Starting phenix.real_space_refine on Sun Jul 5 08:03:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ru1_24693/07_2026/7ru1_24693.cif" } resolution = 2.8 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= -0.000 sd= 0.036 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 126 5.16 5 C 16836 2.51 5 N 4359 2.21 5 O 5172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26493 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8579 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 56, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8579 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 56, 'TRANS': 1041} Chain breaks: 4 Chain: "C" Number of atoms: 8579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8579 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 56, 'TRANS': 1041} Chain breaks: 4 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: "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: "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: "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: "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: "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: "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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.84, per 1000 atoms: 0.22 Number of scatterers: 26493 At special positions: 0 Unit cell: (150.38, 144.2, 179.22, 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 126 16.00 O 5172 8.00 N 4359 7.00 C 16836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.08 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.14 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " 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=2.12 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS C 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.08 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.14 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 705 " - pdb=" SG CYS C 883 " 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=2.12 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.14 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.12 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 17 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN C 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN C1098 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 54 sheets defined 26.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.643A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.546A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.769A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.764A 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 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 1033 removed outlier: 3.958A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.643A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.545A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.769A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.958A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.643A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.546A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.769A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.764A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.947A 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 1033 removed outlier: 3.958A 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.771A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.718A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.380A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.576A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.609A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.514A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.249A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.472A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.725A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.563A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.722A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.752A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.771A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.380A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.576A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.609A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD1, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.515A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.250A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.471A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.725A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.563A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.072A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.722A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.752A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.771A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.380A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.576A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.609A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.250A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.472A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.563A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.722A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.753A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1125 hydrogen bonds defined for protein. 3060 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: 7.55 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7134 1.33 - 1.47: 8729 1.47 - 1.61: 11074 1.61 - 1.76: 24 1.76 - 1.90: 135 Bond restraints: 27096 Sorted by residual: bond pdb=" CB ILE C 312 " pdb=" CG1 ILE C 312 " ideal model delta sigma weight residual 1.530 1.414 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" CB ILE A 312 " pdb=" CG1 ILE A 312 " ideal model delta sigma weight residual 1.530 1.414 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" CB ILE B 312 " pdb=" CG1 ILE B 312 " ideal model delta sigma weight residual 1.530 1.415 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" CG LEU C 916 " pdb=" CD2 LEU C 916 " ideal model delta sigma weight residual 1.521 1.363 0.158 3.30e-02 9.18e+02 2.28e+01 bond pdb=" CG LEU A 916 " pdb=" CD2 LEU A 916 " ideal model delta sigma weight residual 1.521 1.364 0.157 3.30e-02 9.18e+02 2.27e+01 ... (remaining 27091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 36757 7.12 - 14.25: 113 14.25 - 21.37: 0 21.37 - 28.49: 0 28.49 - 35.62: 6 Bond angle restraints: 36876 Sorted by residual: angle pdb=" C2 NAG B1305 " pdb=" N2 NAG B1305 " pdb=" C7 NAG B1305 " ideal model delta sigma weight residual 124.56 160.18 -35.62 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG C1305 " pdb=" N2 NAG C1305 " pdb=" C7 NAG C1305 " ideal model delta sigma weight residual 124.56 160.18 -35.62 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG A1305 " pdb=" N2 NAG A1305 " pdb=" C7 NAG A1305 " ideal model delta sigma weight residual 124.56 160.16 -35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG E 1 " pdb=" N2 NAG E 1 " pdb=" C7 NAG E 1 " ideal model delta sigma weight residual 124.56 159.60 -35.04 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C2 NAG J 1 " pdb=" N2 NAG J 1 " pdb=" C7 NAG J 1 " ideal model delta sigma weight residual 124.56 159.59 -35.03 3.00e+00 1.11e-01 1.36e+02 ... (remaining 36871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 15186 17.84 - 35.68: 387 35.68 - 53.52: 114 53.52 - 71.36: 36 71.36 - 89.20: 21 Dihedral angle restraints: 15744 sinusoidal: 6159 harmonic: 9585 Sorted by residual: dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS C 705 " pdb=" CB CYS C 705 " ideal model delta sinusoidal sigma weight residual 93.00 140.31 -47.31 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS B 705 " pdb=" SG CYS B 705 " pdb=" SG CYS C 883 " pdb=" CB CYS C 883 " ideal model delta sinusoidal sigma weight residual 93.00 140.29 -47.29 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " pdb=" SG CYS B 883 " pdb=" CB CYS B 883 " ideal model delta sinusoidal sigma weight residual 93.00 140.27 -47.27 1 1.00e+01 1.00e-02 3.09e+01 ... (remaining 15741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2981 0.100 - 0.200: 994 0.200 - 0.300: 203 0.300 - 0.400: 97 0.400 - 0.500: 42 Chirality restraints: 4317 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 ... (remaining 4314 not shown) Planarity restraints: 4758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.067 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN B 343 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.104 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.067 2.00e-02 2.50e+03 6.81e-02 5.79e+01 pdb=" CG ASN C 343 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.103 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.067 2.00e-02 2.50e+03 6.81e-02 5.79e+01 pdb=" CG ASN A 343 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.104 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.082 2.00e-02 2.50e+03 ... (remaining 4755 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 10628 2.90 - 3.40: 23782 3.40 - 3.90: 44848 3.90 - 4.40: 52395 4.40 - 4.90: 85830 Nonbonded interactions: 217483 Sorted by model distance: nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.402 3.120 nonbonded pdb=" OE1 GLU C 340 " pdb=" NZ LYS C 356 " model vdw 2.402 3.120 nonbonded pdb=" OE1 GLU B 340 " pdb=" NZ LYS B 356 " model vdw 2.402 3.120 nonbonded pdb=" N ASP A1084 " pdb=" OD1 ASP A1084 " model vdw 2.436 3.120 nonbonded pdb=" N ASP C1084 " pdb=" OD1 ASP C1084 " model vdw 2.436 3.120 ... (remaining 217478 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: 0.08 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' } 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: 8.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.650 Find NCS groups from input model: 0.680 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: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.021 0.158 27198 Z= 1.100 Angle : 1.789 35.616 37134 Z= 1.170 Chirality : 0.117 0.500 4317 Planarity : 0.008 0.046 4716 Dihedral : 10.237 89.199 9438 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.58 (0.14), residues: 3264 helix: 0.29 (0.17), residues: 729 sheet: 1.30 (0.19), residues: 717 loop : 0.15 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 509 TYR 0.065 0.008 TYR A 837 PHE 0.033 0.005 PHE B 58 TRP 0.025 0.007 TRP A 886 HIS 0.011 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.02081 / 1.09 (27096) covalent geometry : angle 1.77931 / 1.17 (36876) SS BOND : bond 0.03770 / 1.98 ( 48) SS BOND : angle 2.39978 / 1.55 ( 96) hydrogen bonds : bond 0.18020 / 11.74 ( 1107) hydrogen bonds : angle 7.88848 / 5.45 ( 3060) link_BETA1-4 : bond 0.07180 / 4.17 ( 12) link_BETA1-4 : angle 4.71102 / 3.24 ( 36) link_NAG-ASN : bond 0.07974 / 5.23 ( 42) link_NAG-ASN : angle 2.41788 / 1.68 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.018 Fit side-chains REVERT: A 505 TYR cc_start: 0.7778 (m-80) cc_final: 0.7078 (t80) REVERT: A 740 MET cc_start: 0.8508 (mmm) cc_final: 0.8298 (mmm) REVERT: A 869 MET cc_start: 0.8716 (mtt) cc_final: 0.8420 (mtt) REVERT: B 505 TYR cc_start: 0.7981 (m-80) cc_final: 0.7214 (t80) REVERT: B 759 PHE cc_start: 0.7095 (t80) cc_final: 0.6877 (t80) REVERT: B 869 MET cc_start: 0.8744 (mtt) cc_final: 0.8540 (mtm) REVERT: C 484 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7367 (tm-30) REVERT: C 505 TYR cc_start: 0.7988 (m-80) cc_final: 0.7283 (t80) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.8445 time to fit residues: 365.0989 Evaluate side-chains 140 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 207 HIS A 388 ASN A 519 HIS A 957 GLN A1010 GLN A1074 ASN A1119 ASN B 115 GLN B 207 HIS B 519 HIS B 641 ASN B 957 GLN B1142 GLN C 115 GLN C 207 HIS C 388 ASN C 606 ASN C 641 ASN C 957 GLN C1074 ASN C1119 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.080274 restraints weight = 44812.096| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.56 r_work: 0.2918 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27198 Z= 0.176 Angle : 0.698 9.759 37134 Z= 0.369 Chirality : 0.048 0.222 4317 Planarity : 0.004 0.045 4716 Dihedral : 5.006 20.630 3537 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.40 % Allowed : 6.12 % Favored : 91.48 % 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: 0.57 (0.14), residues: 3264 helix: 1.63 (0.19), residues: 759 sheet: 1.11 (0.19), residues: 687 loop : -0.44 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 78 TYR 0.027 0.002 TYR B 495 PHE 0.019 0.002 PHE B 497 TRP 0.009 0.001 TRP A 152 HIS 0.010 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (27096) covalent geometry : angle 0.67133 / 0.36 (36876) SS BOND : bond 0.00307 / 0.20 ( 48) SS BOND : angle 1.94741 / 1.22 ( 96) hydrogen bonds : bond 0.06748 / 4.46 ( 1107) hydrogen bonds : angle 6.32376 / 4.37 ( 3060) link_BETA1-4 : bond 0.00669 / 0.37 ( 12) link_BETA1-4 : angle 2.71948 / 1.84 ( 36) link_NAG-ASN : bond 0.00564 / 0.35 ( 42) link_NAG-ASN : angle 2.56343 / 1.67 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 1.015 Fit side-chains REVERT: A 176 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8825 (tt) REVERT: A 309 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: A 505 TYR cc_start: 0.8195 (m-80) cc_final: 0.6935 (t80) REVERT: A 827 THR cc_start: 0.8485 (m) cc_final: 0.8046 (p) REVERT: A 869 MET cc_start: 0.8572 (mtt) cc_final: 0.8278 (mtp) REVERT: A 1002 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7999 (tt0) REVERT: A 1038 LYS cc_start: 0.8630 (mttm) cc_final: 0.8286 (mmtp) REVERT: A 1092 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: B 309 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: B 462 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8060 (mppt) REVERT: B 505 TYR cc_start: 0.8237 (m-80) cc_final: 0.7051 (t80) REVERT: B 646 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8209 (mmm-85) REVERT: B 1002 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7936 (tt0) REVERT: B 1038 LYS cc_start: 0.8636 (mttm) cc_final: 0.8346 (mmtp) REVERT: C 176 LEU cc_start: 0.8988 (mt) cc_final: 0.8756 (tt) REVERT: C 309 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: C 484 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7466 (tm-30) REVERT: C 505 TYR cc_start: 0.8361 (m-80) cc_final: 0.7096 (t80) REVERT: C 1002 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8097 (tt0) REVERT: C 1038 LYS cc_start: 0.8535 (mttm) cc_final: 0.8121 (mmtp) outliers start: 69 outliers final: 23 residues processed: 235 average time/residue: 0.6393 time to fit residues: 176.2681 Evaluate side-chains 162 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 219 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 259 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 957 GLN A1119 ASN A1142 GLN B 481 ASN B 519 HIS B 606 ASN B 644 GLN B1142 GLN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078821 restraints weight = 44983.978| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.55 r_work: 0.2891 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27198 Z= 0.159 Angle : 0.611 10.502 37134 Z= 0.321 Chirality : 0.046 0.237 4317 Planarity : 0.004 0.043 4716 Dihedral : 4.750 26.587 3537 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 2.19 % Allowed : 7.06 % Favored : 90.75 % 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: 0.44 (0.14), residues: 3264 helix: 1.71 (0.19), residues: 759 sheet: 0.53 (0.20), residues: 675 loop : -0.38 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.020 0.001 TYR B 495 PHE 0.015 0.002 PHE B 133 TRP 0.013 0.001 TRP B 886 HIS 0.008 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (27096) covalent geometry : angle 0.58870 / 0.32 (36876) SS BOND : bond 0.00612 / 0.34 ( 48) SS BOND : angle 1.85569 / 1.12 ( 96) hydrogen bonds : bond 0.05811 / 3.82 ( 1107) hydrogen bonds : angle 5.95740 / 4.11 ( 3060) link_BETA1-4 : bond 0.00518 / 0.29 ( 12) link_BETA1-4 : angle 1.68345 / 1.13 ( 36) link_NAG-ASN : bond 0.00439 / 0.29 ( 42) link_NAG-ASN : angle 2.26168 / 1.48 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6967 (ttt) cc_final: 0.6636 (ttp) REVERT: A 214 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7583 (mmp-170) REVERT: A 309 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 505 TYR cc_start: 0.8215 (m-80) cc_final: 0.6863 (t80) REVERT: A 827 THR cc_start: 0.8546 (m) cc_final: 0.8257 (p) REVERT: A 869 MET cc_start: 0.8611 (mtt) cc_final: 0.8300 (mtp) REVERT: A 1002 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8064 (tm-30) REVERT: A 1038 LYS cc_start: 0.8685 (mttm) cc_final: 0.8336 (mmtp) REVERT: B 309 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 505 TYR cc_start: 0.8220 (m-80) cc_final: 0.7020 (t80) REVERT: B 646 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8147 (mtp85) REVERT: B 827 THR cc_start: 0.8483 (m) cc_final: 0.8163 (p) REVERT: B 1002 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7970 (tt0) REVERT: B 1019 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.8054 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8692 (mttm) cc_final: 0.8353 (mmtp) REVERT: C 309 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: C 484 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7503 (tm-30) REVERT: C 505 TYR cc_start: 0.8319 (m-80) cc_final: 0.7108 (t80) REVERT: C 690 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: C 827 THR cc_start: 0.8498 (m) cc_final: 0.8145 (p) REVERT: C 979 ASP cc_start: 0.8136 (m-30) cc_final: 0.7849 (m-30) REVERT: C 1002 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8119 (tt0) REVERT: C 1038 LYS cc_start: 0.8649 (mttm) cc_final: 0.8249 (mmtp) outliers start: 63 outliers final: 21 residues processed: 195 average time/residue: 0.6173 time to fit residues: 142.1850 Evaluate side-chains 162 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 98 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 305 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 481 ASN A 644 GLN A 655 HIS A 957 GLN A1119 ASN A1135 ASN A1142 GLN B 125 ASN B 370 ASN B 606 ASN B 655 HIS B1135 ASN C 125 ASN C 644 GLN C 655 HIS C 957 GLN C1135 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.075359 restraints weight = 45306.969| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.53 r_work: 0.2828 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 27198 Z= 0.251 Angle : 0.672 12.155 37134 Z= 0.349 Chirality : 0.049 0.238 4317 Planarity : 0.005 0.045 4716 Dihedral : 5.034 26.297 3537 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 2.47 % Allowed : 7.33 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3264 helix: 1.53 (0.19), residues: 768 sheet: 0.42 (0.19), residues: 729 loop : -0.75 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1000 TYR 0.023 0.002 TYR B 495 PHE 0.017 0.002 PHE B 275 TRP 0.009 0.002 TRP A 886 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.25 (27096) covalent geometry : angle 0.64743 / 0.34 (36876) SS BOND : bond 0.00481 / 0.30 ( 48) SS BOND : angle 2.48964 / 1.71 ( 96) hydrogen bonds : bond 0.06453 / 4.27 ( 1107) hydrogen bonds : angle 5.98085 / 4.13 ( 3060) link_BETA1-4 : bond 0.00381 / 0.21 ( 12) link_BETA1-4 : angle 1.49182 / 1.01 ( 36) link_NAG-ASN : bond 0.00409 / 0.26 ( 42) link_NAG-ASN : angle 2.22679 / 1.48 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 151 time to evaluate : 1.072 Fit side-chains REVERT: A 177 MET cc_start: 0.7168 (ttt) cc_final: 0.6889 (ttp) REVERT: A 505 TYR cc_start: 0.8202 (m-80) cc_final: 0.6830 (t80) REVERT: A 646 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8311 (mtp85) REVERT: A 827 THR cc_start: 0.8690 (m) cc_final: 0.8428 (p) REVERT: A 1002 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7987 (tt0) REVERT: A 1038 LYS cc_start: 0.8700 (mttm) cc_final: 0.8305 (mmtp) REVERT: B 505 TYR cc_start: 0.8146 (m-80) cc_final: 0.6981 (t80) REVERT: B 646 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8164 (mtp85) REVERT: B 827 THR cc_start: 0.8548 (m) cc_final: 0.8277 (p) REVERT: B 957 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: B 1002 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7940 (tt0) REVERT: B 1019 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8049 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8676 (mttm) cc_final: 0.8299 (mmtp) REVERT: C 406 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8752 (mt-10) REVERT: C 484 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7382 (tm-30) REVERT: C 505 TYR cc_start: 0.8334 (m-80) cc_final: 0.7067 (t80) REVERT: C 646 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8447 (mtp85) REVERT: C 690 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: C 827 THR cc_start: 0.8535 (m) cc_final: 0.8223 (p) REVERT: C 979 ASP cc_start: 0.8215 (m-30) cc_final: 0.7565 (t0) REVERT: C 988 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 1002 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8089 (tt0) REVERT: C 1038 LYS cc_start: 0.8644 (mttm) cc_final: 0.8292 (mmtp) outliers start: 71 outliers final: 28 residues processed: 198 average time/residue: 0.6678 time to fit residues: 154.4718 Evaluate side-chains 168 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 15 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 481 ASN A 957 GLN A1142 GLN B 606 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.075363 restraints weight = 45726.041| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.62 r_work: 0.2821 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27198 Z= 0.220 Angle : 0.638 12.846 37134 Z= 0.331 Chirality : 0.047 0.210 4317 Planarity : 0.004 0.046 4716 Dihedral : 4.956 24.157 3537 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 2.12 % Allowed : 7.92 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3264 helix: 1.61 (0.19), residues: 768 sheet: 0.39 (0.19), residues: 699 loop : -0.84 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.019 0.002 TYR B 495 PHE 0.016 0.002 PHE B 133 TRP 0.013 0.002 TRP C 886 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (27096) covalent geometry : angle 0.61407 / 0.32 (36876) SS BOND : bond 0.00509 / 0.31 ( 48) SS BOND : angle 2.44578 / 1.72 ( 96) hydrogen bonds : bond 0.06116 / 4.05 ( 1107) hydrogen bonds : angle 5.94947 / 4.10 ( 3060) link_BETA1-4 : bond 0.00462 / 0.25 ( 12) link_BETA1-4 : angle 1.27962 / 0.86 ( 36) link_NAG-ASN : bond 0.00362 / 0.24 ( 42) link_NAG-ASN : angle 2.10401 / 1.39 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 1.307 Fit side-chains REVERT: A 309 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: A 505 TYR cc_start: 0.8130 (m-80) cc_final: 0.6800 (t80) REVERT: A 646 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8330 (mtp85) REVERT: A 979 ASP cc_start: 0.8171 (m-30) cc_final: 0.7570 (t70) REVERT: A 1002 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8039 (tt0) REVERT: A 1038 LYS cc_start: 0.8726 (mttm) cc_final: 0.8325 (mmtp) REVERT: B 309 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: B 505 TYR cc_start: 0.8206 (m-80) cc_final: 0.7001 (t80) REVERT: B 646 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8116 (mtp85) REVERT: B 827 THR cc_start: 0.8590 (m) cc_final: 0.8355 (p) REVERT: B 957 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: B 979 ASP cc_start: 0.8247 (m-30) cc_final: 0.7555 (t0) REVERT: B 1002 GLN cc_start: 0.8581 (mm-40) cc_final: 0.7943 (tt0) REVERT: B 1019 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8046 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8602 (mttm) cc_final: 0.8277 (mmtp) REVERT: B 1074 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8329 (m-40) REVERT: C 309 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: C 484 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7354 (tm-30) REVERT: C 505 TYR cc_start: 0.8342 (m-80) cc_final: 0.7027 (t80) REVERT: C 690 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: C 827 THR cc_start: 0.8531 (m) cc_final: 0.8298 (p) REVERT: C 828 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8474 (mt) REVERT: C 979 ASP cc_start: 0.8205 (m-30) cc_final: 0.7614 (t0) REVERT: C 1002 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8054 (tt0) REVERT: C 1038 LYS cc_start: 0.8660 (mttm) cc_final: 0.8305 (mmtp) outliers start: 61 outliers final: 25 residues processed: 194 average time/residue: 0.6488 time to fit residues: 148.2287 Evaluate side-chains 170 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 62 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 957 GLN A1142 GLN B 606 ASN B 784 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074478 restraints weight = 45858.993| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.61 r_work: 0.2804 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27198 Z= 0.255 Angle : 0.662 13.953 37134 Z= 0.343 Chirality : 0.048 0.196 4317 Planarity : 0.005 0.046 4716 Dihedral : 5.053 23.215 3537 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 2.33 % Allowed : 7.99 % Favored : 89.68 % 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: -0.13 (0.14), residues: 3264 helix: 1.47 (0.19), residues: 768 sheet: 0.26 (0.19), residues: 720 loop : -0.95 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.018 0.002 TYR C1067 PHE 0.017 0.002 PHE B 133 TRP 0.007 0.002 TRP A1102 HIS 0.006 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.25 (27096) covalent geometry : angle 0.63938 / 0.34 (36876) SS BOND : bond 0.00477 / 0.31 ( 48) SS BOND : angle 2.49092 / 1.70 ( 96) hydrogen bonds : bond 0.06391 / 4.23 ( 1107) hydrogen bonds : angle 5.95397 / 4.10 ( 3060) link_BETA1-4 : bond 0.00333 / 0.20 ( 12) link_BETA1-4 : angle 1.18814 / 0.81 ( 36) link_NAG-ASN : bond 0.00376 / 0.25 ( 42) link_NAG-ASN : angle 2.11389 / 1.41 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 1.141 Fit side-chains REVERT: A 309 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: A 505 TYR cc_start: 0.8163 (m-80) cc_final: 0.6779 (t80) REVERT: A 646 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8353 (mtp85) REVERT: A 979 ASP cc_start: 0.8130 (m-30) cc_final: 0.7551 (t70) REVERT: A 1002 GLN cc_start: 0.8617 (mm-40) cc_final: 0.7983 (tt0) REVERT: A 1038 LYS cc_start: 0.8772 (mttm) cc_final: 0.8380 (mmtp) REVERT: B 309 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: B 505 TYR cc_start: 0.8208 (m-80) cc_final: 0.6941 (t80) REVERT: B 516 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: B 646 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8099 (mtp85) REVERT: B 827 THR cc_start: 0.8597 (m) cc_final: 0.8372 (p) REVERT: B 957 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: B 979 ASP cc_start: 0.8310 (m-30) cc_final: 0.7621 (t0) REVERT: B 1002 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7913 (tt0) REVERT: B 1019 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8078 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8645 (mttm) cc_final: 0.8307 (mmtp) REVERT: C 309 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: C 503 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8705 (p) REVERT: C 505 TYR cc_start: 0.8351 (m-80) cc_final: 0.7048 (t80) REVERT: C 690 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: C 828 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8581 (mt) REVERT: C 979 ASP cc_start: 0.8161 (m-30) cc_final: 0.7615 (t0) REVERT: C 1002 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8057 (tt0) REVERT: C 1038 LYS cc_start: 0.8715 (mttm) cc_final: 0.8311 (mmtp) outliers start: 67 outliers final: 29 residues processed: 190 average time/residue: 0.6380 time to fit residues: 142.3519 Evaluate side-chains 169 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 300 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 804 GLN A 957 GLN A1119 ASN A1142 GLN B 606 ASN B 804 GLN B1119 ASN C 804 GLN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077674 restraints weight = 45352.097| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.52 r_work: 0.2868 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27198 Z= 0.130 Angle : 0.565 13.087 37134 Z= 0.293 Chirality : 0.045 0.191 4317 Planarity : 0.004 0.042 4716 Dihedral : 4.672 21.200 3537 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 1.18 % Allowed : 9.56 % Favored : 89.26 % 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: 0.09 (0.14), residues: 3264 helix: 1.85 (0.20), residues: 747 sheet: 0.58 (0.19), residues: 699 loop : -0.96 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 646 TYR 0.018 0.001 TYR B 904 PHE 0.013 0.001 PHE C 133 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (27096) covalent geometry : angle 0.54686 / 0.29 (36876) SS BOND : bond 0.00401 / 0.28 ( 48) SS BOND : angle 1.95999 / 1.33 ( 96) hydrogen bonds : bond 0.05147 / 3.40 ( 1107) hydrogen bonds : angle 5.72403 / 3.95 ( 3060) link_BETA1-4 : bond 0.00394 / 0.23 ( 12) link_BETA1-4 : angle 1.03149 / 0.69 ( 36) link_NAG-ASN : bond 0.00309 / 0.20 ( 42) link_NAG-ASN : angle 1.86189 / 1.21 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7506 (mmp-170) REVERT: A 309 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 505 TYR cc_start: 0.8109 (m-80) cc_final: 0.6840 (t80) REVERT: A 979 ASP cc_start: 0.8048 (m-30) cc_final: 0.7538 (t70) REVERT: A 987 PRO cc_start: 0.7839 (Cg_endo) cc_final: 0.7559 (Cg_exo) REVERT: A 1002 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8070 (tm-30) REVERT: A 1038 LYS cc_start: 0.8738 (mttm) cc_final: 0.8326 (mmtp) REVERT: A 1092 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: B 309 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: B 505 TYR cc_start: 0.8183 (m-80) cc_final: 0.6997 (t80) REVERT: B 646 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: B 957 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: B 979 ASP cc_start: 0.8243 (m-30) cc_final: 0.7611 (t0) REVERT: B 1002 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: B 1019 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8022 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8653 (mttm) cc_final: 0.8267 (mmtp) REVERT: C 309 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: C 505 TYR cc_start: 0.8314 (m-80) cc_final: 0.7020 (t80) REVERT: C 690 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: C 828 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 979 ASP cc_start: 0.8103 (m-30) cc_final: 0.7589 (t0) REVERT: C 1002 GLN cc_start: 0.8624 (mm-40) cc_final: 0.7999 (tm-30) REVERT: C 1038 LYS cc_start: 0.8710 (mttm) cc_final: 0.8280 (mmtp) outliers start: 34 outliers final: 12 residues processed: 171 average time/residue: 0.5918 time to fit residues: 120.7042 Evaluate side-chains 151 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 804 GLN A 957 GLN A1142 GLN B 606 ASN B 804 GLN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075642 restraints weight = 45783.992| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.61 r_work: 0.2825 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27198 Z= 0.201 Angle : 0.611 13.338 37134 Z= 0.316 Chirality : 0.047 0.187 4317 Planarity : 0.004 0.048 4716 Dihedral : 4.790 21.986 3537 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.63 % Allowed : 9.70 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3264 helix: 1.71 (0.19), residues: 750 sheet: 0.36 (0.19), residues: 711 loop : -0.96 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1000 TYR 0.018 0.001 TYR C1067 PHE 0.016 0.001 PHE B 133 TRP 0.006 0.001 TRP B 152 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (27096) covalent geometry : angle 0.59143 / 0.31 (36876) SS BOND : bond 0.00420 / 0.28 ( 48) SS BOND : angle 2.16314 / 1.45 ( 96) hydrogen bonds : bond 0.05755 / 3.81 ( 1107) hydrogen bonds : angle 5.73662 / 3.96 ( 3060) link_BETA1-4 : bond 0.00326 / 0.18 ( 12) link_BETA1-4 : angle 1.04126 / 0.71 ( 36) link_NAG-ASN : bond 0.00318 / 0.21 ( 42) link_NAG-ASN : angle 1.91106 / 1.26 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 1.095 Fit side-chains REVERT: A 505 TYR cc_start: 0.8146 (m-80) cc_final: 0.6843 (t80) REVERT: A 979 ASP cc_start: 0.8086 (m-30) cc_final: 0.7573 (t70) REVERT: A 1002 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8050 (tm-30) REVERT: A 1038 LYS cc_start: 0.8763 (mttm) cc_final: 0.8341 (mmtp) REVERT: B 309 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: B 505 TYR cc_start: 0.8207 (m-80) cc_final: 0.6924 (t80) REVERT: B 516 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: B 646 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8126 (mtp85) REVERT: B 957 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: B 979 ASP cc_start: 0.8311 (m-30) cc_final: 0.7673 (t0) REVERT: B 1002 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7960 (tt0) REVERT: B 1019 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8056 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8691 (mttm) cc_final: 0.8311 (mmtp) REVERT: C 309 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: C 505 TYR cc_start: 0.8359 (m-80) cc_final: 0.7063 (t80) REVERT: C 690 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: C 828 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8562 (mt) REVERT: C 979 ASP cc_start: 0.8121 (m-30) cc_final: 0.7609 (t0) REVERT: C 1002 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8021 (tm-30) REVERT: C 1038 LYS cc_start: 0.8667 (mttm) cc_final: 0.8232 (mmtp) outliers start: 47 outliers final: 26 residues processed: 171 average time/residue: 0.6045 time to fit residues: 121.6416 Evaluate side-chains 162 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 167 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 51 optimal weight: 0.8980 chunk 264 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 804 GLN A 957 GLN A1142 GLN B 606 ASN B 804 GLN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078271 restraints weight = 45415.452| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.52 r_work: 0.2882 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27198 Z= 0.123 Angle : 0.549 11.860 37134 Z= 0.284 Chirality : 0.044 0.187 4317 Planarity : 0.004 0.047 4716 Dihedral : 4.518 20.842 3537 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 1.01 % Allowed : 10.39 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3264 helix: 1.87 (0.19), residues: 753 sheet: 0.56 (0.20), residues: 678 loop : -0.95 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 646 TYR 0.019 0.001 TYR A 904 PHE 0.013 0.001 PHE C 133 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (27096) covalent geometry : angle 0.53289 / 0.28 (36876) SS BOND : bond 0.00385 / 0.26 ( 48) SS BOND : angle 1.72863 / 1.14 ( 96) hydrogen bonds : bond 0.04871 / 3.22 ( 1107) hydrogen bonds : angle 5.56277 / 3.86 ( 3060) link_BETA1-4 : bond 0.00381 / 0.22 ( 12) link_BETA1-4 : angle 0.94671 / 0.64 ( 36) link_NAG-ASN : bond 0.00293 / 0.18 ( 42) link_NAG-ASN : angle 1.75927 / 1.14 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.765 Fit side-chains REVERT: A 214 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7468 (mmp-170) REVERT: A 505 TYR cc_start: 0.8051 (m-80) cc_final: 0.6853 (t80) REVERT: A 979 ASP cc_start: 0.8104 (m-30) cc_final: 0.7610 (t70) REVERT: A 1002 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8064 (tm-30) REVERT: A 1038 LYS cc_start: 0.8737 (mttm) cc_final: 0.8339 (mmtp) REVERT: A 1092 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: B 214 ARG cc_start: 0.8188 (mmp80) cc_final: 0.7939 (tpm-80) REVERT: B 309 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: B 505 TYR cc_start: 0.8140 (m-80) cc_final: 0.6907 (t80) REVERT: B 516 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: B 646 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8121 (mtp85) REVERT: B 957 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: B 979 ASP cc_start: 0.8219 (m-30) cc_final: 0.7619 (t0) REVERT: B 1002 GLN cc_start: 0.8565 (mm-40) cc_final: 0.7944 (tt0) REVERT: B 1019 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8035 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8652 (mttm) cc_final: 0.8295 (mmtp) REVERT: C 309 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: C 505 TYR cc_start: 0.8246 (m-80) cc_final: 0.7066 (t80) REVERT: C 690 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: C 740 MET cc_start: 0.8862 (mmm) cc_final: 0.8585 (mtt) REVERT: C 979 ASP cc_start: 0.8060 (m-30) cc_final: 0.7618 (t0) REVERT: C 1002 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8010 (tm-30) REVERT: C 1038 LYS cc_start: 0.8672 (mttm) cc_final: 0.8259 (mmtp) outliers start: 29 outliers final: 16 residues processed: 170 average time/residue: 0.5545 time to fit residues: 111.6484 Evaluate side-chains 157 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 52 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 957 GLN B 606 ASN B 784 GLN B 804 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.075997 restraints weight = 44851.818| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.47 r_work: 0.2863 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27198 Z= 0.199 Angle : 0.604 12.550 37134 Z= 0.313 Chirality : 0.047 0.185 4317 Planarity : 0.005 0.047 4716 Dihedral : 4.708 21.636 3537 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.18 % Allowed : 10.50 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3264 helix: 1.74 (0.19), residues: 756 sheet: 0.34 (0.19), residues: 711 loop : -0.94 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1000 TYR 0.023 0.001 TYR A 904 PHE 0.017 0.002 PHE B 133 TRP 0.007 0.001 TRP A 886 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (27096) covalent geometry : angle 0.58729 / 0.31 (36876) SS BOND : bond 0.00418 / 0.28 ( 48) SS BOND : angle 1.98455 / 1.31 ( 96) hydrogen bonds : bond 0.05674 / 3.76 ( 1107) hydrogen bonds : angle 5.67677 / 3.92 ( 3060) link_BETA1-4 : bond 0.00324 / 0.19 ( 12) link_BETA1-4 : angle 0.97041 / 0.67 ( 36) link_NAG-ASN : bond 0.00304 / 0.20 ( 42) link_NAG-ASN : angle 1.84773 / 1.22 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.048 Fit side-chains REVERT: A 505 TYR cc_start: 0.8280 (m-80) cc_final: 0.7086 (t80) REVERT: A 979 ASP cc_start: 0.8251 (m-30) cc_final: 0.7834 (t70) REVERT: A 1002 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8266 (tm-30) REVERT: A 1038 LYS cc_start: 0.8883 (mttm) cc_final: 0.8571 (mmtp) REVERT: B 214 ARG cc_start: 0.8236 (mmp80) cc_final: 0.8013 (tpm-80) REVERT: B 505 TYR cc_start: 0.8299 (m-80) cc_final: 0.7111 (t80) REVERT: B 646 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8146 (mtp85) REVERT: B 780 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: B 957 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: B 979 ASP cc_start: 0.8386 (m-30) cc_final: 0.7862 (t0) REVERT: B 1002 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8180 (tt0) REVERT: B 1019 ARG cc_start: 0.8762 (ttp-110) cc_final: 0.8261 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8794 (mttm) cc_final: 0.8491 (mmtp) REVERT: C 505 TYR cc_start: 0.8410 (m-80) cc_final: 0.7283 (t80) REVERT: C 690 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: C 828 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8660 (mt) REVERT: C 979 ASP cc_start: 0.8285 (m-30) cc_final: 0.7910 (t0) REVERT: C 1002 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8249 (tm-30) REVERT: C 1038 LYS cc_start: 0.8802 (mttm) cc_final: 0.8474 (mmtp) outliers start: 34 outliers final: 21 residues processed: 166 average time/residue: 0.5899 time to fit residues: 116.0537 Evaluate side-chains 164 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 253 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 0.0050 chunk 215 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 957 GLN A1142 GLN B 606 ASN B 804 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.076687 restraints weight = 44660.171| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.38 r_work: 0.2905 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27198 Z= 0.125 Angle : 0.557 11.384 37134 Z= 0.290 Chirality : 0.045 0.185 4317 Planarity : 0.004 0.046 4716 Dihedral : 4.566 20.746 3537 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 1.08 % Allowed : 10.67 % Favored : 88.25 % 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: 0.06 (0.14), residues: 3264 helix: 1.84 (0.19), residues: 753 sheet: 0.54 (0.20), residues: 663 loop : -0.96 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 646 TYR 0.023 0.001 TYR A 904 PHE 0.013 0.001 PHE B 133 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (27096) covalent geometry : angle 0.54124 / 0.29 (36876) SS BOND : bond 0.00399 / 0.26 ( 48) SS BOND : angle 1.71298 / 1.11 ( 96) hydrogen bonds : bond 0.05039 / 3.33 ( 1107) hydrogen bonds : angle 5.57136 / 3.86 ( 3060) link_BETA1-4 : bond 0.00340 / 0.20 ( 12) link_BETA1-4 : angle 0.93894 / 0.64 ( 36) link_NAG-ASN : bond 0.00296 / 0.19 ( 42) link_NAG-ASN : angle 1.75962 / 1.15 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8525.20 seconds wall clock time: 161 minutes 39.22 seconds (9699.22 seconds total)