Starting phenix.real_space_refine on Thu Mar 5 14:33:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlz_27521/03_2026/8dlz_27521.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlz_27521/03_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_27521/03_2026/8dlz_27521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlz_27521/03_2026/8dlz_27521.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlz_27521/03_2026/8dlz_27521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlz_27521/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 18 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 dihedrals: 21 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.88, per 1000 atoms: 0.21 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: 2.02 Conformation dependent library (CDL) restraints added in 786.2 milliseconds 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: 0.86 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: 5.80 Time building geometry restraints manager: 2.66 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: 13563 17.88 - 35.77: 925 35.77 - 53.65: 162 53.65 - 71.53: 64 71.53 - 89.41: 26 Dihedral angle restraints: 14740 sinusoidal: 6487 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 14737 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.840 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 13.173 89.414 9313 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 covalent geometry : bond 0.00515 (23472) covalent geometry : angle 0.82946 (31945) SS BOND : bond 0.00266 ( 35) SS BOND : angle 1.36632 ( 70) hydrogen bonds : bond 0.12842 ( 870) hydrogen bonds : angle 7.00932 ( 2415) link_BETA1-4 : bond 0.00648 ( 18) link_BETA1-4 : angle 1.22406 ( 54) link_NAG-ASN : bond 0.00762 ( 39) link_NAG-ASN : angle 3.65038 ( 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 : 0.884 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: 0.6233 time to fit residues: 212.1442 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 : 0.851 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 955 ASN A1005 GLN A1011 GLN B 762 GLN B 779 GLN B 901 GLN B 978 ASN C 121 ASN C 196 ASN C 957 GLN C1002 GLN H 35 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.126945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077145 restraints weight = 46280.436| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.82 r_work: 0.3098 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23564 Z= 0.181 Angle : 0.629 12.507 32186 Z= 0.310 Chirality : 0.045 0.266 3819 Planarity : 0.004 0.049 4055 Dihedral : 6.643 57.792 4227 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.49 % Allowed : 6.51 % Favored : 92.00 % 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: 0.29 (0.15), residues: 2788 helix: 2.06 (0.20), residues: 624 sheet: 0.32 (0.20), residues: 626 loop : -0.65 (0.14), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 983 TYR 0.024 0.001 TYR B 28 PHE 0.020 0.001 PHE A 133 TRP 0.017 0.001 TRP A 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00413 (23472) covalent geometry : angle 0.59172 (31945) SS BOND : bond 0.00930 ( 35) SS BOND : angle 1.49316 ( 70) hydrogen bonds : bond 0.04494 ( 870) hydrogen bonds : angle 5.78284 ( 2415) link_BETA1-4 : bond 0.00248 ( 18) link_BETA1-4 : angle 1.12062 ( 54) link_NAG-ASN : bond 0.00650 ( 39) link_NAG-ASN : angle 3.38585 ( 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 192 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8755 (tt0) cc_final: 0.8051 (tm-30) REVERT: B 118 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6481 (mp) REVERT: B 129 LYS cc_start: 0.6194 (mtmt) cc_final: 0.5904 (ttmt) REVERT: B 153 MET cc_start: 0.5494 (mpp) cc_final: 0.4891 (pp-130) REVERT: B 201 PHE cc_start: 0.7306 (t80) cc_final: 0.6744 (t80) REVERT: B 239 GLN cc_start: 0.6894 (tt0) cc_final: 0.6454 (tm-30) REVERT: B 269 TYR cc_start: 0.8337 (m-80) cc_final: 0.8081 (m-80) REVERT: B 327 VAL cc_start: 0.8093 (t) cc_final: 0.7719 (m) REVERT: B 858 LEU cc_start: 0.8774 (mt) cc_final: 0.7908 (pt) REVERT: B 900 MET cc_start: 0.9172 (mtp) cc_final: 0.8932 (ttm) REVERT: B 957 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8328 (pp30) REVERT: C 30 ASN cc_start: 0.7661 (t0) cc_final: 0.7153 (t0) REVERT: C 64 TRP cc_start: 0.7685 (t60) cc_final: 0.7403 (t60) REVERT: C 207 HIS cc_start: 0.7393 (m-70) cc_final: 0.6499 (t-90) REVERT: C 334 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.7104 (p0) REVERT: C 408 ARG cc_start: 0.8450 (ppt170) cc_final: 0.7995 (ptm-80) REVERT: C 420 ASP cc_start: 0.8059 (t0) cc_final: 0.7810 (t0) REVERT: C 421 TYR cc_start: 0.8139 (m-80) cc_final: 0.7908 (m-80) REVERT: C 423 TYR cc_start: 0.7847 (t80) cc_final: 0.7621 (t80) REVERT: C 424 LYS cc_start: 0.8487 (tptt) cc_final: 0.8209 (tptt) REVERT: C 433 VAL cc_start: 0.8346 (t) cc_final: 0.8039 (m) REVERT: C 532 ASN cc_start: 0.8912 (t0) cc_final: 0.8250 (p0) REVERT: C 990 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 1002 GLN cc_start: 0.8985 (tt0) cc_final: 0.8732 (tt0) outliers start: 37 outliers final: 8 residues processed: 184 average time/residue: 0.5645 time to fit residues: 120.9278 Evaluate side-chains 143 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 38 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 239 optimal weight: 0.0980 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 281 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4081 r_free = 0.4081 target = 0.127269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.077869 restraints weight = 46407.655| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.82 r_work: 0.3118 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23564 Z= 0.115 Angle : 0.563 10.425 32186 Z= 0.276 Chirality : 0.044 0.263 3819 Planarity : 0.004 0.048 4055 Dihedral : 5.990 59.843 4227 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.37 % Allowed : 7.91 % Favored : 90.72 % 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: 2.52 (0.21), residues: 616 sheet: 0.26 (0.21), residues: 593 loop : -0.51 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 97 TYR 0.023 0.001 TYR B 28 PHE 0.023 0.001 PHE C 168 TRP 0.011 0.001 TRP B 104 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00255 (23472) covalent geometry : angle 0.52743 (31945) SS BOND : bond 0.00252 ( 35) SS BOND : angle 1.34468 ( 70) hydrogen bonds : bond 0.04034 ( 870) hydrogen bonds : angle 5.45292 ( 2415) link_BETA1-4 : bond 0.00330 ( 18) link_BETA1-4 : angle 1.02207 ( 54) link_NAG-ASN : bond 0.00705 ( 39) link_NAG-ASN : angle 3.09604 ( 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 177 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3341 (pp-130) cc_final: 0.3139 (pp-130) REVERT: A 160 TYR cc_start: 0.5932 (p90) cc_final: 0.5505 (p90) REVERT: A 298 GLU cc_start: 0.8773 (tt0) cc_final: 0.8027 (tm-30) REVERT: A 902 MET cc_start: 0.9231 (tpt) cc_final: 0.8997 (tpt) REVERT: B 102 ARG cc_start: 0.6503 (mmp-170) cc_final: 0.6232 (mmp-170) REVERT: B 118 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6485 (mp) REVERT: B 129 LYS cc_start: 0.6171 (mtmt) cc_final: 0.5886 (ttmt) REVERT: B 153 MET cc_start: 0.5234 (mpp) cc_final: 0.4723 (pp-130) REVERT: B 201 PHE cc_start: 0.7229 (t80) cc_final: 0.6775 (t80) REVERT: B 327 VAL cc_start: 0.8003 (t) cc_final: 0.7584 (m) REVERT: B 554 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7911 (mm-30) REVERT: B 858 LEU cc_start: 0.8849 (mt) cc_final: 0.7991 (pt) REVERT: B 957 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8309 (pp30) REVERT: B 964 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8749 (mmmm) REVERT: C 30 ASN cc_start: 0.7654 (t0) cc_final: 0.7154 (t0) REVERT: C 64 TRP cc_start: 0.7662 (t60) cc_final: 0.7403 (t60) REVERT: C 334 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.7035 (p0) REVERT: C 408 ARG cc_start: 0.8384 (ppt170) cc_final: 0.7894 (ptm-80) REVERT: C 423 TYR cc_start: 0.7854 (t80) cc_final: 0.7562 (t80) REVERT: C 424 LYS cc_start: 0.8551 (tptt) cc_final: 0.8265 (tptt) REVERT: C 433 VAL cc_start: 0.8306 (t) cc_final: 0.8024 (m) REVERT: C 532 ASN cc_start: 0.8904 (t0) cc_final: 0.8236 (p0) REVERT: C 981 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8550 (mm) REVERT: C 990 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7475 (tm-30) REVERT: C 1002 GLN cc_start: 0.8944 (tt0) cc_final: 0.8718 (tt0) REVERT: C 1010 GLN cc_start: 0.8975 (tp40) cc_final: 0.8684 (mp10) outliers start: 34 outliers final: 8 residues processed: 168 average time/residue: 0.4965 time to fit residues: 99.5618 Evaluate side-chains 138 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 470 THR 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: 0.7980 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 824 ASN B1010 GLN C 49 HIS C 196 ASN C 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.124151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074042 restraints weight = 46311.371| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.82 r_work: 0.3052 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 23564 Z= 0.233 Angle : 0.620 14.963 32186 Z= 0.304 Chirality : 0.046 0.285 3819 Planarity : 0.004 0.038 4055 Dihedral : 5.778 52.462 4227 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 8.68 % Favored : 89.35 % 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: 0.29 (0.15), residues: 2788 helix: 2.37 (0.20), residues: 619 sheet: -0.09 (0.19), residues: 650 loop : -0.58 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.022 0.002 TYR C1067 PHE 0.019 0.002 PHE A 135 TRP 0.014 0.002 TRP A 886 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00547 (23472) covalent geometry : angle 0.58169 (31945) SS BOND : bond 0.00621 ( 35) SS BOND : angle 2.09916 ( 70) hydrogen bonds : bond 0.04631 ( 870) hydrogen bonds : angle 5.50857 ( 2415) link_BETA1-4 : bond 0.00271 ( 18) link_BETA1-4 : angle 1.23611 ( 54) link_NAG-ASN : bond 0.00715 ( 39) link_NAG-ASN : angle 3.14844 ( 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 189 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.5798 (p90) cc_final: 0.5401 (p90) REVERT: A 298 GLU cc_start: 0.8763 (tt0) cc_final: 0.8075 (tm-30) REVERT: A 990 GLU cc_start: 0.8170 (tt0) cc_final: 0.7728 (tm-30) REVERT: B 102 ARG cc_start: 0.6577 (mmp-170) cc_final: 0.6377 (mmp-170) REVERT: B 118 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6518 (mp) REVERT: B 129 LYS cc_start: 0.6220 (mtmt) cc_final: 0.5942 (ttmt) REVERT: B 153 MET cc_start: 0.5312 (mpp) cc_final: 0.4629 (pp-130) REVERT: B 201 PHE cc_start: 0.7347 (t80) cc_final: 0.6820 (t80) REVERT: B 239 GLN cc_start: 0.7150 (tt0) cc_final: 0.6705 (tt0) REVERT: B 554 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7927 (mm-30) REVERT: B 740 MET cc_start: 0.8852 (ttt) cc_final: 0.8508 (ttm) REVERT: B 858 LEU cc_start: 0.9036 (mt) cc_final: 0.8142 (pt) REVERT: B 957 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8241 (pp30) REVERT: B 964 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8733 (mmmm) REVERT: B 990 GLU cc_start: 0.8297 (tt0) cc_final: 0.7889 (tm-30) REVERT: C 30 ASN cc_start: 0.7604 (t0) cc_final: 0.7011 (t0) REVERT: C 64 TRP cc_start: 0.7711 (t60) cc_final: 0.7394 (t60) REVERT: C 218 GLN cc_start: 0.8519 (tt0) cc_final: 0.8263 (tp40) REVERT: C 334 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6935 (p0) REVERT: C 408 ARG cc_start: 0.8344 (ppt170) cc_final: 0.7937 (ptm-80) REVERT: C 423 TYR cc_start: 0.7901 (t80) cc_final: 0.7494 (t80) REVERT: C 424 LYS cc_start: 0.8518 (tptt) cc_final: 0.8277 (tptt) REVERT: C 455 LEU cc_start: 0.8372 (tp) cc_final: 0.8044 (pp) REVERT: C 532 ASN cc_start: 0.8914 (t0) cc_final: 0.8227 (p0) REVERT: C 990 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 1002 GLN cc_start: 0.8921 (tt0) cc_final: 0.8678 (tt0) outliers start: 49 outliers final: 14 residues processed: 177 average time/residue: 0.5063 time to fit residues: 105.2959 Evaluate side-chains 145 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 320 VAL 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 C residue 1010 GLN 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: 4.9990 chunk 281 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 236 optimal weight: 0.6980 chunk 282 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 155 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 188 ASN B1010 GLN C 196 ASN C 779 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.125673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075973 restraints weight = 46122.469| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.80 r_work: 0.3091 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23564 Z= 0.115 Angle : 0.553 10.728 32186 Z= 0.269 Chirality : 0.044 0.266 3819 Planarity : 0.003 0.035 4055 Dihedral : 5.315 52.394 4227 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.37 % Allowed : 9.44 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2788 helix: 2.56 (0.21), residues: 625 sheet: 0.24 (0.20), residues: 610 loop : -0.53 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 97 TYR 0.021 0.001 TYR B 28 PHE 0.024 0.001 PHE C 168 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00254 (23472) covalent geometry : angle 0.52187 (31945) SS BOND : bond 0.00327 ( 35) SS BOND : angle 1.09934 ( 70) hydrogen bonds : bond 0.03938 ( 870) hydrogen bonds : angle 5.26481 ( 2415) link_BETA1-4 : bond 0.00335 ( 18) link_BETA1-4 : angle 0.99227 ( 54) link_NAG-ASN : bond 0.00611 ( 39) link_NAG-ASN : angle 2.92534 ( 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 182 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.3153 (OUTLIER) cc_final: 0.2931 (pp-130) REVERT: A 160 TYR cc_start: 0.5901 (p90) cc_final: 0.5651 (p90) REVERT: A 200 TYR cc_start: 0.7347 (m-80) cc_final: 0.6918 (m-80) REVERT: A 298 GLU cc_start: 0.8743 (tt0) cc_final: 0.8050 (tm-30) REVERT: A 856 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.6381 (m110) REVERT: B 118 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6562 (mp) REVERT: B 129 LYS cc_start: 0.6108 (mtmt) cc_final: 0.5804 (ttmt) REVERT: B 153 MET cc_start: 0.5304 (mpp) cc_final: 0.4491 (pp-130) REVERT: B 190 ARG cc_start: 0.7502 (mtp180) cc_final: 0.7098 (ttm170) REVERT: B 201 PHE cc_start: 0.7539 (t80) cc_final: 0.7142 (t80) REVERT: B 239 GLN cc_start: 0.7169 (tt0) cc_final: 0.6219 (tm-30) REVERT: B 269 TYR cc_start: 0.7823 (m-10) cc_final: 0.7607 (m-10) REVERT: B 554 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7916 (mm-30) REVERT: B 740 MET cc_start: 0.8729 (ttt) cc_final: 0.8357 (ttm) REVERT: B 934 ILE cc_start: 0.8360 (mm) cc_final: 0.8147 (mp) REVERT: B 957 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8215 (pp30) REVERT: B 964 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8725 (mmmm) REVERT: B 990 GLU cc_start: 0.8282 (tt0) cc_final: 0.7990 (tm-30) REVERT: C 30 ASN cc_start: 0.7599 (t0) cc_final: 0.7047 (t0) REVERT: C 64 TRP cc_start: 0.7689 (t60) cc_final: 0.7379 (t60) REVERT: C 218 GLN cc_start: 0.8497 (tt0) cc_final: 0.8230 (tp40) REVERT: C 324 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: C 334 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.6827 (p0) REVERT: C 408 ARG cc_start: 0.8294 (ppt170) cc_final: 0.7959 (ptm-80) REVERT: C 424 LYS cc_start: 0.8516 (tptt) cc_final: 0.8220 (tptt) REVERT: C 455 LEU cc_start: 0.8410 (tp) cc_final: 0.8035 (pp) REVERT: C 532 ASN cc_start: 0.8905 (t0) cc_final: 0.8242 (p0) REVERT: C 990 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 1002 GLN cc_start: 0.8916 (tt0) cc_final: 0.8664 (tt0) outliers start: 34 outliers final: 10 residues processed: 173 average time/residue: 0.5649 time to fit residues: 114.0724 Evaluate side-chains 147 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET 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 324 GLU 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 1010 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 35 optimal weight: 0.0770 chunk 251 optimal weight: 0.5980 chunk 238 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 273 optimal weight: 0.0470 chunk 114 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.125704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.075996 restraints weight = 46325.523| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.82 r_work: 0.3096 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23564 Z= 0.117 Angle : 0.546 10.441 32186 Z= 0.264 Chirality : 0.044 0.271 3819 Planarity : 0.003 0.036 4055 Dihedral : 4.929 52.750 4227 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 9.92 % 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: 0.60 (0.16), residues: 2788 helix: 2.68 (0.21), residues: 625 sheet: 0.22 (0.21), residues: 609 loop : -0.48 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 97 TYR 0.020 0.001 TYR H 32 PHE 0.028 0.001 PHE C 400 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00260 (23472) covalent geometry : angle 0.51671 (31945) SS BOND : bond 0.00375 ( 35) SS BOND : angle 0.98730 ( 70) hydrogen bonds : bond 0.03822 ( 870) hydrogen bonds : angle 5.10961 ( 2415) link_BETA1-4 : bond 0.00338 ( 18) link_BETA1-4 : angle 1.03784 ( 54) link_NAG-ASN : bond 0.00593 ( 39) link_NAG-ASN : angle 2.84318 ( 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 185 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6660 (tt) REVERT: A 160 TYR cc_start: 0.5898 (p90) cc_final: 0.5648 (p90) REVERT: A 200 TYR cc_start: 0.7362 (m-80) cc_final: 0.6889 (m-80) REVERT: A 298 GLU cc_start: 0.8743 (tt0) cc_final: 0.8050 (tm-30) REVERT: A 856 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6483 (m110) REVERT: A 983 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7810 (mtm-85) REVERT: B 102 ARG cc_start: 0.6489 (mmp-170) cc_final: 0.6128 (mmp-170) REVERT: B 118 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6434 (mp) REVERT: B 129 LYS cc_start: 0.6172 (mtmt) cc_final: 0.5844 (ttmt) REVERT: B 153 MET cc_start: 0.5405 (mpp) cc_final: 0.4553 (pp-130) REVERT: B 176 LEU cc_start: 0.4190 (OUTLIER) cc_final: 0.3337 (tp) REVERT: B 201 PHE cc_start: 0.7539 (t80) cc_final: 0.7163 (t80) REVERT: B 207 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7100 (t-90) REVERT: B 239 GLN cc_start: 0.7152 (tt0) cc_final: 0.6709 (tt0) REVERT: B 554 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7894 (mm-30) REVERT: B 858 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 957 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8207 (pp30) REVERT: B 964 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8722 (mmmm) REVERT: C 30 ASN cc_start: 0.7593 (t0) cc_final: 0.7030 (t0) REVERT: C 64 TRP cc_start: 0.7695 (t60) cc_final: 0.7393 (t60) REVERT: C 187 LYS cc_start: 0.6630 (mmtp) cc_final: 0.6324 (ptpt) REVERT: C 218 GLN cc_start: 0.8494 (tt0) cc_final: 0.8226 (tp40) REVERT: C 324 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: C 334 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6843 (p0) REVERT: C 455 LEU cc_start: 0.8383 (tp) cc_final: 0.8010 (pp) REVERT: C 532 ASN cc_start: 0.8892 (t0) cc_final: 0.8328 (OUTLIER) REVERT: C 773 GLU cc_start: 0.8402 (tt0) cc_final: 0.8159 (tt0) REVERT: C 957 GLN cc_start: 0.8662 (tt0) cc_final: 0.8267 (tm-30) REVERT: C 990 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 1002 GLN cc_start: 0.8894 (tt0) cc_final: 0.8684 (tt0) outliers start: 41 outliers final: 13 residues processed: 174 average time/residue: 0.5908 time to fit residues: 120.0260 Evaluate side-chains 156 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 856 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 176 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 212 LEU 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 C residue 1010 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 125 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 0.0270 chunk 198 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 755 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 = 0.4047 r_free = 0.4047 target = 0.124927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075225 restraints weight = 46168.873| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.80 r_work: 0.3073 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23564 Z= 0.146 Angle : 0.554 10.448 32186 Z= 0.269 Chirality : 0.044 0.274 3819 Planarity : 0.003 0.037 4055 Dihedral : 4.871 52.020 4227 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.57 % Allowed : 10.53 % 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: 0.57 (0.16), residues: 2788 helix: 2.62 (0.20), residues: 631 sheet: 0.16 (0.20), residues: 623 loop : -0.48 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.023 0.001 TYR H 32 PHE 0.030 0.001 PHE B 194 TRP 0.010 0.001 TRP A 104 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00335 (23472) covalent geometry : angle 0.52574 (31945) SS BOND : bond 0.00153 ( 35) SS BOND : angle 0.86482 ( 70) hydrogen bonds : bond 0.03948 ( 870) hydrogen bonds : angle 5.08575 ( 2415) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 1.04905 ( 54) link_NAG-ASN : bond 0.00592 ( 39) link_NAG-ASN : angle 2.84144 ( 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 178 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7668 (mm) REVERT: A 117 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6695 (tt) REVERT: A 160 TYR cc_start: 0.5881 (p90) cc_final: 0.5652 (p90) REVERT: A 298 GLU cc_start: 0.8786 (tt0) cc_final: 0.8084 (tm-30) REVERT: A 856 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6504 (m110) REVERT: A 983 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7866 (mtm-85) REVERT: B 102 ARG cc_start: 0.6529 (mmp-170) cc_final: 0.6243 (mmp-170) REVERT: B 118 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6449 (mp) REVERT: B 129 LYS cc_start: 0.6217 (mtmt) cc_final: 0.5845 (ttmt) REVERT: B 153 MET cc_start: 0.5222 (mpp) cc_final: 0.4338 (pp-130) REVERT: B 190 ARG cc_start: 0.7375 (ttm170) cc_final: 0.7149 (ttm170) REVERT: B 201 PHE cc_start: 0.7558 (t80) cc_final: 0.7170 (t80) REVERT: B 239 GLN cc_start: 0.7215 (tt0) cc_final: 0.6777 (tt0) REVERT: B 554 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7936 (mm-30) REVERT: B 858 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8154 (pt) REVERT: B 957 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8232 (pp30) REVERT: B 964 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8761 (mmmm) REVERT: B 990 GLU cc_start: 0.8320 (tt0) cc_final: 0.7923 (tm-30) REVERT: C 30 ASN cc_start: 0.7599 (t0) cc_final: 0.7035 (t0) REVERT: C 64 TRP cc_start: 0.7701 (t60) cc_final: 0.7490 (t60) REVERT: C 187 LYS cc_start: 0.6712 (mmtp) cc_final: 0.6371 (ptpt) REVERT: C 218 GLN cc_start: 0.8483 (tt0) cc_final: 0.8253 (tp40) REVERT: C 324 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: C 334 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6791 (p0) REVERT: C 455 LEU cc_start: 0.8364 (tp) cc_final: 0.7978 (pp) REVERT: C 532 ASN cc_start: 0.9040 (t0) cc_final: 0.8335 (OUTLIER) REVERT: C 957 GLN cc_start: 0.8684 (tt0) cc_final: 0.8293 (tm-30) REVERT: C 990 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 1002 GLN cc_start: 0.8927 (tt0) cc_final: 0.8712 (tt0) outliers start: 39 outliers final: 15 residues processed: 168 average time/residue: 0.5734 time to fit residues: 112.5818 Evaluate side-chains 150 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG 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 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 C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN 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: 0.9980 chunk 157 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 0.0020 chunk 88 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 188 optimal weight: 0.1980 chunk 151 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 overall best weight: 0.6448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.125653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.076171 restraints weight = 45876.381| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.80 r_work: 0.3099 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 23564 Z= 0.110 Angle : 0.547 13.765 32186 Z= 0.267 Chirality : 0.044 0.266 3819 Planarity : 0.003 0.037 4055 Dihedral : 4.709 52.623 4227 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.41 % Allowed : 10.85 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2788 helix: 2.72 (0.21), residues: 625 sheet: 0.23 (0.21), residues: 619 loop : -0.44 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.027 0.001 TYR H 32 PHE 0.024 0.001 PHE C 168 TRP 0.011 0.001 TRP A 104 HIS 0.004 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00250 (23472) covalent geometry : angle 0.51593 (31945) SS BOND : bond 0.00258 ( 35) SS BOND : angle 1.77214 ( 70) hydrogen bonds : bond 0.03763 ( 870) hydrogen bonds : angle 5.02393 ( 2415) link_BETA1-4 : bond 0.00329 ( 18) link_BETA1-4 : angle 0.97981 ( 54) link_NAG-ASN : bond 0.00567 ( 39) link_NAG-ASN : angle 2.72934 ( 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 173 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6631 (tt) REVERT: A 160 TYR cc_start: 0.5866 (p90) cc_final: 0.5631 (p90) REVERT: A 200 TYR cc_start: 0.7571 (m-80) cc_final: 0.7271 (t80) REVERT: A 298 GLU cc_start: 0.8764 (tt0) cc_final: 0.8060 (tm-30) REVERT: A 856 ASN cc_start: 0.6748 (OUTLIER) cc_final: 0.6443 (m110) REVERT: A 983 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7844 (mtm-85) REVERT: B 102 ARG cc_start: 0.6396 (mmp-170) cc_final: 0.6140 (mmp-170) REVERT: B 118 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6429 (mp) REVERT: B 129 LYS cc_start: 0.6124 (mtmt) cc_final: 0.5754 (tttt) REVERT: B 153 MET cc_start: 0.5229 (mpp) cc_final: 0.4326 (pp-130) REVERT: B 190 ARG cc_start: 0.7369 (ttm170) cc_final: 0.7089 (ttm170) REVERT: B 201 PHE cc_start: 0.7533 (t80) cc_final: 0.7185 (t80) REVERT: B 207 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7353 (t70) REVERT: B 239 GLN cc_start: 0.7138 (tt0) cc_final: 0.6702 (tt0) REVERT: B 554 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7907 (mm-30) REVERT: B 957 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8198 (pp30) REVERT: B 964 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8693 (mmmm) REVERT: C 30 ASN cc_start: 0.7622 (t0) cc_final: 0.7048 (t0) REVERT: C 64 TRP cc_start: 0.7722 (t60) cc_final: 0.7485 (t60) REVERT: C 187 LYS cc_start: 0.6725 (mmtp) cc_final: 0.6377 (ptpt) REVERT: C 218 GLN cc_start: 0.8455 (tt0) cc_final: 0.8220 (tp40) REVERT: C 324 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: C 334 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.6809 (p0) REVERT: C 421 TYR cc_start: 0.8290 (m-80) cc_final: 0.7677 (m-80) REVERT: C 455 LEU cc_start: 0.8339 (tp) cc_final: 0.7956 (pp) REVERT: C 532 ASN cc_start: 0.9020 (t0) cc_final: 0.8295 (OUTLIER) REVERT: C 957 GLN cc_start: 0.8649 (tt0) cc_final: 0.8271 (tm-30) REVERT: C 990 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 1002 GLN cc_start: 0.8911 (tt0) cc_final: 0.8699 (tt0) outliers start: 35 outliers final: 15 residues processed: 164 average time/residue: 0.5596 time to fit residues: 107.1166 Evaluate side-chains 153 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 533 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG 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 858 LEU 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 C residue 1010 GLN 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: 0.9990 chunk 109 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 169 optimal weight: 0.0870 chunk 133 optimal weight: 0.6980 chunk 279 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 136 optimal weight: 0.0060 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.125948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076724 restraints weight = 46307.856| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.79 r_work: 0.3086 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23564 Z= 0.105 Angle : 0.537 11.527 32186 Z= 0.262 Chirality : 0.043 0.267 3819 Planarity : 0.003 0.047 4055 Dihedral : 4.554 52.846 4227 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.37 % Allowed : 11.05 % Favored : 87.59 % 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: 0.68 (0.16), residues: 2788 helix: 2.73 (0.21), residues: 625 sheet: 0.27 (0.21), residues: 629 loop : -0.42 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.032 0.001 TYR H 32 PHE 0.025 0.001 PHE C 168 TRP 0.011 0.001 TRP A 104 HIS 0.005 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00232 (23472) covalent geometry : angle 0.51060 (31945) SS BOND : bond 0.00400 ( 35) SS BOND : angle 0.91267 ( 70) hydrogen bonds : bond 0.03655 ( 870) hydrogen bonds : angle 4.94450 ( 2415) link_BETA1-4 : bond 0.00317 ( 18) link_BETA1-4 : angle 0.98216 ( 54) link_NAG-ASN : bond 0.00558 ( 39) link_NAG-ASN : angle 2.66774 ( 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 172 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.5865 (p90) cc_final: 0.5640 (p90) REVERT: A 200 TYR cc_start: 0.7579 (m-80) cc_final: 0.7343 (t80) REVERT: A 298 GLU cc_start: 0.8777 (tt0) cc_final: 0.8083 (tm-30) REVERT: A 856 ASN cc_start: 0.6792 (OUTLIER) cc_final: 0.6422 (m110) REVERT: A 983 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7860 (mtp180) REVERT: B 88 ASP cc_start: 0.7690 (m-30) cc_final: 0.6717 (p0) REVERT: B 118 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6438 (mp) REVERT: B 129 LYS cc_start: 0.6031 (mtmt) cc_final: 0.5649 (ttmt) REVERT: B 153 MET cc_start: 0.5327 (mpp) cc_final: 0.4380 (pp-130) REVERT: B 190 ARG cc_start: 0.7306 (ttm170) cc_final: 0.7062 (ttm170) REVERT: B 201 PHE cc_start: 0.7537 (t80) cc_final: 0.7171 (t80) REVERT: B 207 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.7316 (t70) REVERT: B 239 GLN cc_start: 0.7115 (tt0) cc_final: 0.6667 (tt0) REVERT: B 269 TYR cc_start: 0.7946 (m-80) cc_final: 0.7714 (m-80) REVERT: B 554 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7916 (mm-30) REVERT: B 858 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8136 (pt) REVERT: B 957 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8212 (pp30) REVERT: B 964 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8718 (mmmm) REVERT: C 30 ASN cc_start: 0.7716 (t0) cc_final: 0.7069 (t0) REVERT: C 64 TRP cc_start: 0.7721 (t60) cc_final: 0.7516 (t60) REVERT: C 134 GLN cc_start: 0.7359 (mm110) cc_final: 0.6667 (mm110) REVERT: C 187 LYS cc_start: 0.6852 (mmtp) cc_final: 0.6487 (ptpt) REVERT: C 218 GLN cc_start: 0.8455 (tt0) cc_final: 0.8213 (tp40) REVERT: C 324 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: C 334 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6868 (p0) REVERT: C 421 TYR cc_start: 0.8378 (m-80) cc_final: 0.8141 (m-80) REVERT: C 455 LEU cc_start: 0.8354 (tp) cc_final: 0.7983 (pp) REVERT: C 532 ASN cc_start: 0.9026 (t0) cc_final: 0.8301 (OUTLIER) REVERT: C 957 GLN cc_start: 0.8663 (tt0) cc_final: 0.8292 (tm-30) REVERT: C 985 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7638 (p0) REVERT: C 990 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7554 (tm-30) REVERT: H 34 MET cc_start: 0.6073 (pmm) cc_final: 0.3000 (mpp) REVERT: H 98 VAL cc_start: 0.6708 (OUTLIER) cc_final: 0.6262 (m) outliers start: 34 outliers final: 13 residues processed: 162 average time/residue: 0.5638 time to fit residues: 107.1166 Evaluate side-chains 151 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL 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 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 858 LEU Chi-restraints excluded: chain B residue 934 ILE 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 985 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 162 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 223 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B1010 GLN C 196 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.124834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075230 restraints weight = 46191.057| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.83 r_work: 0.3060 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 23564 Z= 0.162 Angle : 0.577 18.797 32186 Z= 0.283 Chirality : 0.044 0.274 3819 Planarity : 0.004 0.058 4055 Dihedral : 4.640 52.103 4227 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.17 % Allowed : 11.57 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2788 helix: 2.66 (0.21), residues: 626 sheet: 0.08 (0.20), residues: 628 loop : -0.46 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 102 TYR 0.034 0.001 TYR H 32 PHE 0.021 0.001 PHE C 400 TRP 0.013 0.001 TRP C 353 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00382 (23472) covalent geometry : angle 0.54232 (31945) SS BOND : bond 0.00476 ( 35) SS BOND : angle 2.33642 ( 70) hydrogen bonds : bond 0.03965 ( 870) hydrogen bonds : angle 5.06628 ( 2415) link_BETA1-4 : bond 0.00288 ( 18) link_BETA1-4 : angle 1.05754 ( 54) link_NAG-ASN : bond 0.00570 ( 39) link_NAG-ASN : angle 2.71693 ( 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 164 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.5944 (p90) cc_final: 0.5683 (p90) REVERT: A 200 TYR cc_start: 0.7732 (m-80) cc_final: 0.7425 (t80) REVERT: A 298 GLU cc_start: 0.8770 (tt0) cc_final: 0.8118 (tm-30) REVERT: A 856 ASN cc_start: 0.6755 (OUTLIER) cc_final: 0.6449 (m110) REVERT: A 983 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7907 (mtp180) REVERT: B 118 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6243 (mp) REVERT: B 129 LYS cc_start: 0.6196 (mtmt) cc_final: 0.5817 (ttmt) REVERT: B 153 MET cc_start: 0.5268 (mpp) cc_final: 0.4293 (pp-130) REVERT: B 190 ARG cc_start: 0.7308 (ttm170) cc_final: 0.7015 (ttm170) REVERT: B 201 PHE cc_start: 0.7524 (t80) cc_final: 0.7150 (t80) REVERT: B 207 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.7276 (t70) REVERT: B 239 GLN cc_start: 0.7126 (tt0) cc_final: 0.6681 (tt0) REVERT: B 554 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7896 (mm-30) REVERT: B 964 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8719 (mmmm) REVERT: B 990 GLU cc_start: 0.8275 (tt0) cc_final: 0.7990 (tm-30) REVERT: C 64 TRP cc_start: 0.7742 (t60) cc_final: 0.7535 (t60) REVERT: C 218 GLN cc_start: 0.8442 (tt0) cc_final: 0.8215 (tp40) REVERT: C 324 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: C 421 TYR cc_start: 0.8279 (m-80) cc_final: 0.8059 (m-80) REVERT: C 455 LEU cc_start: 0.8394 (tp) cc_final: 0.8051 (pp) REVERT: C 532 ASN cc_start: 0.8979 (t0) cc_final: 0.8490 (m110) REVERT: C 869 MET cc_start: 0.9251 (mtt) cc_final: 0.8892 (mtt) REVERT: C 957 GLN cc_start: 0.8657 (tt0) cc_final: 0.8273 (tm-30) REVERT: C 985 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7670 (p0) REVERT: C 990 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7543 (tm-30) REVERT: H 98 VAL cc_start: 0.6642 (t) cc_final: 0.6304 (m) outliers start: 29 outliers final: 12 residues processed: 157 average time/residue: 0.5711 time to fit residues: 105.0482 Evaluate side-chains 148 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG 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 534 VAL 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 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1010 GLN 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: 9.9990 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 210 optimal weight: 0.9990 chunk 258 optimal weight: 0.7980 chunk 260 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B1010 GLN C 196 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.125041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075628 restraints weight = 46253.541| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.80 r_work: 0.3088 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23564 Z= 0.130 Angle : 0.549 11.164 32186 Z= 0.269 Chirality : 0.044 0.269 3819 Planarity : 0.003 0.055 4055 Dihedral : 4.569 52.368 4225 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.00 % Allowed : 11.69 % Favored : 87.30 % 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: 2.71 (0.20), residues: 625 sheet: 0.25 (0.20), residues: 632 loop : -0.44 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 457 TYR 0.034 0.001 TYR H 32 PHE 0.025 0.001 PHE C 168 TRP 0.013 0.001 TRP A 104 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00298 (23472) covalent geometry : angle 0.52406 (31945) SS BOND : bond 0.00166 ( 35) SS BOND : angle 0.89033 ( 70) hydrogen bonds : bond 0.03801 ( 870) hydrogen bonds : angle 5.00452 ( 2415) link_BETA1-4 : bond 0.00293 ( 18) link_BETA1-4 : angle 0.98978 ( 54) link_NAG-ASN : bond 0.00558 ( 39) link_NAG-ASN : angle 2.66301 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12137.14 seconds wall clock time: 206 minutes 17.51 seconds (12377.51 seconds total)