angle 0.91193 / 0.62 ( 54) link_NAG-ASN : bond 0.00490 / 0.26 ( 42) link_NAG-ASN : angle 2.38556 / 2.00 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4591 (ptt) cc_final: 0.3752 (tpt) REVERT: A 1002 GLN cc_start: 0.9251 (tt0) cc_final: 0.8765 (tm-30) REVERT: A 1010 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8479 (mp10) REVERT: B 104 TRP cc_start: 0.7712 (m-90) cc_final: 0.7470 (m-90) REVERT: B 200 TYR cc_start: 0.8975 (m-80) cc_final: 0.8717 (m-80) REVERT: B 394 ASN cc_start: 0.8261 (m-40) cc_final: 0.7829 (m110) REVERT: B 985 ASP cc_start: 0.8229 (p0) cc_final: 0.7926 (p0) REVERT: B 1145 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8588 (tm) REVERT: C 378 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8428 (ttpt) REVERT: C 408 ARG cc_start: 0.9079 (tmm-80) cc_final: 0.8870 (tmm-80) REVERT: C 414 GLN cc_start: 0.9022 (mm-40) cc_final: 0.7912 (tm130) REVERT: C 456 PHE cc_start: 0.8586 (m-10) cc_final: 0.8290 (m-10) REVERT: C 858 LEU cc_start: 0.9187 (mp) cc_final: 0.8807 (pp) outliers start: 22 outliers final: 7 residues processed: 89 average time/residue: 0.6229 time to fit residues: 64.9489 Evaluate side-chains 77 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 571 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 271 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 957 GLN C 824 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.072353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.044711 restraints weight = 97815.796| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.44 r_work: 0.2764 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 25905 Z= 0.303 Angle : 0.638 9.679 35388 Z= 0.316 Chirality : 0.046 0.249 4158 Planarity : 0.004 0.043 4476 Dihedral : 4.453 21.737 3342 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.02 % Allowed : 8.23 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3072 helix: 1.88 (0.20), residues: 701 sheet: -0.12 (0.19), residues: 678 loop : -0.55 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1014 TYR 0.021 0.002 TYR C 756 PHE 0.019 0.002 PHE B 898 TRP 0.011 0.002 TRP A 886 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.30 (25803) covalent geometry : angle 0.61828 / 0.31 (35124) SS BOND : bond 0.00215 / 0.14 ( 42) SS BOND : angle 0.72674 / 0.48 ( 84) hydrogen bonds : bond 0.04684 / 3.12 ( 852) hydrogen bonds : angle 5.47044 / 3.71 ( 2373) link_BETA1-4 : bond 0.00227 / 0.12 ( 18) link_BETA1-4 : angle 1.36317 / 0.94 ( 54) link_NAG-ASN : bond 0.00669 / 0.41 ( 42) link_NAG-ASN : angle 2.58389 / 2.08 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4664 (ptt) cc_final: 0.3922 (tpt) REVERT: A 740 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8702 (tmm) REVERT: A 1002 GLN cc_start: 0.9300 (tt0) cc_final: 0.8819 (tm-30) REVERT: A 1010 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: B 104 TRP cc_start: 0.7910 (m-90) cc_final: 0.7675 (m-90) REVERT: C 456 PHE cc_start: 0.8707 (m-10) cc_final: 0.8449 (m-10) REVERT: C 1010 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8746 (mp10) outliers start: 28 outliers final: 8 residues processed: 90 average time/residue: 0.5968 time to fit residues: 63.2394 Evaluate side-chains 75 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 156 optimal weight: 0.9980 chunk 151 optimal weight: 0.4980 chunk 299 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 290 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.073865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.046249 restraints weight = 97445.977| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.55 r_work: 0.2812 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25905 Z= 0.106 Angle : 0.512 10.075 35388 Z= 0.254 Chirality : 0.043 0.244 4158 Planarity : 0.003 0.043 4476 Dihedral : 4.082 18.893 3342 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.88 % Allowed : 9.15 % Favored : 89.97 % 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: 0.41 (0.15), residues: 3072 helix: 2.26 (0.20), residues: 687 sheet: -0.04 (0.19), residues: 674 loop : -0.39 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1014 TYR 0.014 0.001 TYR B 369 PHE 0.016 0.001 PHE A 392 TRP 0.007 0.001 TRP B 436 HIS 0.003 0.000 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (25803) covalent geometry : angle 0.49413 / 0.25 (35124) SS BOND : bond 0.00133 / 0.09 ( 42) SS BOND : angle 0.53584 / 0.36 ( 84) hydrogen bonds : bond 0.03887 / 2.60 ( 852) hydrogen bonds : angle 5.13918 / 3.48 ( 2373) link_BETA1-4 : bond 0.00314 / 0.21 ( 18) link_BETA1-4 : angle 0.84006 / 0.57 ( 54) link_NAG-ASN : bond 0.00469 / 0.24 ( 42) link_NAG-ASN : angle 2.26585 / 1.89 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5013 (ptt) cc_final: 0.4143 (tpt) REVERT: A 347 PHE cc_start: 0.5498 (t80) cc_final: 0.5258 (t80) REVERT: A 740 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8785 (tmm) REVERT: A 1002 GLN cc_start: 0.9278 (tt0) cc_final: 0.8780 (tm-30) REVERT: A 1010 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: B 104 TRP cc_start: 0.7699 (m-90) cc_final: 0.7494 (m-90) REVERT: B 200 TYR cc_start: 0.8736 (m-80) cc_final: 0.8447 (m-80) REVERT: B 1145 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8601 (tm) REVERT: C 408 ARG cc_start: 0.9052 (tmm-80) cc_final: 0.8630 (tmm-80) REVERT: C 414 GLN cc_start: 0.9054 (mm-40) cc_final: 0.7954 (tm-30) REVERT: C 456 PHE cc_start: 0.8696 (m-10) cc_final: 0.8407 (m-10) REVERT: C 1010 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8706 (mp10) outliers start: 24 outliers final: 8 residues processed: 88 average time/residue: 0.6104 time to fit residues: 63.7151 Evaluate side-chains 77 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 171 optimal weight: 0.6980 chunk 257 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 302 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 63 optimal weight: 0.0070 chunk 156 optimal weight: 0.4980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN C 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.074112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046592 restraints weight = 97432.920| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.50 r_work: 0.2833 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25905 Z= 0.099 Angle : 0.502 10.248 35388 Z= 0.248 Chirality : 0.043 0.243 4158 Planarity : 0.003 0.044 4476 Dihedral : 3.919 17.949 3342 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.95 % Allowed : 9.22 % Favored : 89.83 % 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: 0.52 (0.15), residues: 3072 helix: 2.36 (0.20), residues: 690 sheet: 0.04 (0.20), residues: 664 loop : -0.34 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.016 0.001 TYR C 200 PHE 0.018 0.001 PHE A 392 TRP 0.008 0.001 TRP B 436 HIS 0.005 0.000 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (25803) covalent geometry : angle 0.48476 / 0.24 (35124) SS BOND : bond 0.00118 / 0.08 ( 42) SS BOND : angle 0.51430 / 0.35 ( 84) hydrogen bonds : bond 0.03672 / 2.45 ( 852) hydrogen bonds : angle 4.95505 / 3.36 ( 2373) link_BETA1-4 : bond 0.00296 / 0.19 ( 18) link_BETA1-4 : angle 0.87818 / 0.60 ( 54) link_NAG-ASN : bond 0.00462 / 0.24 ( 42) link_NAG-ASN : angle 2.21352 / 1.84 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4736 (ptt) cc_final: 0.4163 (tpt) REVERT: A 740 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8871 (tmm) REVERT: A 1002 GLN cc_start: 0.9229 (tt0) cc_final: 0.8760 (tm-30) REVERT: A 1010 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8409 (mp10) REVERT: B 104 TRP cc_start: 0.7678 (m-90) cc_final: 0.7459 (m-90) REVERT: B 200 TYR cc_start: 0.8731 (m-80) cc_final: 0.8428 (m-80) REVERT: B 1145 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8573 (tm) REVERT: C 408 ARG cc_start: 0.9103 (tmm-80) cc_final: 0.8886 (tmm-80) REVERT: C 414 GLN cc_start: 0.9100 (mm-40) cc_final: 0.7950 (tm130) REVERT: C 456 PHE cc_start: 0.8674 (m-10) cc_final: 0.8435 (m-10) REVERT: C 1010 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8704 (mp10) outliers start: 26 outliers final: 7 residues processed: 95 average time/residue: 0.5603 time to fit residues: 63.1244 Evaluate side-chains 79 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 18 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 281 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.073696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045972 restraints weight = 97743.825| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.61 r_work: 0.2805 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25905 Z= 0.152 Angle : 0.526 10.305 35388 Z= 0.259 Chirality : 0.044 0.334 4158 Planarity : 0.003 0.042 4476 Dihedral : 3.937 18.309 3342 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.91 % Allowed : 9.55 % Favored : 89.54 % 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: 0.51 (0.15), residues: 3072 helix: 2.29 (0.20), residues: 702 sheet: -0.06 (0.19), residues: 713 loop : -0.29 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 509 TYR 0.015 0.001 TYR B 449 PHE 0.020 0.001 PHE A 392 TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (25803) covalent geometry : angle 0.50832 / 0.26 (35124) SS BOND : bond 0.00133 / 0.09 ( 42) SS BOND : angle 0.52160 / 0.35 ( 84) hydrogen bonds : bond 0.03813 / 2.55 ( 852) hydrogen bonds : angle 5.01662 / 3.40 ( 2373) link_BETA1-4 : bond 0.00238 / 0.16 ( 18) link_BETA1-4 : angle 0.95214 / 0.65 ( 54) link_NAG-ASN : bond 0.00465 / 0.25 ( 42) link_NAG-ASN : angle 2.23093 / 1.84 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4623 (ptt) cc_final: 0.4103 (tpt) REVERT: A 740 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8772 (tmm) REVERT: A 1002 GLN cc_start: 0.9346 (tt0) cc_final: 0.8742 (tm-30) REVERT: A 1010 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: B 104 TRP cc_start: 0.7705 (m-90) cc_final: 0.7438 (m-90) REVERT: B 153 MET cc_start: 0.4023 (tmm) cc_final: 0.3760 (tmm) REVERT: B 200 TYR cc_start: 0.8740 (m-80) cc_final: 0.8469 (m-80) REVERT: C 408 ARG cc_start: 0.9076 (tmm-80) cc_final: 0.8642 (tmm-80) REVERT: C 414 GLN cc_start: 0.9034 (mm-40) cc_final: 0.7934 (tm-30) REVERT: C 456 PHE cc_start: 0.8685 (m-10) cc_final: 0.8446 (m-10) REVERT: C 1010 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8806 (mp10) outliers start: 25 outliers final: 9 residues processed: 88 average time/residue: 0.6124 time to fit residues: 63.7750 Evaluate side-chains 81 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 200 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 271 optimal weight: 0.5980 chunk 222 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 314 GLN C 580 GLN C 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.072611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.044852 restraints weight = 98791.895| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.65 r_work: 0.2768 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 25905 Z= 0.250 Angle : 0.586 10.334 35388 Z= 0.290 Chirality : 0.045 0.316 4158 Planarity : 0.004 0.042 4476 Dihedral : 4.164 20.653 3342 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.95 % Allowed : 9.59 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3072 helix: 2.19 (0.20), residues: 702 sheet: -0.18 (0.19), residues: 687 loop : -0.36 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.015 0.001 TYR B1067 PHE 0.022 0.001 PHE C 497 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 (25803) covalent geometry : angle 0.56903 / 0.29 (35124) SS BOND : bond 0.00182 / 0.12 ( 42) SS BOND : angle 0.63704 / 0.43 ( 84) hydrogen bonds : bond 0.04245 / 2.84 ( 852) hydrogen bonds : angle 5.25159 / 3.57 ( 2373) link_BETA1-4 : bond 0.00197 / 0.11 ( 18) link_BETA1-4 : angle 1.08887 / 0.74 ( 54) link_NAG-ASN : bond 0.00545 / 0.32 ( 42) link_NAG-ASN : angle 2.35007 / 1.91 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5362 (ptt) cc_final: 0.4496 (tpt) REVERT: A 740 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8742 (tmm) REVERT: A 1002 GLN cc_start: 0.9370 (tt0) cc_final: 0.8782 (tm-30) REVERT: A 1010 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: B 153 MET cc_start: 0.4124 (tmm) cc_final: 0.3858 (tmm) REVERT: B 200 TYR cc_start: 0.8754 (m-80) cc_final: 0.8521 (m-80) REVERT: C 456 PHE cc_start: 0.8719 (m-10) cc_final: 0.8485 (m-10) REVERT: C 1010 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8824 (mp10) outliers start: 26 outliers final: 10 residues processed: 89 average time/residue: 0.5765 time to fit residues: 61.5651 Evaluate side-chains 76 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 204 optimal weight: 0.9980 chunk 255 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 71 optimal weight: 0.0050 chunk 50 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 487 ASN B1005 GLN C 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.073539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045871 restraints weight = 97738.638| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.70 r_work: 0.2800 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 25905 Z= 0.128 Angle : 0.529 10.688 35388 Z= 0.261 Chirality : 0.044 0.304 4158 Planarity : 0.003 0.043 4476 Dihedral : 4.007 19.402 3342 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.62 % Allowed : 10.25 % Favored : 89.13 % 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: 3072 helix: 2.28 (0.20), residues: 702 sheet: -0.14 (0.19), residues: 693 loop : -0.32 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 983 TYR 0.015 0.001 TYR B 449 PHE 0.020 0.001 PHE A 392 TRP 0.018 0.001 TRP B 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (25803) covalent geometry : angle 0.51290 / 0.26 (35124) SS BOND : bond 0.00137 / 0.09 ( 42) SS BOND : angle 0.54362 / 0.36 ( 84) hydrogen bonds : bond 0.03846 / 2.58 ( 852) hydrogen bonds : angle 5.06393 / 3.43 ( 2373) link_BETA1-4 : bond 0.00283 / 0.19 ( 18) link_BETA1-4 : angle 0.86726 / 0.59 ( 54) link_NAG-ASN : bond 0.00448 / 0.23 ( 42) link_NAG-ASN : angle 2.21167 / 1.84 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5349 (ptt) cc_final: 0.4509 (tpt) REVERT: A 740 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8817 (tmm) REVERT: A 1002 GLN cc_start: 0.9360 (tt0) cc_final: 0.8758 (tm-30) REVERT: A 1010 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8557 (mp10) REVERT: B 153 MET cc_start: 0.4178 (tmm) cc_final: 0.3919 (tmm) REVERT: B 200 TYR cc_start: 0.8755 (m-80) cc_final: 0.8522 (m-80) REVERT: C 456 PHE cc_start: 0.8727 (m-10) cc_final: 0.8497 (m-10) REVERT: C 1010 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8781 (mp10) outliers start: 17 outliers final: 9 residues processed: 73 average time/residue: 0.5492 time to fit residues: 48.1032 Evaluate side-chains 72 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 287 optimal weight: 0.5980 chunk 268 optimal weight: 0.0870 chunk 120 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN ** C1002 GLN ** 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 = 0.3718 r_free = 0.3718 target = 0.072965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.045267 restraints weight = 97524.832| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.69 r_work: 0.2784 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 25905 Z= 0.188 Angle : 0.554 10.612 35388 Z= 0.273 Chirality : 0.044 0.301 4158 Planarity : 0.003 0.042 4476 Dihedral : 4.040 19.281 3342 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.62 % Allowed : 10.14 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3072 helix: 2.28 (0.20), residues: 702 sheet: -0.22 (0.20), residues: 676 loop : -0.35 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.014 0.001 TYR C 489 PHE 0.026 0.001 PHE C 497 TRP 0.029 0.001 TRP B 104 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (25803) covalent geometry : angle 0.53718 / 0.27 (35124) SS BOND : bond 0.00166 / 0.11 ( 42) SS BOND : angle 0.58362 / 0.38 ( 84) hydrogen bonds : bond 0.04004 / 2.68 ( 852) hydrogen bonds : angle 5.11722 / 3.47 ( 2373) link_BETA1-4 : bond 0.00185 / 0.12 ( 18) link_BETA1-4 : angle 1.00093 / 0.69 ( 54) link_NAG-ASN : bond 0.00486 / 0.27 ( 42) link_NAG-ASN : angle 2.27661 / 1.86 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7395.11 seconds wall clock time: 127 minutes 28.58 seconds (7648.58 seconds total)