Starting phenix.real_space_refine on Fri Mar 6 00:27:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru1_24693/03_2026/7ru1_24693.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru1_24693/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ru1_24693/03_2026/7ru1_24693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru1_24693/03_2026/7ru1_24693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ru1_24693/03_2026/7ru1_24693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru1_24693/03_2026/7ru1_24693.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.96, 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: 2.42 Conformation dependent library (CDL) restraints added in 1.4 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: 1.36 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: 8.38 Time building geometry restraints manager: 3.27 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: 16272 17.84 - 35.68: 408 35.68 - 53.52: 138 53.52 - 71.36: 39 71.36 - 89.20: 21 Dihedral angle restraints: 16878 sinusoidal: 7293 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 16875 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: 0.04 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: 8.250 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: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.640 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 10.143 89.199 10572 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 covalent geometry : bond 0.02081 (27096) covalent geometry : angle 1.77931 (36876) SS BOND : bond 0.03770 ( 48) SS BOND : angle 2.39978 ( 96) hydrogen bonds : bond 0.18020 ( 1107) hydrogen bonds : angle 7.88848 ( 3060) link_BETA1-4 : bond 0.07180 ( 12) link_BETA1-4 : angle 4.71102 ( 36) link_NAG-ASN : bond 0.07974 ( 42) link_NAG-ASN : angle 2.41788 ( 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 : 1.037 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: 0.8452 time to fit residues: 363.8825 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 : 1.016 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3376 r_free = 0.3376 target = 0.100423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.080091 restraints weight = 44823.738| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.57 r_work: 0.2915 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2128 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= 0.183 Angle : 0.707 9.247 37134 Z= 0.377 Chirality : 0.048 0.216 4317 Planarity : 0.004 0.043 4716 Dihedral : 5.836 49.186 4671 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.26 % Allowed : 6.33 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3264 helix: 1.65 (0.19), residues: 759 sheet: 1.14 (0.19), residues: 687 loop : -0.41 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 78 TYR 0.027 0.002 TYR B 495 PHE 0.019 0.002 PHE B 497 TRP 0.010 0.002 TRP A 152 HIS 0.010 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00410 (27096) covalent geometry : angle 0.67779 (36876) SS BOND : bond 0.00340 ( 48) SS BOND : angle 2.24040 ( 96) hydrogen bonds : bond 0.07026 ( 1107) hydrogen bonds : angle 6.35518 ( 3060) link_BETA1-4 : bond 0.00792 ( 12) link_BETA1-4 : angle 3.00518 ( 36) link_NAG-ASN : bond 0.00650 ( 42) link_NAG-ASN : angle 2.52316 ( 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 255 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.957 Fit side-chains REVERT: A 176 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8828 (tt) REVERT: A 309 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: A 505 TYR cc_start: 0.8201 (m-80) cc_final: 0.6927 (t80) REVERT: A 827 THR cc_start: 0.8481 (m) cc_final: 0.8020 (p) REVERT: A 869 MET cc_start: 0.8577 (mtt) cc_final: 0.8278 (mtp) REVERT: A 1002 GLN cc_start: 0.8584 (mm-40) cc_final: 0.7999 (tt0) REVERT: A 1038 LYS cc_start: 0.8650 (mttm) cc_final: 0.8296 (mmtp) REVERT: A 1092 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: B 309 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: B 462 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8057 (mppt) REVERT: B 505 TYR cc_start: 0.8271 (m-80) cc_final: 0.7046 (t80) REVERT: B 646 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8217 (mmm-85) REVERT: B 1002 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7925 (tt0) REVERT: B 1038 LYS cc_start: 0.8634 (mttm) cc_final: 0.8340 (mmtp) REVERT: C 309 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: C 484 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7474 (tm-30) REVERT: C 505 TYR cc_start: 0.8354 (m-80) cc_final: 0.7096 (t80) REVERT: C 827 THR cc_start: 0.8450 (m) cc_final: 0.7949 (p) REVERT: C 1002 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8060 (tt0) REVERT: C 1038 LYS cc_start: 0.8530 (mttm) cc_final: 0.8114 (mmtp) outliers start: 65 outliers final: 24 residues processed: 234 average time/residue: 0.6413 time to fit residues: 174.7335 Evaluate side-chains 163 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 705 CYS 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 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 1029 MET 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: 6.9990 chunk 192 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 259 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 957 GLN A1119 ASN A1142 GLN B 481 ASN B 519 HIS B 606 ASN B 644 GLN B 655 HIS C 655 HIS C 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078325 restraints weight = 44970.452| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.54 r_work: 0.2883 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27198 Z= 0.167 Angle : 0.616 11.078 37134 Z= 0.324 Chirality : 0.047 0.223 4317 Planarity : 0.004 0.052 4716 Dihedral : 5.560 57.684 4671 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.33 % Rotamer: Outliers : 2.26 % Allowed : 6.95 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3264 helix: 1.74 (0.19), residues: 753 sheet: 0.53 (0.20), residues: 675 loop : -0.42 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.022 0.001 TYR B 495 PHE 0.016 0.002 PHE B 133 TRP 0.013 0.001 TRP A 886 HIS 0.009 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00385 (27096) covalent geometry : angle 0.59368 (36876) SS BOND : bond 0.00271 ( 48) SS BOND : angle 1.83872 ( 96) hydrogen bonds : bond 0.05908 ( 1107) hydrogen bonds : angle 5.96308 ( 3060) link_BETA1-4 : bond 0.00574 ( 12) link_BETA1-4 : angle 1.94122 ( 36) link_NAG-ASN : bond 0.00538 ( 42) link_NAG-ASN : angle 2.25684 ( 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 219 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 154 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6934 (ttt) cc_final: 0.6595 (ttp) REVERT: A 214 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7622 (mmp-170) REVERT: A 309 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: A 505 TYR cc_start: 0.8225 (m-80) cc_final: 0.6856 (t80) REVERT: A 827 THR cc_start: 0.8522 (m) cc_final: 0.8243 (p) REVERT: A 1002 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8062 (tm-30) REVERT: A 1038 LYS cc_start: 0.8700 (mttm) cc_final: 0.8324 (mmtp) REVERT: B 309 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 505 TYR cc_start: 0.8221 (m-80) cc_final: 0.7014 (t80) REVERT: B 646 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8147 (mtp85) REVERT: B 827 THR cc_start: 0.8503 (m) cc_final: 0.8160 (p) REVERT: B 1002 GLN cc_start: 0.8577 (mm-40) cc_final: 0.7964 (tt0) REVERT: B 1019 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8062 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8695 (mttm) cc_final: 0.8350 (mmtp) REVERT: C 309 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: C 484 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7501 (tm-30) REVERT: C 505 TYR cc_start: 0.8315 (m-80) cc_final: 0.7100 (t80) REVERT: C 646 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8337 (mpp80) REVERT: C 690 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: C 827 THR cc_start: 0.8492 (m) cc_final: 0.8129 (p) REVERT: C 979 ASP cc_start: 0.8140 (m-30) cc_final: 0.7865 (m-30) REVERT: C 1002 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8111 (tt0) REVERT: C 1038 LYS cc_start: 0.8653 (mttm) cc_final: 0.8244 (mmtp) outliers start: 65 outliers final: 21 residues processed: 196 average time/residue: 0.6132 time to fit residues: 141.0401 Evaluate side-chains 159 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 645 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 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 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 646 ARG 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: 0.9990 chunk 65 optimal weight: 4.9990 chunk 305 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B1135 ASN C 125 ASN C 644 GLN C 957 GLN C1135 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.076136 restraints weight = 45180.133| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.54 r_work: 0.2840 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27198 Z= 0.213 Angle : 0.645 12.818 37134 Z= 0.335 Chirality : 0.048 0.250 4317 Planarity : 0.004 0.044 4716 Dihedral : 5.605 55.435 4671 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 2.29 % Allowed : 7.37 % Favored : 90.34 % 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: 0.23 (0.14), residues: 3264 helix: 1.68 (0.19), residues: 750 sheet: 0.50 (0.19), residues: 723 loop : -0.66 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.023 0.002 TYR B 495 PHE 0.015 0.002 PHE A 133 TRP 0.013 0.002 TRP B 886 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00515 (27096) covalent geometry : angle 0.61942 (36876) SS BOND : bond 0.00408 ( 48) SS BOND : angle 2.49330 ( 96) hydrogen bonds : bond 0.06116 ( 1107) hydrogen bonds : angle 5.92050 ( 3060) link_BETA1-4 : bond 0.00461 ( 12) link_BETA1-4 : angle 1.69741 ( 36) link_NAG-ASN : bond 0.00439 ( 42) link_NAG-ASN : angle 2.14676 ( 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 215 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7155 (ttt) cc_final: 0.6882 (ttp) REVERT: A 214 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7636 (mmp-170) REVERT: A 505 TYR cc_start: 0.8192 (m-80) cc_final: 0.6828 (t80) REVERT: A 646 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8308 (mtp85) REVERT: A 827 THR cc_start: 0.8636 (m) cc_final: 0.8399 (p) REVERT: A 1002 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8042 (tt0) REVERT: A 1038 LYS cc_start: 0.8695 (mttm) cc_final: 0.8309 (mmtp) REVERT: B 505 TYR cc_start: 0.8147 (m-80) cc_final: 0.6986 (t80) REVERT: B 646 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8138 (mtp85) REVERT: B 827 THR cc_start: 0.8579 (m) cc_final: 0.8308 (p) REVERT: B 957 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: B 1002 GLN cc_start: 0.8591 (mm-40) cc_final: 0.7959 (tt0) REVERT: B 1019 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8025 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8680 (mttm) cc_final: 0.8334 (mmtp) REVERT: C 484 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7452 (tm-30) REVERT: C 505 TYR cc_start: 0.8350 (m-80) cc_final: 0.7089 (t80) REVERT: C 690 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: C 827 THR cc_start: 0.8529 (m) cc_final: 0.8244 (p) REVERT: C 979 ASP cc_start: 0.8195 (m-30) cc_final: 0.7555 (t0) REVERT: C 1002 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8103 (tt0) REVERT: C 1038 LYS cc_start: 0.8647 (mttm) cc_final: 0.8294 (mmtp) outliers start: 66 outliers final: 25 residues processed: 193 average time/residue: 0.6425 time to fit residues: 144.6169 Evaluate side-chains 167 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 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 1111 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 120 VAL 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 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: 3.9990 chunk 212 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3276 r_free = 0.3276 target = 0.094145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.073914 restraints weight = 45915.307| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.62 r_work: 0.2790 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 27198 Z= 0.302 Angle : 0.704 13.735 37134 Z= 0.366 Chirality : 0.050 0.216 4317 Planarity : 0.005 0.048 4716 Dihedral : 5.916 56.608 4671 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 2.19 % Allowed : 8.03 % Favored : 89.78 % 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: -0.12 (0.14), residues: 3264 helix: 1.42 (0.19), residues: 768 sheet: 0.33 (0.19), residues: 720 loop : -0.94 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1000 TYR 0.022 0.002 TYR C 495 PHE 0.019 0.002 PHE B 275 TRP 0.016 0.002 TRP C 886 HIS 0.008 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00741 (27096) covalent geometry : angle 0.67930 (36876) SS BOND : bond 0.00498 ( 48) SS BOND : angle 2.67446 ( 96) hydrogen bonds : bond 0.06834 ( 1107) hydrogen bonds : angle 6.09962 ( 3060) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 1.48468 ( 36) link_NAG-ASN : bond 0.00453 ( 42) link_NAG-ASN : angle 2.20513 ( 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 208 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 1.030 Fit side-chains REVERT: A 309 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: A 503 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 505 TYR cc_start: 0.8199 (m-80) cc_final: 0.6770 (t80) REVERT: A 646 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (mtp85) REVERT: A 979 ASP cc_start: 0.8208 (m-30) cc_final: 0.7608 (t70) REVERT: A 1002 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8016 (tt0) REVERT: A 1038 LYS cc_start: 0.8733 (mttm) cc_final: 0.8327 (mmtp) REVERT: B 309 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 505 TYR cc_start: 0.8190 (m-80) cc_final: 0.6946 (t80) REVERT: B 646 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8121 (mtp85) REVERT: B 827 THR cc_start: 0.8593 (m) cc_final: 0.8342 (p) REVERT: B 957 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: B 1038 LYS cc_start: 0.8637 (mttm) cc_final: 0.8300 (mmtp) REVERT: C 503 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8618 (p) REVERT: C 505 TYR cc_start: 0.8356 (m-80) cc_final: 0.7042 (t80) REVERT: C 690 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: C 827 THR cc_start: 0.8601 (m) cc_final: 0.8346 (p) REVERT: C 979 ASP cc_start: 0.8244 (m-30) cc_final: 0.7651 (t0) REVERT: C 1002 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8067 (tt0) REVERT: C 1038 LYS cc_start: 0.8716 (mttm) cc_final: 0.8315 (mmtp) outliers start: 63 outliers final: 27 residues processed: 190 average time/residue: 0.6550 time to fit residues: 144.4343 Evaluate side-chains 166 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 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 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 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 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 1096 VAL Chi-restraints excluded: chain C residue 1111 GLU 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: 0.9980 chunk 184 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 321 optimal weight: 0.9990 chunk 239 optimal weight: 0.9980 chunk 241 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 957 GLN A1142 GLN B 784 GLN B 804 GLN B1119 ASN C 804 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.076868 restraints weight = 45628.622| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.52 r_work: 0.2850 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27198 Z= 0.153 Angle : 0.593 13.227 37134 Z= 0.307 Chirality : 0.046 0.191 4317 Planarity : 0.004 0.042 4716 Dihedral : 5.532 54.791 4671 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 1.88 % Allowed : 8.65 % Favored : 89.47 % 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: 1.69 (0.19), residues: 750 sheet: 0.58 (0.20), residues: 669 loop : -0.93 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 78 TYR 0.017 0.001 TYR B 904 PHE 0.013 0.001 PHE C 133 TRP 0.007 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00355 (27096) covalent geometry : angle 0.57100 (36876) SS BOND : bond 0.00408 ( 48) SS BOND : angle 2.21700 ( 96) hydrogen bonds : bond 0.05528 ( 1107) hydrogen bonds : angle 5.80545 ( 3060) link_BETA1-4 : bond 0.00452 ( 12) link_BETA1-4 : angle 1.38470 ( 36) link_NAG-ASN : bond 0.00364 ( 42) link_NAG-ASN : angle 1.96842 ( 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 200 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7515 (mmp-170) REVERT: A 309 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: A 505 TYR cc_start: 0.8130 (m-80) cc_final: 0.6884 (t80) REVERT: A 979 ASP cc_start: 0.8100 (m-30) cc_final: 0.7560 (t70) REVERT: A 1002 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8067 (tm-30) REVERT: A 1038 LYS cc_start: 0.8744 (mttm) cc_final: 0.8373 (mmtp) REVERT: B 309 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: B 505 TYR cc_start: 0.8201 (m-80) cc_final: 0.7004 (t80) REVERT: B 646 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8085 (mtp85) REVERT: B 957 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: B 979 ASP cc_start: 0.8294 (m-30) cc_final: 0.7634 (t0) REVERT: B 1002 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7974 (tt0) REVERT: B 1019 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8086 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8638 (mttm) cc_final: 0.8264 (mmtp) REVERT: C 309 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: C 505 TYR cc_start: 0.8329 (m-80) cc_final: 0.7026 (t80) REVERT: C 690 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: C 979 ASP cc_start: 0.8140 (m-30) cc_final: 0.7621 (t0) REVERT: C 1002 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8086 (tm-30) REVERT: C 1038 LYS cc_start: 0.8704 (mttm) cc_final: 0.8276 (mmtp) outliers start: 54 outliers final: 20 residues processed: 188 average time/residue: 0.6439 time to fit residues: 141.4281 Evaluate side-chains 158 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 326 ILE Chi-restraints excluded: chain B residue 493 GLN 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 1096 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 646 ARG Chi-restraints excluded: chain C residue 690 GLN 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: 0.0070 chunk 199 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 300 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 804 GLN A 957 GLN A1142 GLN B 784 GLN C 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 = 0.3338 r_free = 0.3338 target = 0.098002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078277 restraints weight = 45261.063| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.52 r_work: 0.2878 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27198 Z= 0.120 Angle : 0.553 12.565 37134 Z= 0.286 Chirality : 0.044 0.186 4317 Planarity : 0.004 0.045 4716 Dihedral : 5.244 53.976 4671 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 1.39 % Allowed : 9.38 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3264 helix: 1.89 (0.20), residues: 747 sheet: 0.31 (0.19), residues: 750 loop : -0.81 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.018 0.001 TYR B 904 PHE 0.012 0.001 PHE C 133 TRP 0.007 0.001 TRP B 152 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00267 (27096) covalent geometry : angle 0.53554 (36876) SS BOND : bond 0.00431 ( 48) SS BOND : angle 1.81820 ( 96) hydrogen bonds : bond 0.04913 ( 1107) hydrogen bonds : angle 5.60235 ( 3060) link_BETA1-4 : bond 0.00443 ( 12) link_BETA1-4 : angle 1.23600 ( 36) link_NAG-ASN : bond 0.00335 ( 42) link_NAG-ASN : angle 1.81418 ( 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 183 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7648 (mmp-170) REVERT: A 309 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: A 505 TYR cc_start: 0.8105 (m-80) cc_final: 0.6855 (t80) REVERT: A 979 ASP cc_start: 0.8116 (m-30) cc_final: 0.7616 (t70) REVERT: A 1002 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8072 (tm-30) REVERT: A 1038 LYS cc_start: 0.8765 (mttm) cc_final: 0.8335 (mmtp) REVERT: A 1092 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: B 309 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: B 505 TYR cc_start: 0.8172 (m-80) cc_final: 0.6951 (t80) REVERT: B 516 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8219 (mt-10) REVERT: B 646 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8095 (mtp85) REVERT: B 780 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: B 979 ASP cc_start: 0.8218 (m-30) cc_final: 0.7606 (t0) REVERT: B 1002 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: B 1019 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8048 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8689 (mttm) cc_final: 0.8320 (mmtp) REVERT: B 1074 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8307 (m-40) REVERT: C 309 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: C 406 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8850 (mt-10) REVERT: C 505 TYR cc_start: 0.8337 (m-80) cc_final: 0.7077 (t80) REVERT: C 646 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8297 (mpp80) REVERT: C 690 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: C 740 MET cc_start: 0.8873 (mmm) cc_final: 0.8591 (mtt) REVERT: C 979 ASP cc_start: 0.8102 (m-30) cc_final: 0.7627 (t0) REVERT: C 1002 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8022 (tm-30) REVERT: C 1038 LYS cc_start: 0.8718 (mttm) cc_final: 0.8303 (mmtp) REVERT: C 1092 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7953 (pm20) outliers start: 40 outliers final: 14 residues processed: 174 average time/residue: 0.6091 time to fit residues: 123.9407 Evaluate side-chains 160 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 516 GLU 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 1002 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 C residue 309 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 1092 GLU 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: 5.9990 chunk 55 optimal weight: 0.0470 chunk 310 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 804 GLN A 957 GLN A1142 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 = 0.3284 r_free = 0.3284 target = 0.094597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.074452 restraints weight = 46030.203| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.61 r_work: 0.2801 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 27198 Z= 0.273 Angle : 0.663 13.671 37134 Z= 0.343 Chirality : 0.049 0.189 4317 Planarity : 0.005 0.049 4716 Dihedral : 5.694 56.927 4671 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 1.63 % Allowed : 9.35 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3264 helix: 1.58 (0.19), residues: 768 sheet: 0.13 (0.19), residues: 747 loop : -0.99 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 403 TYR 0.018 0.002 TYR C 495 PHE 0.018 0.002 PHE B 133 TRP 0.010 0.002 TRP B 886 HIS 0.008 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00671 (27096) covalent geometry : angle 0.64312 (36876) SS BOND : bond 0.00475 ( 48) SS BOND : angle 2.31528 ( 96) hydrogen bonds : bond 0.06359 ( 1107) hydrogen bonds : angle 5.88052 ( 3060) link_BETA1-4 : bond 0.00369 ( 12) link_BETA1-4 : angle 1.25834 ( 36) link_NAG-ASN : bond 0.00386 ( 42) link_NAG-ASN : angle 2.01177 ( 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 189 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.813 Fit side-chains REVERT: A 503 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 505 TYR cc_start: 0.8139 (m-80) cc_final: 0.6776 (t80) REVERT: A 979 ASP cc_start: 0.8089 (m-30) cc_final: 0.7573 (t70) REVERT: A 1002 GLN cc_start: 0.8618 (mm-40) cc_final: 0.7982 (tt0) REVERT: A 1038 LYS cc_start: 0.8771 (mttm) cc_final: 0.8366 (mmtp) REVERT: B 505 TYR cc_start: 0.8164 (m-80) cc_final: 0.6849 (t80) REVERT: B 516 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: B 646 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8134 (mtp85) REVERT: B 957 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: B 964 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8063 (tptp) REVERT: B 979 ASP cc_start: 0.8332 (m-30) cc_final: 0.7683 (t0) REVERT: B 1002 GLN cc_start: 0.8581 (mm-40) cc_final: 0.7923 (tt0) REVERT: B 1038 LYS cc_start: 0.8690 (mttm) cc_final: 0.8309 (mmtp) REVERT: C 503 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8702 (p) REVERT: C 505 TYR cc_start: 0.8334 (m-80) cc_final: 0.7038 (t80) REVERT: C 690 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: C 740 MET cc_start: 0.8858 (mmm) cc_final: 0.8603 (mtt) REVERT: C 979 ASP cc_start: 0.8213 (m-30) cc_final: 0.7701 (t0) REVERT: C 1002 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8079 (tt0) REVERT: C 1038 LYS cc_start: 0.8687 (mttm) cc_final: 0.8244 (mmtp) outliers start: 47 outliers final: 27 residues processed: 173 average time/residue: 0.6488 time to fit residues: 130.7036 Evaluate side-chains 166 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 176 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU 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 957 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 503 VAL 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 724 THR 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: 0.9990 chunk 196 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 264 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 804 GLN A 957 GLN A1142 GLN B 804 GLN C 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 = 0.3337 r_free = 0.3337 target = 0.097132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077588 restraints weight = 44925.960| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.39 r_work: 0.2892 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27198 Z= 0.133 Angle : 0.571 12.278 37134 Z= 0.297 Chirality : 0.045 0.186 4317 Planarity : 0.004 0.046 4716 Dihedral : 5.389 54.771 4671 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.15 % Allowed : 10.11 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3264 helix: 1.84 (0.20), residues: 747 sheet: 0.39 (0.19), residues: 714 loop : -0.96 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.022 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 A 519 Details of bonding type rmsd covalent geometry : bond 0.00301 (27096) covalent geometry : angle 0.55408 (36876) SS BOND : bond 0.00386 ( 48) SS BOND : angle 1.81941 ( 96) hydrogen bonds : bond 0.05216 ( 1107) hydrogen bonds : angle 5.66546 ( 3060) link_BETA1-4 : bond 0.00417 ( 12) link_BETA1-4 : angle 1.17792 ( 36) link_NAG-ASN : bond 0.00339 ( 42) link_NAG-ASN : angle 1.85482 ( 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 171 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.037 Fit side-chains REVERT: A 214 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7554 (mmp-170) REVERT: A 505 TYR cc_start: 0.8200 (m-80) cc_final: 0.7123 (t80) REVERT: A 979 ASP cc_start: 0.8236 (m-30) cc_final: 0.7824 (t70) REVERT: A 1002 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8257 (tm-30) REVERT: A 1038 LYS cc_start: 0.8848 (mttm) cc_final: 0.8547 (mmtp) REVERT: B 505 TYR cc_start: 0.8291 (m-80) cc_final: 0.7132 (t80) REVERT: B 646 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8093 (mtp85) REVERT: B 979 ASP cc_start: 0.8337 (m-30) cc_final: 0.7813 (t0) REVERT: B 1002 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8187 (tt0) REVERT: B 1019 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8103 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8746 (mttm) cc_final: 0.8468 (mmtp) REVERT: C 505 TYR cc_start: 0.8433 (m-80) cc_final: 0.7277 (t80) REVERT: C 646 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8267 (mpp80) REVERT: C 690 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: C 740 MET cc_start: 0.8980 (mmm) cc_final: 0.8722 (mtt) REVERT: C 979 ASP cc_start: 0.8255 (m-30) cc_final: 0.7892 (t0) REVERT: C 1002 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8266 (tm-30) REVERT: C 1038 LYS cc_start: 0.8790 (mttm) cc_final: 0.8468 (mmtp) outliers start: 33 outliers final: 17 residues processed: 162 average time/residue: 0.6001 time to fit residues: 114.8804 Evaluate side-chains 152 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 1128 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 646 ARG 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: 4.9990 chunk 261 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 957 GLN C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077092 restraints weight = 44849.320| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.39 r_work: 0.2885 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27198 Z= 0.162 Angle : 0.579 11.915 37134 Z= 0.301 Chirality : 0.046 0.186 4317 Planarity : 0.004 0.046 4716 Dihedral : 5.390 55.198 4671 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.01 % Allowed : 10.29 % Favored : 88.70 % 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: 1.79 (0.19), residues: 753 sheet: 0.46 (0.19), residues: 696 loop : -0.97 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.023 0.001 TYR A 904 PHE 0.015 0.001 PHE B 133 TRP 0.006 0.001 TRP B 152 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00384 (27096) covalent geometry : angle 0.56177 (36876) SS BOND : bond 0.00401 ( 48) SS BOND : angle 1.89584 ( 96) hydrogen bonds : bond 0.05357 ( 1107) hydrogen bonds : angle 5.63759 ( 3060) link_BETA1-4 : bond 0.00399 ( 12) link_BETA1-4 : angle 1.14028 ( 36) link_NAG-ASN : bond 0.00329 ( 42) link_NAG-ASN : angle 1.83541 ( 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 167 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.960 Fit side-chains REVERT: A 505 TYR cc_start: 0.8275 (m-80) cc_final: 0.7127 (t80) REVERT: A 979 ASP cc_start: 0.8231 (m-30) cc_final: 0.7828 (t70) REVERT: A 1002 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8263 (tm-30) REVERT: A 1038 LYS cc_start: 0.8835 (mttm) cc_final: 0.8528 (mmtp) REVERT: B 505 TYR cc_start: 0.8272 (m-80) cc_final: 0.7102 (t80) REVERT: B 646 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8113 (mtp85) REVERT: B 964 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8179 (tptp) REVERT: B 979 ASP cc_start: 0.8334 (m-30) cc_final: 0.7809 (t0) REVERT: B 1002 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8187 (tt0) REVERT: B 1019 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8098 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8742 (mttm) cc_final: 0.8506 (mmtp) REVERT: C 505 TYR cc_start: 0.8383 (m-80) cc_final: 0.7270 (t80) REVERT: C 690 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: C 979 ASP cc_start: 0.8266 (m-30) cc_final: 0.7889 (t0) REVERT: C 1002 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8262 (tm-30) REVERT: C 1038 LYS cc_start: 0.8795 (mttm) cc_final: 0.8472 (mmtp) outliers start: 29 outliers final: 21 residues processed: 160 average time/residue: 0.5974 time to fit residues: 112.3490 Evaluate side-chains 158 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1128 VAL 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 964 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 646 ARG 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 253 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 89 optimal weight: 0.0670 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 215 optimal weight: 0.2980 chunk 266 optimal weight: 0.3980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 957 GLN A1142 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.078452 restraints weight = 44611.877| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.38 r_work: 0.2930 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27198 Z= 0.106 Angle : 0.529 10.609 37134 Z= 0.275 Chirality : 0.044 0.187 4317 Planarity : 0.004 0.045 4716 Dihedral : 5.104 53.578 4671 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 0.76 % Allowed : 10.53 % Favored : 88.70 % 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: 0.17 (0.14), residues: 3264 helix: 1.97 (0.20), residues: 753 sheet: 0.56 (0.20), residues: 666 loop : -0.88 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.022 0.001 TYR A 904 PHE 0.013 0.001 PHE C 133 TRP 0.007 0.001 TRP B 152 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00224 (27096) covalent geometry : angle 0.51400 (36876) SS BOND : bond 0.00384 ( 48) SS BOND : angle 1.51582 ( 96) hydrogen bonds : bond 0.04517 ( 1107) hydrogen bonds : angle 5.44181 ( 3060) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 1.03759 ( 36) link_NAG-ASN : bond 0.00319 ( 42) link_NAG-ASN : angle 1.71909 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7888.35 seconds wall clock time: 135 minutes 8.39 seconds (8108.39 seconds total)