Starting phenix.real_space_refine on Thu Mar 5 20:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ub0_26433/03_2026/7ub0_26433.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ub0_26433/03_2026/7ub0_26433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ub0_26433/03_2026/7ub0_26433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ub0_26433/03_2026/7ub0_26433.map" model { file = "/net/cci-nas-00/data/ceres_data/7ub0_26433/03_2026/7ub0_26433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ub0_26433/03_2026/7ub0_26433.cif" } resolution = 3.31 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= -0.003 sd= 0.154 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 114 5.16 5 C 15950 2.51 5 N 4092 2.21 5 O 4837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 24993 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8152 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 50, 'TRANS': 991} Chain breaks: 6 Chain: "B" Number of atoms: 8031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8031 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8110 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.51, per 1000 atoms: 0.22 Number of scatterers: 24993 At special positions: 0 Unit cell: (129.6, 140.4, 174.96, 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 114 16.00 O 4837 8.00 N 4092 7.00 C 15950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 B 840 " - pdb=" SG CYS B 851 " 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 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 234 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 978.2 milliseconds 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5818 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 45 sheets defined 26.7% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.825A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.946A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.648A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 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: 3.636A 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 835 through 841 Processing helix chain 'A' and resid 848 through 857 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.264A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.589A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.834A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.804A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.878A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 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: 4.383A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.863A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.184A 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 removed outlier: 3.828A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.061A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.158A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) 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: 3.564A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.090A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.324A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.544A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.901A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.634A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.792A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.576A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.537A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.672A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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: 3.563A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.100A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.491A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.238A 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: 6.470A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.810A 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 removed outlier: 5.921A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.156A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.869A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.728A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.632A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.590A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.648A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.506A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.608A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.839A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.241A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.812A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.846A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.856A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.714A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.287A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.275A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.577A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.560A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.619A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.651A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.565A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.588A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.212A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.633A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.605A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.549A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.812A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.341A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2919 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: 5.83 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7933 1.35 - 1.47: 6455 1.47 - 1.59: 11016 1.59 - 1.71: 0 1.71 - 1.84: 141 Bond restraints: 25545 Sorted by residual: bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 25540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 33585 1.25 - 2.51: 909 2.51 - 3.76: 223 3.76 - 5.01: 11 5.01 - 6.27: 10 Bond angle restraints: 34738 Sorted by residual: angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 108.54 5.86 2.30e+00 1.89e-01 6.48e+00 angle pdb=" C ARG B 102 " pdb=" N GLY B 103 " pdb=" CA GLY B 103 " ideal model delta sigma weight residual 121.22 116.13 5.09 2.05e+00 2.38e-01 6.18e+00 angle pdb=" N VAL A 620 " pdb=" CA VAL A 620 " pdb=" C VAL A 620 " ideal model delta sigma weight residual 108.88 113.95 -5.07 2.16e+00 2.14e-01 5.51e+00 angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 119.57 -5.17 2.30e+00 1.89e-01 5.05e+00 angle pdb=" CB GLN A 173 " pdb=" CG GLN A 173 " pdb=" CD GLN A 173 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.70e+00 3.46e-01 5.05e+00 ... (remaining 34733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14386 17.89 - 35.78: 1211 35.78 - 53.67: 214 53.67 - 71.56: 47 71.56 - 89.44: 14 Dihedral angle restraints: 15872 sinusoidal: 6827 harmonic: 9045 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.87 82.87 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.96 72.96 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.35 71.35 1 1.00e+01 1.00e-02 6.53e+01 ... (remaining 15869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2939 0.042 - 0.084: 756 0.084 - 0.125: 373 0.125 - 0.167: 20 0.167 - 0.209: 4 Chirality restraints: 4092 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C2 NAG C1310 " pdb=" C1 NAG C1310 " pdb=" C3 NAG C1310 " pdb=" N2 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 4089 not shown) Planarity restraints: 4463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 295 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 738 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C CYS C 738 " 0.030 2.00e-02 2.50e+03 pdb=" O CYS C 738 " -0.011 2.00e-02 2.50e+03 pdb=" N THR C 739 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 4460 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2076 2.74 - 3.28: 22740 3.28 - 3.82: 40571 3.82 - 4.36: 47447 4.36 - 4.90: 85556 Nonbonded interactions: 198390 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.205 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A1100 " pdb=" O7 NAG G 1 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.248 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.279 3.040 ... (remaining 198385 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' and (resid 24 through 68 or resid 81 through 137 or resid 166 through \ 210 or resid 215 through 243 or resid 263 through 621 or resid 641 through 674 \ or resid 691 through 1146 or resid 1303 through 1310)) selection = (chain 'B' and (resid 24 through 137 or resid 166 through 621 or resid 641 throu \ gh 1308)) selection = (chain 'C' and (resid 24 through 68 or resid 81 through 177 or resid 187 through \ 210 or resid 215 through 243 or resid 263 through 621 or resid 641 through 674 \ or resid 691 through 1146 or resid 1303 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.020 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: 0.070 Set scattering table: 0.060 Process input model: 23.820 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.003 0.054 25637 Z= 0.161 Angle : 0.527 6.265 34972 Z= 0.266 Chirality : 0.044 0.209 4092 Planarity : 0.004 0.050 4423 Dihedral : 13.231 89.444 9928 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3065 helix: 1.41 (0.19), residues: 713 sheet: 0.39 (0.18), residues: 720 loop : -0.99 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B 559 TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00339 (25545) covalent geometry : angle 0.51492 (34738) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.20654 ( 84) hydrogen bonds : bond 0.07925 ( 1051) hydrogen bonds : angle 5.49375 ( 2919) link_BETA1-4 : bond 0.00429 ( 10) link_BETA1-4 : angle 1.33275 ( 30) link_NAG-ASN : bond 0.00192 ( 40) link_NAG-ASN : angle 1.63348 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.955 Fit side-chains REVERT: B 468 ILE cc_start: 0.8943 (pt) cc_final: 0.8581 (tp) REVERT: B 1029 MET cc_start: 0.9355 (tpp) cc_final: 0.8984 (tpp) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1338 time to fit residues: 15.0536 Evaluate side-chains 51 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 613 GLN B 901 GLN C 901 GLN C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.079942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056570 restraints weight = 64609.049| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.70 r_work: 0.2663 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 25637 Z= 0.296 Angle : 0.615 9.421 34972 Z= 0.316 Chirality : 0.048 0.184 4092 Planarity : 0.004 0.044 4423 Dihedral : 7.110 59.726 4381 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3065 helix: 1.54 (0.20), residues: 711 sheet: 0.20 (0.18), residues: 722 loop : -1.02 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1014 TYR 0.025 0.002 TYR C1067 PHE 0.020 0.002 PHE B 559 TRP 0.014 0.002 TRP C 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00725 (25545) covalent geometry : angle 0.60267 (34738) SS BOND : bond 0.00532 ( 42) SS BOND : angle 1.37536 ( 84) hydrogen bonds : bond 0.05615 ( 1051) hydrogen bonds : angle 5.43919 ( 2919) link_BETA1-4 : bond 0.00252 ( 10) link_BETA1-4 : angle 1.30838 ( 30) link_NAG-ASN : bond 0.00315 ( 40) link_NAG-ASN : angle 1.83752 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8185 (t80) cc_final: 0.7984 (t80) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.1367 time to fit residues: 13.0682 Evaluate side-chains 48 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain C residue 200 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 143 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN A 804 GLN A 935 GLN C 414 GLN C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056773 restraints weight = 64560.464| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.67 r_work: 0.2687 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25637 Z= 0.212 Angle : 0.541 9.393 34972 Z= 0.278 Chirality : 0.045 0.231 4092 Planarity : 0.003 0.037 4423 Dihedral : 6.698 58.827 4381 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.52 % Allowed : 6.78 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3065 helix: 1.71 (0.20), residues: 717 sheet: 0.17 (0.18), residues: 721 loop : -0.99 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.023 0.001 TYR C1067 PHE 0.016 0.001 PHE B 559 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00516 (25545) covalent geometry : angle 0.52940 (34738) SS BOND : bond 0.00443 ( 42) SS BOND : angle 1.20089 ( 84) hydrogen bonds : bond 0.04955 ( 1051) hydrogen bonds : angle 5.29867 ( 2919) link_BETA1-4 : bond 0.00283 ( 10) link_BETA1-4 : angle 1.18836 ( 30) link_NAG-ASN : bond 0.00226 ( 40) link_NAG-ASN : angle 1.68552 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.935 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1269 time to fit residues: 14.5532 Evaluate side-chains 54 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 123 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 259 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.079994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056625 restraints weight = 64339.528| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.76 r_work: 0.2652 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25637 Z= 0.210 Angle : 0.541 9.503 34972 Z= 0.277 Chirality : 0.045 0.238 4092 Planarity : 0.003 0.036 4423 Dihedral : 6.490 58.886 4381 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.70 % Allowed : 7.82 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3065 helix: 1.78 (0.20), residues: 717 sheet: 0.12 (0.18), residues: 733 loop : -0.98 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.021 0.001 TYR C1067 PHE 0.015 0.001 PHE A1121 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00510 (25545) covalent geometry : angle 0.52857 (34738) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.24552 ( 84) hydrogen bonds : bond 0.04929 ( 1051) hydrogen bonds : angle 5.26270 ( 2919) link_BETA1-4 : bond 0.00266 ( 10) link_BETA1-4 : angle 1.18331 ( 30) link_NAG-ASN : bond 0.00239 ( 40) link_NAG-ASN : angle 1.69846 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 375 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: A 377 PHE cc_start: 0.8154 (t80) cc_final: 0.7947 (t80) outliers start: 19 outliers final: 11 residues processed: 64 average time/residue: 0.1405 time to fit residues: 16.1172 Evaluate side-chains 57 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 69 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 304 optimal weight: 0.4980 chunk 269 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 284 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 755 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.081097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.057338 restraints weight = 63698.621| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.71 r_work: 0.2707 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25637 Z= 0.129 Angle : 0.483 9.537 34972 Z= 0.248 Chirality : 0.043 0.247 4092 Planarity : 0.003 0.034 4423 Dihedral : 6.153 58.504 4381 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.74 % Allowed : 8.48 % Favored : 90.77 % 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: 0.11 (0.15), residues: 3065 helix: 2.01 (0.20), residues: 721 sheet: 0.21 (0.18), residues: 737 loop : -0.92 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.019 0.001 TYR C1067 PHE 0.013 0.001 PHE A1121 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (25545) covalent geometry : angle 0.47171 (34738) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.07693 ( 84) hydrogen bonds : bond 0.04252 ( 1051) hydrogen bonds : angle 5.05828 ( 2919) link_BETA1-4 : bond 0.00351 ( 10) link_BETA1-4 : angle 1.10636 ( 30) link_NAG-ASN : bond 0.00207 ( 40) link_NAG-ASN : angle 1.55392 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.910 Fit side-chains REVERT: A 135 PHE cc_start: 0.5071 (OUTLIER) cc_final: 0.2946 (m-10) REVERT: A 375 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: A 377 PHE cc_start: 0.8091 (t80) cc_final: 0.7843 (t80) REVERT: C 486 PHE cc_start: 0.8985 (t80) cc_final: 0.8620 (t80) outliers start: 20 outliers final: 15 residues processed: 66 average time/residue: 0.1473 time to fit residues: 17.4836 Evaluate side-chains 61 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 45 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 177 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.081883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058279 restraints weight = 63762.124| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.69 r_work: 0.2729 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25637 Z= 0.094 Angle : 0.458 9.575 34972 Z= 0.234 Chirality : 0.043 0.250 4092 Planarity : 0.003 0.033 4423 Dihedral : 5.906 57.711 4381 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.70 % Allowed : 9.04 % Favored : 90.26 % 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: 0.25 (0.15), residues: 3065 helix: 2.18 (0.20), residues: 721 sheet: 0.29 (0.18), residues: 728 loop : -0.84 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.017 0.001 TYR C1067 PHE 0.011 0.001 PHE A1121 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00211 (25545) covalent geometry : angle 0.44843 (34738) SS BOND : bond 0.00341 ( 42) SS BOND : angle 0.92070 ( 84) hydrogen bonds : bond 0.03857 ( 1051) hydrogen bonds : angle 4.90233 ( 2919) link_BETA1-4 : bond 0.00388 ( 10) link_BETA1-4 : angle 1.06821 ( 30) link_NAG-ASN : bond 0.00215 ( 40) link_NAG-ASN : angle 1.46946 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.855 Fit side-chains REVERT: A 375 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: A 377 PHE cc_start: 0.8031 (t80) cc_final: 0.7778 (t80) REVERT: B 1029 MET cc_start: 0.9433 (tpp) cc_final: 0.9047 (tpp) REVERT: C 486 PHE cc_start: 0.8999 (t80) cc_final: 0.8620 (t80) outliers start: 19 outliers final: 15 residues processed: 65 average time/residue: 0.1285 time to fit residues: 15.6359 Evaluate side-chains 61 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 844 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 231 optimal weight: 0.5980 chunk 212 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 262 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 283 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.080361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056603 restraints weight = 64079.899| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.70 r_work: 0.2687 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 25637 Z= 0.203 Angle : 0.536 14.884 34972 Z= 0.272 Chirality : 0.045 0.242 4092 Planarity : 0.003 0.033 4423 Dihedral : 6.094 59.920 4381 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.00 % Allowed : 9.30 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3065 helix: 2.00 (0.20), residues: 721 sheet: 0.22 (0.18), residues: 726 loop : -0.88 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.020 0.001 TYR C1067 PHE 0.015 0.001 PHE B 759 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00495 (25545) covalent geometry : angle 0.52111 (34738) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.77973 ( 84) hydrogen bonds : bond 0.04677 ( 1051) hydrogen bonds : angle 5.10974 ( 2919) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 1.17015 ( 30) link_NAG-ASN : bond 0.00233 ( 40) link_NAG-ASN : angle 1.62444 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.930 Fit side-chains REVERT: A 135 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.2686 (m-10) REVERT: A 375 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: A 377 PHE cc_start: 0.8086 (t80) cc_final: 0.7856 (t80) REVERT: C 486 PHE cc_start: 0.9010 (t80) cc_final: 0.8621 (t80) outliers start: 27 outliers final: 20 residues processed: 73 average time/residue: 0.1246 time to fit residues: 16.8005 Evaluate side-chains 68 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 286 optimal weight: 2.9990 chunk 205 optimal weight: 0.0970 chunk 236 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 279 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 276 optimal weight: 0.0980 chunk 79 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059333 restraints weight = 63484.867| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.72 r_work: 0.2740 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25637 Z= 0.086 Angle : 0.453 9.764 34972 Z= 0.231 Chirality : 0.042 0.253 4092 Planarity : 0.003 0.034 4423 Dihedral : 5.695 57.324 4381 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.82 % Allowed : 9.63 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3065 helix: 2.22 (0.20), residues: 721 sheet: 0.35 (0.18), residues: 735 loop : -0.77 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 995 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE A1121 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00187 (25545) covalent geometry : angle 0.44273 (34738) SS BOND : bond 0.00301 ( 42) SS BOND : angle 1.19413 ( 84) hydrogen bonds : bond 0.03573 ( 1051) hydrogen bonds : angle 4.81034 ( 2919) link_BETA1-4 : bond 0.00436 ( 10) link_BETA1-4 : angle 1.03152 ( 30) link_NAG-ASN : bond 0.00260 ( 40) link_NAG-ASN : angle 1.38140 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.823 Fit side-chains REVERT: A 375 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: A 377 PHE cc_start: 0.8068 (t80) cc_final: 0.7835 (t80) REVERT: B 1029 MET cc_start: 0.9422 (tpp) cc_final: 0.9057 (tpp) REVERT: C 486 PHE cc_start: 0.9004 (t80) cc_final: 0.8612 (t80) outliers start: 22 outliers final: 12 residues processed: 71 average time/residue: 0.1293 time to fit residues: 16.9071 Evaluate side-chains 60 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 154 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 222 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 0.0040 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059206 restraints weight = 63874.061| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.67 r_work: 0.2757 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25637 Z= 0.090 Angle : 0.454 10.071 34972 Z= 0.230 Chirality : 0.042 0.250 4092 Planarity : 0.003 0.032 4423 Dihedral : 5.584 57.790 4381 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.67 % Allowed : 9.86 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3065 helix: 2.35 (0.20), residues: 722 sheet: 0.40 (0.18), residues: 738 loop : -0.70 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.015 0.001 TYR C1067 PHE 0.011 0.001 PHE A1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00203 (25545) covalent geometry : angle 0.44367 (34738) SS BOND : bond 0.00350 ( 42) SS BOND : angle 1.17884 ( 84) hydrogen bonds : bond 0.03561 ( 1051) hydrogen bonds : angle 4.75195 ( 2919) link_BETA1-4 : bond 0.00372 ( 10) link_BETA1-4 : angle 1.05942 ( 30) link_NAG-ASN : bond 0.00171 ( 40) link_NAG-ASN : angle 1.39573 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.967 Fit side-chains REVERT: A 375 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: A 377 PHE cc_start: 0.8006 (t80) cc_final: 0.7763 (t80) REVERT: B 1029 MET cc_start: 0.9434 (tpp) cc_final: 0.9110 (tpp) REVERT: C 486 PHE cc_start: 0.8994 (t80) cc_final: 0.8611 (t80) outliers start: 18 outliers final: 14 residues processed: 66 average time/residue: 0.1400 time to fit residues: 17.9906 Evaluate side-chains 63 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 127 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 10 optimal weight: 0.0020 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 chunk 199 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057958 restraints weight = 64047.920| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.70 r_work: 0.2725 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25637 Z= 0.134 Angle : 0.479 9.680 34972 Z= 0.242 Chirality : 0.043 0.246 4092 Planarity : 0.003 0.031 4423 Dihedral : 5.648 58.196 4381 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.74 % Allowed : 9.86 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3065 helix: 2.29 (0.20), residues: 721 sheet: 0.39 (0.18), residues: 735 loop : -0.74 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1039 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE A1121 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00323 (25545) covalent geometry : angle 0.46772 (34738) SS BOND : bond 0.00399 ( 42) SS BOND : angle 1.31001 ( 84) hydrogen bonds : bond 0.04016 ( 1051) hydrogen bonds : angle 4.86182 ( 2919) link_BETA1-4 : bond 0.00345 ( 10) link_BETA1-4 : angle 1.10072 ( 30) link_NAG-ASN : bond 0.00151 ( 40) link_NAG-ASN : angle 1.44085 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.982 Fit side-chains REVERT: A 135 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.2424 (m-10) REVERT: A 375 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: A 377 PHE cc_start: 0.8064 (t80) cc_final: 0.7843 (t80) REVERT: B 1029 MET cc_start: 0.9434 (tpp) cc_final: 0.9191 (tpp) REVERT: C 486 PHE cc_start: 0.8996 (t80) cc_final: 0.8607 (t80) outliers start: 20 outliers final: 16 residues processed: 68 average time/residue: 0.1253 time to fit residues: 15.7221 Evaluate side-chains 67 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 218 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.081978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058360 restraints weight = 63693.819| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.70 r_work: 0.2736 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25637 Z= 0.110 Angle : 0.465 10.475 34972 Z= 0.235 Chirality : 0.043 0.248 4092 Planarity : 0.003 0.032 4423 Dihedral : 5.573 57.886 4381 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.85 % Allowed : 9.82 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3065 helix: 2.32 (0.20), residues: 722 sheet: 0.41 (0.18), residues: 737 loop : -0.70 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 905 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE A1121 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00258 (25545) covalent geometry : angle 0.45441 (34738) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.19323 ( 84) hydrogen bonds : bond 0.03825 ( 1051) hydrogen bonds : angle 4.80906 ( 2919) link_BETA1-4 : bond 0.00368 ( 10) link_BETA1-4 : angle 1.07163 ( 30) link_NAG-ASN : bond 0.00157 ( 40) link_NAG-ASN : angle 1.39881 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.76 seconds wall clock time: 72 minutes 24.59 seconds (4344.59 seconds total)