Starting phenix.real_space_refine on Sat Jul 4 19:48:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dlz_27521/07_2026/8dlz_27521.cif" } resolution = 2.57 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= 0.022 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 100 5.16 5 C 14605 2.51 5 N 3756 2.21 5 O 4513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22974 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6549 Classifications: {'peptide': 840} Link IDs: {'PTRANS': 45, 'TRANS': 794} Chain breaks: 8 Chain: "B" Number of atoms: 6572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6572 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 45, 'TRANS': 797} Chain breaks: 8 Chain: "C" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.42, per 1000 atoms: 0.24 Number of scatterers: 22974 At special positions: 0 Unit cell: (140, 146, 183, 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 100 16.00 O 4513 8.00 N 3756 7.00 C 14605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5322 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 36 sheets defined 25.4% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.085A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.675A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.955A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.040A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.542A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.965A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.582A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.510A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.909A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.972A 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 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.844A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.532A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.075A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.308A 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 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.882A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.652A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.948A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.552A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.330A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.550A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.409A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.504A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.019A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 11.330A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.692A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.182A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.050A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.817A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.834A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.293A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.730A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB4, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 5.994A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.133A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.569A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.756A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.595A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.631A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.885A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.347A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC5, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 6.346A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.004A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.481A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.172A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.610A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.279A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.863A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.201A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.59 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7019 1.34 - 1.46: 5741 1.46 - 1.58: 10580 1.58 - 1.71: 2 1.71 - 1.83: 130 Bond restraints: 23472 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.528 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1 NAG C1304 " pdb=" C2 NAG C1304 " ideal model delta sigma weight residual 1.532 1.591 -0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.26e+00 ... (remaining 23467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 30949 2.15 - 4.31: 902 4.31 - 6.46: 71 6.46 - 8.62: 18 8.62 - 10.77: 5 Bond angle restraints: 31945 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.66 -5.96 1.22e+00 6.72e-01 2.39e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.24 -5.54 1.22e+00 6.72e-01 2.06e+01 angle pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 112.00 105.76 6.24 1.40e+00 5.10e-01 1.99e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.93 -5.23 1.22e+00 6.72e-01 1.83e+01 angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 119.36 -6.76 1.70e+00 3.46e-01 1.58e+01 ... (remaining 31940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12473 17.88 - 35.77: 862 35.77 - 53.65: 131 53.65 - 71.53: 51 71.53 - 89.41: 26 Dihedral angle restraints: 13543 sinusoidal: 5290 harmonic: 8253 Sorted by residual: dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 129.87 -36.87 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA VAL C 483 " pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 13540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2953 0.063 - 0.126: 747 0.126 - 0.189: 101 0.189 - 0.252: 15 0.252 - 0.314: 3 Chirality restraints: 3819 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3816 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.044 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO H 14 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C MET C 902 " 0.040 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 551 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C VAL C 551 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL C 551 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 552 " 0.013 2.00e-02 2.50e+03 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6431 2.82 - 3.34: 19506 3.34 - 3.86: 39344 3.86 - 4.38: 45075 4.38 - 4.90: 77310 Nonbonded interactions: 187666 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.309 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.332 3.040 ... (remaining 187661 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 330 or resid 531 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.890 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 23564 Z= 0.243 Angle : 0.859 15.231 32186 Z= 0.451 Chirality : 0.056 0.314 3819 Planarity : 0.006 0.064 4055 Dihedral : 13.330 89.414 8116 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 2788 helix: 1.24 (0.19), residues: 603 sheet: 0.31 (0.19), residues: 670 loop : -0.82 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 19 TYR 0.033 0.002 TYR C1067 PHE 0.034 0.002 PHE A 275 TRP 0.030 0.002 TRP A 886 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (23472) covalent geometry : angle 0.82946 / 0.45 (31945) SS BOND : bond 0.00266 / 0.16 ( 35) SS BOND : angle 1.36632 / 0.81 ( 70) hydrogen bonds : bond 0.12842 / 8.56 ( 870) hydrogen bonds : angle 7.00932 / 4.95 ( 2415) link_BETA1-4 : bond 0.00648 / 0.39 ( 18) link_BETA1-4 : angle 1.22406 / 0.81 ( 54) link_NAG-ASN : bond 0.00762 / 0.55 ( 39) link_NAG-ASN : angle 3.65038 / 2.43 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.5413 (p90) cc_final: 0.5038 (p90) REVERT: A 541 PHE cc_start: 0.7652 (p90) cc_final: 0.7374 (p90) REVERT: A 985 ASP cc_start: 0.7780 (m-30) cc_final: 0.7393 (m-30) REVERT: A 1029 MET cc_start: 0.9340 (tpp) cc_final: 0.9062 (tpp) REVERT: B 129 LYS cc_start: 0.6367 (mtmt) cc_final: 0.6126 (tppp) REVERT: B 153 MET cc_start: 0.5560 (mpp) cc_final: 0.4993 (pp-130) REVERT: B 201 PHE cc_start: 0.7093 (t80) cc_final: 0.6729 (t80) REVERT: B 207 HIS cc_start: 0.6566 (t-170) cc_final: 0.5705 (t-170) REVERT: B 327 VAL cc_start: 0.8520 (t) cc_final: 0.8246 (m) REVERT: B 858 LEU cc_start: 0.8449 (mt) cc_final: 0.7859 (pt) REVERT: B 900 MET cc_start: 0.8616 (mtp) cc_final: 0.8401 (ttm) REVERT: C 30 ASN cc_start: 0.7538 (t0) cc_final: 0.7202 (t0) REVERT: C 54 LEU cc_start: 0.8734 (mm) cc_final: 0.8226 (mt) REVERT: C 104 TRP cc_start: 0.7491 (m-90) cc_final: 0.7280 (m-90) REVERT: C 133 PHE cc_start: 0.6047 (m-80) cc_final: 0.5396 (m-80) REVERT: C 207 HIS cc_start: 0.7147 (m-70) cc_final: 0.6541 (t-90) REVERT: C 334 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7049 (p0) REVERT: C 378 LYS cc_start: 0.8778 (mttm) cc_final: 0.8568 (mttp) REVERT: C 396 TYR cc_start: 0.6994 (m-80) cc_final: 0.5138 (m-10) REVERT: C 403 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7357 (ptt-90) REVERT: C 424 LYS cc_start: 0.8762 (tptt) cc_final: 0.8532 (tptt) REVERT: C 433 VAL cc_start: 0.8709 (t) cc_final: 0.8390 (m) REVERT: C 532 ASN cc_start: 0.8530 (t0) cc_final: 0.8250 (p0) REVERT: C 987 PRO cc_start: 0.7958 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: C 988 GLU cc_start: 0.8083 (mp0) cc_final: 0.7657 (mp0) REVERT: C 1002 GLN cc_start: 0.8456 (tt0) cc_final: 0.8211 (tt0) outliers start: 3 outliers final: 0 residues processed: 297 average time/residue: 0.6197 time to fit residues: 212.1037 Evaluate side-chains 139 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 955 ASN A1011 GLN B 762 GLN B 779 GLN B 901 GLN B 978 ASN C 49 HIS C 121 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN H 35 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.127007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077285 restraints weight = 46251.185| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.83 r_work: 0.3103 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 23564 Z= 0.182 Angle : 0.624 11.747 32186 Z= 0.308 Chirality : 0.046 0.256 3819 Planarity : 0.005 0.052 4055 Dihedral : 4.578 43.194 3030 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.29 % Allowed : 6.83 % Favored : 91.88 % 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: 0.28 (0.15), residues: 2788 helix: 2.05 (0.20), residues: 624 sheet: 0.29 (0.20), residues: 624 loop : -0.64 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 983 TYR 0.021 0.001 TYR B 28 PHE 0.021 0.001 PHE A 133 TRP 0.017 0.001 TRP A 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (23472) covalent geometry : angle 0.58705 / 0.30 (31945) SS BOND : bond 0.00881 / 0.51 ( 35) SS BOND : angle 1.49829 / 1.16 ( 70) hydrogen bonds : bond 0.04649 / 3.06 ( 870) hydrogen bonds : angle 5.81184 / 4.05 ( 2415) link_BETA1-4 : bond 0.00237 / 0.13 ( 18) link_BETA1-4 : angle 1.06796 / 0.72 ( 54) link_NAG-ASN : bond 0.00863 / 0.54 ( 39) link_NAG-ASN : angle 3.36364 / 2.40 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8758 (tt0) cc_final: 0.8051 (tm-30) REVERT: B 102 ARG cc_start: 0.6852 (mmp-170) cc_final: 0.6527 (mmp-170) REVERT: B 118 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6578 (mp) REVERT: B 129 LYS cc_start: 0.6195 (mtmt) cc_final: 0.5901 (ttmt) REVERT: B 153 MET cc_start: 0.5489 (mpp) cc_final: 0.4887 (pp-130) REVERT: B 201 PHE cc_start: 0.7343 (t80) cc_final: 0.6777 (t80) REVERT: B 239 GLN cc_start: 0.6896 (tt0) cc_final: 0.6424 (tm-30) REVERT: B 269 TYR cc_start: 0.8381 (m-80) cc_final: 0.8088 (m-80) REVERT: B 327 VAL cc_start: 0.8108 (t) cc_final: 0.7736 (m) REVERT: B 858 LEU cc_start: 0.8768 (mt) cc_final: 0.7903 (pt) REVERT: B 900 MET cc_start: 0.9174 (mtp) cc_final: 0.8925 (ttm) REVERT: B 957 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8328 (pp30) REVERT: C 30 ASN cc_start: 0.7663 (t0) cc_final: 0.7152 (t0) REVERT: C 64 TRP cc_start: 0.7689 (t60) cc_final: 0.7380 (t60) REVERT: C 207 HIS cc_start: 0.7415 (m-70) cc_final: 0.6521 (t-90) REVERT: C 334 ASN cc_start: 0.7477 (OUTLIER) cc_final: 0.7090 (p0) REVERT: C 378 LYS cc_start: 0.8461 (mttm) cc_final: 0.8237 (mttp) REVERT: C 408 ARG cc_start: 0.8447 (ppt170) cc_final: 0.7991 (ptm-80) REVERT: C 424 LYS cc_start: 0.8490 (tptt) cc_final: 0.8208 (tptt) REVERT: C 433 VAL cc_start: 0.8357 (t) cc_final: 0.8060 (m) REVERT: C 532 ASN cc_start: 0.8908 (t0) cc_final: 0.8240 (p0) REVERT: C 990 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 1002 GLN cc_start: 0.8984 (tt0) cc_final: 0.8740 (tt0) outliers start: 32 outliers final: 10 residues processed: 176 average time/residue: 0.5864 time to fit residues: 120.5835 Evaluate side-chains 142 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain H residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 38 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 239 optimal weight: 0.2980 chunk 147 optimal weight: 0.0060 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 281 optimal weight: 6.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A1005 GLN B1010 GLN C 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.127015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.077862 restraints weight = 46272.989| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.79 r_work: 0.3122 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23564 Z= 0.118 Angle : 0.560 10.356 32186 Z= 0.275 Chirality : 0.044 0.254 3819 Planarity : 0.004 0.040 4055 Dihedral : 4.300 39.995 3030 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.45 % Allowed : 7.79 % Favored : 90.76 % 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: 0.50 (0.15), residues: 2788 helix: 2.44 (0.21), residues: 622 sheet: 0.26 (0.20), residues: 602 loop : -0.50 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.023 0.001 TYR B 28 PHE 0.023 0.001 PHE C 168 TRP 0.012 0.001 TRP B 104 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (23472) covalent geometry : angle 0.52761 / 0.27 (31945) SS BOND : bond 0.00299 / 0.23 ( 35) SS BOND : angle 1.31198 / 1.18 ( 70) hydrogen bonds : bond 0.04049 / 2.67 ( 870) hydrogen bonds : angle 5.43858 / 3.79 ( 2415) link_BETA1-4 : bond 0.00354 / 0.22 ( 18) link_BETA1-4 : angle 0.91671 / 0.61 ( 54) link_NAG-ASN : bond 0.00703 / 0.48 ( 39) link_NAG-ASN : angle 2.99214 / 2.13 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.5893 (p90) cc_final: 0.5474 (p90) REVERT: A 298 GLU cc_start: 0.8772 (tt0) cc_final: 0.8024 (tm-30) REVERT: B 118 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6503 (mp) REVERT: B 129 LYS cc_start: 0.6193 (mtmt) cc_final: 0.5914 (ttmt) REVERT: B 153 MET cc_start: 0.5216 (mpp) cc_final: 0.4713 (pp-130) REVERT: B 201 PHE cc_start: 0.7278 (t80) cc_final: 0.6773 (t80) REVERT: B 327 VAL cc_start: 0.8006 (t) cc_final: 0.7591 (m) REVERT: B 554 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7951 (mm-30) REVERT: B 858 LEU cc_start: 0.8906 (mt) cc_final: 0.8062 (pt) REVERT: B 957 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8311 (pp30) REVERT: B 964 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8743 (mmmm) REVERT: C 30 ASN cc_start: 0.7658 (t0) cc_final: 0.7157 (t0) REVERT: C 64 TRP cc_start: 0.7685 (t60) cc_final: 0.7441 (t60) REVERT: C 334 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.7060 (p0) REVERT: C 378 LYS cc_start: 0.8516 (mttm) cc_final: 0.8294 (mttp) REVERT: C 408 ARG cc_start: 0.8387 (ppt170) cc_final: 0.7898 (ptm-80) REVERT: C 433 VAL cc_start: 0.8324 (t) cc_final: 0.8032 (m) REVERT: C 455 LEU cc_start: 0.8459 (tp) cc_final: 0.8063 (pp) REVERT: C 532 ASN cc_start: 0.8919 (t0) cc_final: 0.8257 (p0) REVERT: C 981 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 990 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7502 (tm-30) REVERT: C 1002 GLN cc_start: 0.8932 (tt0) cc_final: 0.8710 (tt0) outliers start: 36 outliers final: 10 residues processed: 177 average time/residue: 0.5418 time to fit residues: 113.2418 Evaluate side-chains 144 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 193 optimal weight: 3.9990 chunk 249 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 185 optimal weight: 0.0570 chunk 203 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B1010 GLN C 196 ASN C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.126842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.077661 restraints weight = 46295.779| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.78 r_work: 0.3118 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23564 Z= 0.118 Angle : 0.548 10.281 32186 Z= 0.268 Chirality : 0.044 0.255 3819 Planarity : 0.003 0.037 4055 Dihedral : 4.176 38.015 3030 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.45 % Allowed : 8.76 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2788 helix: 2.60 (0.21), residues: 617 sheet: 0.27 (0.20), residues: 619 loop : -0.48 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.026 0.001 TYR B 28 PHE 0.024 0.001 PHE C 168 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23472) covalent geometry : angle 0.51681 / 0.26 (31945) SS BOND : bond 0.00365 / 0.28 ( 35) SS BOND : angle 1.39927 / 1.30 ( 70) hydrogen bonds : bond 0.03861 / 2.52 ( 870) hydrogen bonds : angle 5.27635 / 3.68 ( 2415) link_BETA1-4 : bond 0.00328 / 0.20 ( 18) link_BETA1-4 : angle 0.92399 / 0.62 ( 54) link_NAG-ASN : bond 0.00634 / 0.44 ( 39) link_NAG-ASN : angle 2.87534 / 2.03 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.5733 (p90) cc_final: 0.5411 (p90) REVERT: A 298 GLU cc_start: 0.8776 (tt0) cc_final: 0.8027 (tm-30) REVERT: A 643 PHE cc_start: 0.7563 (t80) cc_final: 0.7348 (t80) REVERT: A 856 ASN cc_start: 0.6803 (OUTLIER) cc_final: 0.6462 (m110) REVERT: B 102 ARG cc_start: 0.6436 (mmp-170) cc_final: 0.6198 (mmp-170) REVERT: B 118 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6465 (mp) REVERT: B 129 LYS cc_start: 0.6219 (mtmt) cc_final: 0.5934 (ttmt) REVERT: B 153 MET cc_start: 0.5232 (mpp) cc_final: 0.4699 (pp-130) REVERT: B 201 PHE cc_start: 0.7361 (t80) cc_final: 0.6929 (t80) REVERT: B 239 GLN cc_start: 0.7273 (tt0) cc_final: 0.6347 (tm-30) REVERT: B 269 TYR cc_start: 0.8089 (m-80) cc_final: 0.7852 (m-10) REVERT: B 327 VAL cc_start: 0.8020 (t) cc_final: 0.7605 (m) REVERT: B 554 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7902 (mm-30) REVERT: B 740 MET cc_start: 0.8829 (ttt) cc_final: 0.8506 (ttm) REVERT: B 858 LEU cc_start: 0.8964 (mt) cc_final: 0.8027 (pt) REVERT: B 957 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8277 (pp30) REVERT: B 964 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8735 (mmmm) REVERT: C 30 ASN cc_start: 0.7643 (t0) cc_final: 0.7148 (t0) REVERT: C 64 TRP cc_start: 0.7669 (t60) cc_final: 0.7416 (t60) REVERT: C 227 VAL cc_start: 0.8866 (t) cc_final: 0.8664 (m) REVERT: C 334 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.6961 (p0) REVERT: C 378 LYS cc_start: 0.8507 (mttm) cc_final: 0.8275 (mttp) REVERT: C 408 ARG cc_start: 0.8347 (ppt170) cc_final: 0.7973 (ptm-80) REVERT: C 433 VAL cc_start: 0.8318 (t) cc_final: 0.8030 (m) REVERT: C 455 LEU cc_start: 0.8442 (tp) cc_final: 0.8040 (pp) REVERT: C 532 ASN cc_start: 0.8922 (t0) cc_final: 0.8263 (OUTLIER) REVERT: C 990 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 1002 GLN cc_start: 0.8958 (tt0) cc_final: 0.8718 (tt0) REVERT: C 1010 GLN cc_start: 0.8947 (tp40) cc_final: 0.8674 (mp10) REVERT: H 32 TYR cc_start: 0.3935 (p90) cc_final: 0.3233 (p90) outliers start: 36 outliers final: 13 residues processed: 176 average time/residue: 0.5152 time to fit residues: 108.0870 Evaluate side-chains 149 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 221 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B 188 ASN B 755 GLN B 824 ASN B1010 GLN C 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.125354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075466 restraints weight = 46268.455| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.83 r_work: 0.3079 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23564 Z= 0.164 Angle : 0.572 10.765 32186 Z= 0.277 Chirality : 0.045 0.264 3819 Planarity : 0.004 0.036 4055 Dihedral : 4.208 36.622 3030 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.69 % Allowed : 9.36 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 2788 helix: 2.63 (0.21), residues: 618 sheet: 0.16 (0.20), residues: 593 loop : -0.52 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.023 0.001 TYR B 28 PHE 0.024 0.001 PHE C 168 TRP 0.013 0.001 TRP H 47 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (23472) covalent geometry : angle 0.54233 / 0.27 (31945) SS BOND : bond 0.00324 / 0.25 ( 35) SS BOND : angle 1.09936 / 0.97 ( 70) hydrogen bonds : bond 0.04123 / 2.68 ( 870) hydrogen bonds : angle 5.24733 / 3.67 ( 2415) link_BETA1-4 : bond 0.00246 / 0.14 ( 18) link_BETA1-4 : angle 0.98468 / 0.65 ( 54) link_NAG-ASN : bond 0.00619 / 0.43 ( 39) link_NAG-ASN : angle 2.89609 / 2.03 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6636 (tt) REVERT: A 298 GLU cc_start: 0.8758 (tt0) cc_final: 0.8085 (tm-30) REVERT: A 643 PHE cc_start: 0.7638 (t80) cc_final: 0.7413 (t80) REVERT: A 856 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.6452 (m110) REVERT: B 102 ARG cc_start: 0.6467 (mmp-170) cc_final: 0.6244 (mmp-170) REVERT: B 118 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6423 (mp) REVERT: B 129 LYS cc_start: 0.6179 (mtmt) cc_final: 0.5901 (ttmt) REVERT: B 153 MET cc_start: 0.5271 (mpp) cc_final: 0.4645 (pp-130) REVERT: B 201 PHE cc_start: 0.7480 (t80) cc_final: 0.7090 (t80) REVERT: B 239 GLN cc_start: 0.7145 (tt0) cc_final: 0.6146 (tm-30) REVERT: B 554 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7915 (mm-30) REVERT: B 858 LEU cc_start: 0.8961 (mt) cc_final: 0.8067 (pt) REVERT: B 934 ILE cc_start: 0.8331 (mm) cc_final: 0.8102 (mp) REVERT: B 957 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8205 (pp30) REVERT: B 964 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8681 (mmmm) REVERT: B 990 GLU cc_start: 0.8287 (tt0) cc_final: 0.7888 (tm-30) REVERT: C 30 ASN cc_start: 0.7630 (t0) cc_final: 0.7124 (t0) REVERT: C 64 TRP cc_start: 0.7670 (t60) cc_final: 0.7351 (t60) REVERT: C 218 GLN cc_start: 0.8483 (tt0) cc_final: 0.8203 (tp40) REVERT: C 324 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: C 334 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.6784 (p0) REVERT: C 378 LYS cc_start: 0.8431 (mttm) cc_final: 0.8228 (mttp) REVERT: C 408 ARG cc_start: 0.8302 (ppt170) cc_final: 0.7941 (ptm-80) REVERT: C 433 VAL cc_start: 0.8206 (t) cc_final: 0.7937 (m) REVERT: C 455 LEU cc_start: 0.8358 (tp) cc_final: 0.7991 (pp) REVERT: C 532 ASN cc_start: 0.8913 (t0) cc_final: 0.8211 (OUTLIER) REVERT: C 990 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 1002 GLN cc_start: 0.8934 (tt0) cc_final: 0.8683 (tt0) REVERT: C 1010 GLN cc_start: 0.8965 (tp40) cc_final: 0.8736 (mp10) REVERT: H 32 TYR cc_start: 0.3875 (p90) cc_final: 0.3350 (p90) outliers start: 42 outliers final: 14 residues processed: 180 average time/residue: 0.5011 time to fit residues: 107.1771 Evaluate side-chains 153 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 35 optimal weight: 0.0980 chunk 251 optimal weight: 0.9980 chunk 238 optimal weight: 0.0470 chunk 192 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B1010 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.126477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077004 restraints weight = 46348.731| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.83 r_work: 0.3108 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23564 Z= 0.103 Angle : 0.542 10.367 32186 Z= 0.262 Chirality : 0.043 0.253 3819 Planarity : 0.003 0.036 4055 Dihedral : 4.006 35.026 3030 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.29 % Allowed : 10.29 % Favored : 88.43 % 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: 0.67 (0.16), residues: 2788 helix: 2.79 (0.21), residues: 612 sheet: 0.38 (0.21), residues: 603 loop : -0.48 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.020 0.001 TYR B 28 PHE 0.023 0.001 PHE C 168 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (23472) covalent geometry : angle 0.51443 / 0.26 (31945) SS BOND : bond 0.00143 / 0.11 ( 35) SS BOND : angle 1.21914 / 1.13 ( 70) hydrogen bonds : bond 0.03722 / 2.42 ( 870) hydrogen bonds : angle 5.05574 / 3.52 ( 2415) link_BETA1-4 : bond 0.00366 / 0.22 ( 18) link_BETA1-4 : angle 0.85856 / 0.57 ( 54) link_NAG-ASN : bond 0.00591 / 0.41 ( 39) link_NAG-ASN : angle 2.72911 / 1.91 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7629 (mm) REVERT: A 200 TYR cc_start: 0.7323 (m-80) cc_final: 0.6842 (m-80) REVERT: A 298 GLU cc_start: 0.8775 (tt0) cc_final: 0.8075 (tm-30) REVERT: A 856 ASN cc_start: 0.6806 (OUTLIER) cc_final: 0.6456 (m110) REVERT: B 118 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6502 (mp) REVERT: B 129 LYS cc_start: 0.6245 (mtmt) cc_final: 0.5850 (ttmt) REVERT: B 153 MET cc_start: 0.5257 (mpp) cc_final: 0.4525 (pp-130) REVERT: B 201 PHE cc_start: 0.7557 (t80) cc_final: 0.7168 (t80) REVERT: B 207 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7115 (t-90) REVERT: B 239 GLN cc_start: 0.7262 (tt0) cc_final: 0.6249 (tm-30) REVERT: B 554 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7924 (mm-30) REVERT: B 957 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8228 (pp30) REVERT: B 964 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8767 (mmmm) REVERT: C 30 ASN cc_start: 0.7595 (t0) cc_final: 0.7100 (t0) REVERT: C 64 TRP cc_start: 0.7644 (t60) cc_final: 0.7349 (t60) REVERT: C 218 GLN cc_start: 0.8437 (tt0) cc_final: 0.8199 (tp40) REVERT: C 324 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: C 334 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.6857 (p0) REVERT: C 408 ARG cc_start: 0.8324 (ppt170) cc_final: 0.7986 (ptm-80) REVERT: C 455 LEU cc_start: 0.8398 (tp) cc_final: 0.7998 (pp) REVERT: C 532 ASN cc_start: 0.8895 (t0) cc_final: 0.8308 (OUTLIER) REVERT: C 773 GLU cc_start: 0.8437 (tt0) cc_final: 0.8197 (tt0) REVERT: C 957 GLN cc_start: 0.8690 (tt0) cc_final: 0.8318 (tm-30) REVERT: C 990 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 1002 GLN cc_start: 0.8931 (tt0) cc_final: 0.8712 (tt0) REVERT: H 32 TYR cc_start: 0.3572 (OUTLIER) cc_final: 0.3146 (p90) outliers start: 32 outliers final: 13 residues processed: 170 average time/residue: 0.5118 time to fit residues: 101.7494 Evaluate side-chains 148 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 125 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 274 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B1010 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.124594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.074737 restraints weight = 46166.051| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.81 r_work: 0.3039 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23564 Z= 0.179 Angle : 0.578 10.478 32186 Z= 0.281 Chirality : 0.045 0.269 3819 Planarity : 0.004 0.036 4055 Dihedral : 4.161 34.363 3030 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.41 % Allowed : 10.45 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 2788 helix: 2.63 (0.20), residues: 625 sheet: 0.15 (0.20), residues: 606 loop : -0.54 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.019 0.001 TYR C1067 PHE 0.023 0.001 PHE C 400 TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (23472) covalent geometry : angle 0.54995 / 0.27 (31945) SS BOND : bond 0.00218 / 0.14 ( 35) SS BOND : angle 1.17570 / 1.03 ( 70) hydrogen bonds : bond 0.04188 / 2.72 ( 870) hydrogen bonds : angle 5.15511 / 3.59 ( 2415) link_BETA1-4 : bond 0.00241 / 0.13 ( 18) link_BETA1-4 : angle 1.04619 / 0.68 ( 54) link_NAG-ASN : bond 0.00604 / 0.42 ( 39) link_NAG-ASN : angle 2.82509 / 1.98 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7692 (mm) REVERT: A 298 GLU cc_start: 0.8782 (tt0) cc_final: 0.8146 (tm-30) REVERT: A 856 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6465 (m110) REVERT: A 983 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7831 (mtm-85) REVERT: B 102 ARG cc_start: 0.6655 (mmp-170) cc_final: 0.6152 (mmp-170) REVERT: B 118 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6382 (mp) REVERT: B 129 LYS cc_start: 0.6251 (mtmt) cc_final: 0.5871 (ttmt) REVERT: B 153 MET cc_start: 0.5217 (mpp) cc_final: 0.4381 (pp-130) REVERT: B 201 PHE cc_start: 0.7545 (t80) cc_final: 0.7171 (t80) REVERT: B 207 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7057 (t-90) REVERT: B 239 GLN cc_start: 0.7155 (tt0) cc_final: 0.6735 (tt0) REVERT: B 554 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7893 (mm-30) REVERT: B 957 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8240 (pp30) REVERT: B 964 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (mmmm) REVERT: B 990 GLU cc_start: 0.8337 (tt0) cc_final: 0.7935 (tm-30) REVERT: C 30 ASN cc_start: 0.7602 (t0) cc_final: 0.7025 (t0) REVERT: C 64 TRP cc_start: 0.7781 (t60) cc_final: 0.7556 (t60) REVERT: C 113 LYS cc_start: 0.8370 (mttp) cc_final: 0.8084 (tptp) REVERT: C 187 LYS cc_start: 0.6700 (mmtp) cc_final: 0.6343 (ptpt) REVERT: C 218 GLN cc_start: 0.8476 (tt0) cc_final: 0.8210 (tp40) REVERT: C 324 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: C 334 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6758 (p0) REVERT: C 455 LEU cc_start: 0.8337 (tp) cc_final: 0.7959 (pp) REVERT: C 532 ASN cc_start: 0.8992 (t0) cc_final: 0.8296 (OUTLIER) REVERT: C 990 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 1002 GLN cc_start: 0.8924 (tt0) cc_final: 0.8720 (tt0) outliers start: 35 outliers final: 11 residues processed: 162 average time/residue: 0.5266 time to fit residues: 100.6770 Evaluate side-chains 147 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 236 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 0.0470 chunk 88 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.125782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076304 restraints weight = 45825.620| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.80 r_work: 0.3079 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23564 Z= 0.111 Angle : 0.539 10.482 32186 Z= 0.262 Chirality : 0.044 0.258 3819 Planarity : 0.003 0.038 4055 Dihedral : 4.001 33.290 3030 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.96 % Allowed : 11.13 % Favored : 87.91 % 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: 0.65 (0.16), residues: 2788 helix: 2.69 (0.21), residues: 631 sheet: 0.30 (0.21), residues: 610 loop : -0.46 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.021 0.001 TYR B 170 PHE 0.014 0.001 PHE A 898 TRP 0.011 0.001 TRP A 104 HIS 0.003 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (23472) covalent geometry : angle 0.51307 / 0.26 (31945) SS BOND : bond 0.00177 / 0.13 ( 35) SS BOND : angle 1.03341 / 0.91 ( 70) hydrogen bonds : bond 0.03739 / 2.42 ( 870) hydrogen bonds : angle 4.97258 / 3.46 ( 2415) link_BETA1-4 : bond 0.00335 / 0.21 ( 18) link_BETA1-4 : angle 0.84736 / 0.56 ( 54) link_NAG-ASN : bond 0.00553 / 0.39 ( 39) link_NAG-ASN : angle 2.66232 / 1.84 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8768 (tt0) cc_final: 0.8074 (tm-30) REVERT: A 856 ASN cc_start: 0.6835 (OUTLIER) cc_final: 0.6469 (m110) REVERT: B 118 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6418 (mp) REVERT: B 129 LYS cc_start: 0.6139 (mtmt) cc_final: 0.5778 (ttmt) REVERT: B 153 MET cc_start: 0.5197 (mpp) cc_final: 0.4307 (pp-130) REVERT: B 201 PHE cc_start: 0.7507 (t80) cc_final: 0.7142 (t80) REVERT: B 207 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6977 (t-90) REVERT: B 239 GLN cc_start: 0.7125 (tt0) cc_final: 0.6678 (tt0) REVERT: B 554 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7870 (mm-30) REVERT: B 934 ILE cc_start: 0.8224 (mm) cc_final: 0.7984 (mp) REVERT: B 957 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8221 (pp30) REVERT: B 964 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8721 (mmmm) REVERT: C 30 ASN cc_start: 0.7674 (t0) cc_final: 0.7070 (t0) REVERT: C 113 LYS cc_start: 0.8352 (mttp) cc_final: 0.8042 (tptp) REVERT: C 187 LYS cc_start: 0.6725 (mmtp) cc_final: 0.6373 (ptpt) REVERT: C 218 GLN cc_start: 0.8474 (tt0) cc_final: 0.8224 (tp40) REVERT: C 324 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: C 334 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6787 (p0) REVERT: C 455 LEU cc_start: 0.8431 (tp) cc_final: 0.8025 (pp) REVERT: C 532 ASN cc_start: 0.8992 (t0) cc_final: 0.8467 (m110) REVERT: C 773 GLU cc_start: 0.8455 (tt0) cc_final: 0.8220 (tt0) REVERT: C 957 GLN cc_start: 0.8679 (tt0) cc_final: 0.8303 (tm-30) REVERT: C 985 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7578 (p0) REVERT: C 990 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7579 (tm-30) REVERT: C 1002 GLN cc_start: 0.8932 (tt0) cc_final: 0.8719 (tt0) REVERT: C 1010 GLN cc_start: 0.8959 (tp40) cc_final: 0.8720 (mp10) outliers start: 24 outliers final: 11 residues processed: 155 average time/residue: 0.5241 time to fit residues: 96.0548 Evaluate side-chains 149 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 207 optimal weight: 2.9990 chunk 125 optimal weight: 0.0170 chunk 109 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 169 optimal weight: 0.0170 chunk 133 optimal weight: 0.8980 chunk 279 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 136 optimal weight: 0.3980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077132 restraints weight = 46331.355| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.80 r_work: 0.3113 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23564 Z= 0.096 Angle : 0.527 10.482 32186 Z= 0.257 Chirality : 0.043 0.256 3819 Planarity : 0.003 0.037 4055 Dihedral : 3.876 30.461 3030 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.80 % Allowed : 11.49 % Favored : 87.71 % 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: 0.72 (0.16), residues: 2788 helix: 2.80 (0.21), residues: 626 sheet: 0.29 (0.21), residues: 616 loop : -0.40 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.024 0.001 TYR C 421 PHE 0.025 0.001 PHE C 168 TRP 0.015 0.001 TRP C 64 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (23472) covalent geometry : angle 0.50288 / 0.25 (31945) SS BOND : bond 0.00148 / 0.11 ( 35) SS BOND : angle 0.95043 / 0.84 ( 70) hydrogen bonds : bond 0.03537 / 2.29 ( 870) hydrogen bonds : angle 4.85927 / 3.38 ( 2415) link_BETA1-4 : bond 0.00326 / 0.20 ( 18) link_BETA1-4 : angle 0.84276 / 0.56 ( 54) link_NAG-ASN : bond 0.00543 / 0.38 ( 39) link_NAG-ASN : angle 2.57391 / 1.77 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8745 (tt0) cc_final: 0.8059 (tm-30) REVERT: A 856 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6408 (m110) REVERT: B 88 ASP cc_start: 0.7737 (m-30) cc_final: 0.6774 (p0) REVERT: B 102 ARG cc_start: 0.6566 (mmp-170) cc_final: 0.6354 (mmp-170) REVERT: B 118 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6256 (mp) REVERT: B 129 LYS cc_start: 0.6181 (mtmt) cc_final: 0.5809 (tttt) REVERT: B 153 MET cc_start: 0.5284 (mpp) cc_final: 0.4436 (pp-130) REVERT: B 207 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.6975 (t-90) REVERT: B 239 GLN cc_start: 0.7094 (tt0) cc_final: 0.6132 (tm-30) REVERT: B 554 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7916 (mm-30) REVERT: B 934 ILE cc_start: 0.8095 (mm) cc_final: 0.7864 (mp) REVERT: B 957 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8201 (pp30) REVERT: B 964 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8697 (mmmm) REVERT: C 30 ASN cc_start: 0.7663 (t0) cc_final: 0.7091 (t0) REVERT: C 64 TRP cc_start: 0.7420 (t60) cc_final: 0.7164 (t60) REVERT: C 187 LYS cc_start: 0.6726 (mmtp) cc_final: 0.6400 (ptpt) REVERT: C 218 GLN cc_start: 0.8447 (tt0) cc_final: 0.8215 (tp40) REVERT: C 324 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: C 421 TYR cc_start: 0.8059 (m-80) cc_final: 0.7667 (m-80) REVERT: C 455 LEU cc_start: 0.8407 (tp) cc_final: 0.7995 (pp) REVERT: C 532 ASN cc_start: 0.9011 (t0) cc_final: 0.8489 (m110) REVERT: C 773 GLU cc_start: 0.8399 (tt0) cc_final: 0.8152 (tt0) REVERT: C 869 MET cc_start: 0.9240 (mtt) cc_final: 0.8937 (mtt) REVERT: C 957 GLN cc_start: 0.8650 (tt0) cc_final: 0.8270 (tm-30) REVERT: C 990 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 1002 GLN cc_start: 0.8906 (tt0) cc_final: 0.8688 (tt0) outliers start: 20 outliers final: 10 residues processed: 151 average time/residue: 0.5738 time to fit residues: 102.2909 Evaluate side-chains 146 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 162 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 223 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.124980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075438 restraints weight = 46130.916| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.79 r_work: 0.3079 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23564 Z= 0.151 Angle : 0.554 10.451 32186 Z= 0.271 Chirality : 0.044 0.266 3819 Planarity : 0.003 0.037 4055 Dihedral : 3.949 16.585 3028 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.76 % Allowed : 11.57 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2788 helix: 2.71 (0.20), residues: 631 sheet: 0.14 (0.20), residues: 629 loop : -0.46 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.022 0.001 TYR B 170 PHE 0.019 0.001 PHE C 400 TRP 0.015 0.001 TRP H 47 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (23472) covalent geometry : angle 0.52855 / 0.27 (31945) SS BOND : bond 0.00174 / 0.12 ( 35) SS BOND : angle 1.01043 / 0.90 ( 70) hydrogen bonds : bond 0.03927 / 2.54 ( 870) hydrogen bonds : angle 4.96083 / 3.45 ( 2415) link_BETA1-4 : bond 0.00272 / 0.15 ( 18) link_BETA1-4 : angle 0.96101 / 0.63 ( 54) link_NAG-ASN : bond 0.00545 / 0.38 ( 39) link_NAG-ASN : angle 2.64360 / 1.82 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7673 (m-80) cc_final: 0.7437 (t80) REVERT: A 298 GLU cc_start: 0.8754 (tt0) cc_final: 0.8113 (tm-30) REVERT: B 102 ARG cc_start: 0.6559 (mmp-170) cc_final: 0.6313 (mmp-170) REVERT: B 118 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6264 (mp) REVERT: B 129 LYS cc_start: 0.6146 (mtmt) cc_final: 0.5734 (ttmt) REVERT: B 153 MET cc_start: 0.5212 (mpp) cc_final: 0.4277 (pp-130) REVERT: B 201 PHE cc_start: 0.7287 (t80) cc_final: 0.6575 (t80) REVERT: B 207 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: B 239 GLN cc_start: 0.7106 (tt0) cc_final: 0.6715 (tt0) REVERT: B 554 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7900 (mm-30) REVERT: B 934 ILE cc_start: 0.8197 (mm) cc_final: 0.7966 (mp) REVERT: B 964 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8711 (mmmm) REVERT: B 990 GLU cc_start: 0.8275 (tt0) cc_final: 0.7999 (tm-30) REVERT: C 64 TRP cc_start: 0.7444 (t60) cc_final: 0.7205 (t60) REVERT: C 324 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: C 421 TYR cc_start: 0.8014 (m-80) cc_final: 0.7678 (m-80) REVERT: C 455 LEU cc_start: 0.8465 (tp) cc_final: 0.8072 (pp) REVERT: C 532 ASN cc_start: 0.8989 (t0) cc_final: 0.8465 (m110) REVERT: C 773 GLU cc_start: 0.8411 (tt0) cc_final: 0.8171 (tt0) REVERT: C 957 GLN cc_start: 0.8634 (tt0) cc_final: 0.8247 (tm-30) REVERT: C 990 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 1002 GLN cc_start: 0.8904 (tt0) cc_final: 0.8678 (tt0) REVERT: C 1010 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8657 (mm110) outliers start: 19 outliers final: 10 residues processed: 145 average time/residue: 0.5743 time to fit residues: 98.6206 Evaluate side-chains 144 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 198 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 82 optimal weight: 0.0050 chunk 210 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.074365 restraints weight = 46133.451| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.79 r_work: 0.3062 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23564 Z= 0.183 Angle : 0.577 10.455 32186 Z= 0.283 Chirality : 0.045 0.266 3819 Planarity : 0.004 0.037 4055 Dihedral : 4.100 17.303 3028 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.92 % Allowed : 11.53 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2788 helix: 2.61 (0.20), residues: 632 sheet: 0.07 (0.20), residues: 633 loop : -0.52 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 457 TYR 0.021 0.001 TYR C 421 PHE 0.026 0.001 PHE C 168 TRP 0.017 0.002 TRP H 47 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (23472) covalent geometry : angle 0.55186 / 0.28 (31945) SS BOND : bond 0.00197 / 0.14 ( 35) SS BOND : angle 1.05405 / 0.93 ( 70) hydrogen bonds : bond 0.04164 / 2.69 ( 870) hydrogen bonds : angle 5.06506 / 3.53 ( 2415) link_BETA1-4 : bond 0.00275 / 0.15 ( 18) link_BETA1-4 : angle 0.99518 / 0.65 ( 54) link_NAG-ASN : bond 0.00567 / 0.40 ( 39) link_NAG-ASN : angle 2.70721 / 1.86 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11835.10 seconds wall clock time: 201 minutes 35.65 seconds (12095.65 seconds total)