Starting phenix.real_space_refine on Sun Jul 5 20:19:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz8_26882/07_2026/7uz8_26882.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 132 5.16 5 C 19188 2.51 5 N 4944 2.21 5 O 5811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30075 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8113 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 56, 'TRANS': 982} Chain breaks: 7 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8113 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 56, 'TRANS': 982} Chain breaks: 7 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8113 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 56, 'TRANS': 982} Chain breaks: 7 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "P" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 chiralities: 9 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 chiralities: 9 Chain: "C" 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 chiralities: 9 Time building chain proxies: 7.27, per 1000 atoms: 0.24 Number of scatterers: 30075 At special positions: 0 Unit cell: (153.92, 159.744, 188.864, 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 132 16.00 O 5811 8.00 N 4944 7.00 C 19188 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 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " 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-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN B 343 " " NAG F 1 " - " ASN C 343 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 59 sheets defined 21.9% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.759A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.559A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.028A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.132A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.632A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.690A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.179A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.514A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.178A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) 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 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 removed outlier: 3.545A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.047A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.160A 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 337 through 343 removed outlier: 3.585A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.618A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.077A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.759A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.533A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.274A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.637A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.190A 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 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.512A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.093A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 498 through 502 removed outlier: 3.641A pdb=" N GLY C 502 " --> pdb=" O PRO C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 757 removed outlier: 3.551A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.510A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.566A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.178A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.217A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.550A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) 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 removed outlier: 3.735A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.570A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.403A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.833A pdb=" N ASN H 36 " --> pdb=" O ASN H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 72 Processing helix chain 'H' and resid 82 through 85 Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'M' and resid 29 through 37 removed outlier: 3.900A pdb=" N ASN M 36 " --> pdb=" O ASN M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 72 Processing helix chain 'M' and resid 82 through 85 Processing helix chain 'N' and resid 27 through 29 No H-bonds generated for 'chain 'N' and resid 27 through 29' Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.834A pdb=" N ASN P 36 " --> pdb=" O ASN P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 72 Processing helix chain 'P' and resid 82 through 85 Processing helix chain 'Q' and resid 27 through 29 No H-bonds generated for 'chain 'Q' and resid 27 through 29' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.045A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.792A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 3.540A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 172 removed outlier: 3.609A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.266A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.052A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.611A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.790A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.625A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.693A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.325A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.084A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.770A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.918A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.504A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 141 removed outlier: 10.539A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.221A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.036A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.857A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.588A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.661A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.707A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.387A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.840A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.480A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.522A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 135 through 141 removed outlier: 10.498A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.224A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.606A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (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 654 through 655 removed outlier: 5.860A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.693A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.766A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.524A pdb=" N THR H 79 " --> pdb=" O TYR H 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 50 through 55 removed outlier: 5.070A pdb=" N TRP H 52 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.786A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.361A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR L 103 " --> pdb=" O TYR L 42 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'M' and resid 18 through 19 removed outlier: 3.504A pdb=" N THR M 79 " --> pdb=" O TYR M 88 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 50 through 55 removed outlier: 5.066A pdb=" N TRP M 52 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS M 43 " --> pdb=" O TRP M 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.764A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE N 87 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 66 through 67 removed outlier: 3.541A pdb=" N TYR N 55 " --> pdb=" O THR N 66 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR N 55 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR N 103 " --> pdb=" O TYR N 42 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'P' and resid 18 through 19 Processing sheet with id=AG3, first strand: chain 'P' and resid 50 through 55 removed outlier: 5.103A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 4 through 6 removed outlier: 3.776A pdb=" N THR Q 5 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS Q 23 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE Q 87 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 66 through 67 removed outlier: 3.502A pdb=" N TYR Q 55 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR Q 55 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU Q 39 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR Q 103 " --> pdb=" O TYR Q 42 " (cutoff:3.500A) 1097 hydrogen bonds defined for protein. 2961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.18 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9562 1.34 - 1.46: 6843 1.46 - 1.58: 14195 1.58 - 1.70: 0 1.70 - 1.82: 171 Bond restraints: 30771 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 30766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 40880 1.74 - 3.48: 886 3.48 - 5.22: 97 5.22 - 6.96: 22 6.96 - 8.70: 1 Bond angle restraints: 41886 Sorted by residual: angle pdb=" C LEU A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 120.09 124.82 -4.73 1.25e+00 6.40e-01 1.43e+01 angle pdb=" C LEU C 371 " pdb=" N ALA C 372 " pdb=" CA ALA C 372 " ideal model delta sigma weight residual 120.09 124.65 -4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" N GLY C1124 " pdb=" CA GLY C1124 " pdb=" C GLY C1124 " ideal model delta sigma weight residual 111.21 114.96 -3.75 1.04e+00 9.25e-01 1.30e+01 angle pdb=" C LEU B 371 " pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 120.09 124.59 -4.50 1.25e+00 6.40e-01 1.30e+01 angle pdb=" C GLN H 72 " pdb=" N ASP H 74 " pdb=" CA ASP H 74 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.24e+01 ... (remaining 41881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16543 17.98 - 35.96: 1199 35.96 - 53.94: 232 53.94 - 71.92: 57 71.92 - 89.90: 20 Dihedral angle restraints: 18051 sinusoidal: 6984 harmonic: 11067 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 104 " pdb=" CB CYS N 104 " ideal model delta sinusoidal sigma weight residual 93.00 172.73 -79.73 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 104 " pdb=" CB CYS Q 104 " ideal model delta sinusoidal sigma weight residual 93.00 167.03 -74.03 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 166.16 -73.16 1 1.00e+01 1.00e-02 6.82e+01 ... (remaining 18048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4288 0.075 - 0.150: 528 0.150 - 0.225: 13 0.225 - 0.300: 0 0.300 - 0.376: 1 Chirality restraints: 4830 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 4827 not shown) Planarity restraints: 5394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO A 82 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO A 217 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C1142 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO C1143 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C1143 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C1143 " 0.036 5.00e-02 4.00e+02 ... (remaining 5391 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 303 2.65 - 3.21: 27943 3.21 - 3.77: 46389 3.77 - 4.34: 66105 4.34 - 4.90: 107424 Nonbonded interactions: 248164 Sorted by model distance: nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.085 3.040 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.144 3.120 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.172 3.040 nonbonded pdb=" O LEU C 176 " pdb=" NH1 ARG C 190 " model vdw 2.175 3.120 ... (remaining 248159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 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: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.510 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.004 0.059 30846 Z= 0.197 Angle : 0.653 20.274 42069 Z= 0.345 Chirality : 0.045 0.376 4830 Planarity : 0.004 0.075 5364 Dihedral : 13.179 89.896 10809 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3741 helix: 1.39 (0.20), residues: 639 sheet: -0.06 (0.17), residues: 903 loop : -0.63 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 190 TYR 0.039 0.001 TYR A 756 PHE 0.025 0.001 PHE C 906 TRP 0.029 0.002 TRP C 64 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (30771) covalent geometry : angle 0.61587 / 0.34 (41886) SS BOND : bond 0.00484 / 0.34 ( 42) SS BOND : angle 1.42002 / 0.93 ( 84) hydrogen bonds : bond 0.20561 / 13.31 ( 1067) hydrogen bonds : angle 8.85868 / 6.15 ( 2961) link_BETA1-4 : bond 0.00549 / 0.24 ( 3) link_BETA1-4 : angle 1.61959 / 0.94 ( 9) link_NAG-ASN : bond 0.00739 / 0.56 ( 30) link_NAG-ASN : angle 4.53051 / 3.58 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.4409 (OUTLIER) cc_final: 0.4104 (p0) REVERT: B 84 LEU cc_start: 0.6793 (mt) cc_final: 0.6353 (mp) REVERT: B 965 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7896 (mm-40) REVERT: C 196 ASN cc_start: 0.7130 (t0) cc_final: 0.6876 (t0) REVERT: C 574 ASP cc_start: 0.7229 (t0) cc_final: 0.7015 (t0) REVERT: C 969 LYS cc_start: 0.8601 (mttm) cc_final: 0.8028 (mmmt) outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.1777 time to fit residues: 73.1955 Evaluate side-chains 193 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 957 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 949 GLN B 957 GLN C 755 GLN C 762 GLN C 949 GLN Q 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.234323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.179704 restraints weight = 39845.663| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 3.04 r_work: 0.3341 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30846 Z= 0.175 Angle : 0.627 19.466 42069 Z= 0.316 Chirality : 0.047 0.287 4830 Planarity : 0.004 0.055 5364 Dihedral : 4.479 61.010 4079 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.64 % Allowed : 6.17 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 3741 helix: 1.59 (0.21), residues: 609 sheet: -0.05 (0.17), residues: 867 loop : -0.62 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.023 0.001 TYR C1067 PHE 0.019 0.001 PHE B 906 TRP 0.015 0.001 TRP B 64 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (30771) covalent geometry : angle 0.59117 / 0.31 (41886) SS BOND : bond 0.00536 / 0.37 ( 42) SS BOND : angle 1.38388 / 0.91 ( 84) hydrogen bonds : bond 0.04605 / 2.94 ( 1067) hydrogen bonds : angle 6.82496 / 4.74 ( 2961) link_BETA1-4 : bond 0.00553 / 0.24 ( 3) link_BETA1-4 : angle 1.50996 / 0.88 ( 9) link_NAG-ASN : bond 0.00707 / 0.52 ( 30) link_NAG-ASN : angle 4.37053 / 3.46 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1092 GLU cc_start: 0.7969 (tp30) cc_final: 0.7757 (tt0) REVERT: B 84 LEU cc_start: 0.6799 (mt) cc_final: 0.6524 (mp) REVERT: B 99 ASN cc_start: 0.8205 (m-40) cc_final: 0.7901 (m-40) REVERT: B 102 ARG cc_start: 0.6240 (mmm160) cc_final: 0.5947 (mmm160) REVERT: B 574 ASP cc_start: 0.8301 (t0) cc_final: 0.8085 (t0) REVERT: C 196 ASN cc_start: 0.7388 (t0) cc_final: 0.7097 (t0) REVERT: C 271 GLN cc_start: 0.8145 (tt0) cc_final: 0.7790 (mt0) REVERT: C 574 ASP cc_start: 0.8178 (t0) cc_final: 0.7730 (t0) REVERT: C 969 LYS cc_start: 0.8476 (mttm) cc_final: 0.7966 (mmtp) outliers start: 21 outliers final: 15 residues processed: 235 average time/residue: 0.1760 time to fit residues: 71.1558 Evaluate side-chains 215 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 215 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 247 optimal weight: 40.0000 chunk 305 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 297 optimal weight: 0.9990 chunk 294 optimal weight: 4.9990 chunk 225 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 ASN A 762 GLN A 957 GLN B 121 ASN B 957 GLN C 245 HIS C 762 GLN C 949 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.233409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.178878 restraints weight = 39780.486| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.05 r_work: 0.3352 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30846 Z= 0.175 Angle : 0.602 18.627 42069 Z= 0.299 Chirality : 0.047 0.275 4830 Planarity : 0.004 0.052 5364 Dihedral : 4.328 21.559 4077 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.43 % Allowed : 8.76 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.22 (0.13), residues: 3741 helix: 1.61 (0.21), residues: 615 sheet: -0.05 (0.17), residues: 846 loop : -0.67 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.023 0.001 TYR C1067 PHE 0.017 0.001 PHE B 906 TRP 0.016 0.001 TRP C 64 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (30771) covalent geometry : angle 0.56649 / 0.29 (41886) SS BOND : bond 0.00570 / 0.39 ( 42) SS BOND : angle 1.32900 / 0.86 ( 84) hydrogen bonds : bond 0.04259 / 2.73 ( 1067) hydrogen bonds : angle 6.34235 / 4.39 ( 2961) link_BETA1-4 : bond 0.00409 / 0.18 ( 3) link_BETA1-4 : angle 1.53981 / 0.88 ( 9) link_NAG-ASN : bond 0.00683 / 0.51 ( 30) link_NAG-ASN : angle 4.27330 / 3.37 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6349 (mmt90) cc_final: 0.5740 (mmm160) REVERT: A 1092 GLU cc_start: 0.7967 (tp30) cc_final: 0.7744 (tt0) REVERT: B 84 LEU cc_start: 0.6945 (mt) cc_final: 0.6739 (mp) REVERT: B 574 ASP cc_start: 0.8288 (t0) cc_final: 0.7980 (t0) REVERT: C 192 PHE cc_start: 0.7433 (m-80) cc_final: 0.7112 (m-80) REVERT: C 196 ASN cc_start: 0.7350 (t0) cc_final: 0.7098 (t0) REVERT: C 271 GLN cc_start: 0.8207 (tt0) cc_final: 0.7844 (mt0) REVERT: C 314 GLN cc_start: 0.8356 (tt0) cc_final: 0.8009 (tm-30) REVERT: C 574 ASP cc_start: 0.8143 (t0) cc_final: 0.7701 (t0) REVERT: C 969 LYS cc_start: 0.8467 (mttm) cc_final: 0.8011 (mmtp) outliers start: 47 outliers final: 33 residues processed: 247 average time/residue: 0.1771 time to fit residues: 75.1338 Evaluate side-chains 230 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 76 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 166 optimal weight: 0.0980 chunk 371 optimal weight: 40.0000 chunk 24 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 957 GLN C 957 GLN L 105 GLN N 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.235601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181236 restraints weight = 39605.884| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.94 r_work: 0.3401 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 30846 Z= 0.109 Angle : 0.569 18.017 42069 Z= 0.280 Chirality : 0.045 0.272 4830 Planarity : 0.004 0.050 5364 Dihedral : 4.113 20.464 4077 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.43 % Allowed : 10.07 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3741 helix: 1.89 (0.21), residues: 615 sheet: 0.07 (0.17), residues: 864 loop : -0.56 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.001 PHE A 192 TRP 0.011 0.001 TRP C 64 HIS 0.004 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (30771) covalent geometry : angle 0.53292 / 0.27 (41886) SS BOND : bond 0.00313 / 0.22 ( 42) SS BOND : angle 1.57148 / 1.18 ( 84) hydrogen bonds : bond 0.03755 / 2.40 ( 1067) hydrogen bonds : angle 5.99098 / 4.16 ( 2961) link_BETA1-4 : bond 0.00522 / 0.24 ( 3) link_BETA1-4 : angle 1.50273 / 0.86 ( 9) link_NAG-ASN : bond 0.00737 / 0.54 ( 30) link_NAG-ASN : angle 4.10403 / 3.25 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6271 (mmt90) cc_final: 0.5986 (mmp-170) REVERT: B 574 ASP cc_start: 0.8261 (t0) cc_final: 0.7898 (t0) REVERT: C 192 PHE cc_start: 0.7382 (m-80) cc_final: 0.7029 (m-80) REVERT: C 196 ASN cc_start: 0.7302 (t0) cc_final: 0.7085 (t0) REVERT: C 314 GLN cc_start: 0.8219 (tt0) cc_final: 0.7939 (tm-30) REVERT: C 574 ASP cc_start: 0.8079 (t70) cc_final: 0.7633 (t0) REVERT: C 969 LYS cc_start: 0.8446 (mttm) cc_final: 0.8015 (mmtp) outliers start: 47 outliers final: 30 residues processed: 250 average time/residue: 0.1752 time to fit residues: 75.5795 Evaluate side-chains 229 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 103 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 246 optimal weight: 30.0000 chunk 347 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 chunk 274 optimal weight: 0.7980 chunk 351 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 363 optimal weight: 50.0000 chunk 211 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 762 GLN A 957 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 HIS B 949 GLN B 957 GLN C 762 GLN C 949 GLN C 957 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN P 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.230008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178717 restraints weight = 39768.245| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.86 r_work: 0.3313 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 30846 Z= 0.327 Angle : 0.710 18.386 42069 Z= 0.354 Chirality : 0.051 0.307 4830 Planarity : 0.005 0.047 5364 Dihedral : 4.626 21.690 4077 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.26 % Allowed : 11.84 % Favored : 85.90 % 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 (0.13), residues: 3741 helix: 1.12 (0.20), residues: 630 sheet: -0.18 (0.16), residues: 921 loop : -0.76 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 190 TYR 0.026 0.002 TYR C1067 PHE 0.027 0.002 PHE B 759 TRP 0.017 0.002 TRP C 64 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.33 (30771) covalent geometry : angle 0.67593 / 0.35 (41886) SS BOND : bond 0.01126 / 0.77 ( 42) SS BOND : angle 1.94758 / 1.39 ( 84) hydrogen bonds : bond 0.04594 / 2.98 ( 1067) hydrogen bonds : angle 6.39340 / 4.43 ( 2961) link_BETA1-4 : bond 0.00343 / 0.15 ( 3) link_BETA1-4 : angle 1.62220 / 0.95 ( 9) link_NAG-ASN : bond 0.00620 / 0.46 ( 30) link_NAG-ASN : angle 4.40368 / 3.44 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6593 (mmt90) cc_final: 0.6138 (mmp-170) REVERT: A 580 GLN cc_start: 0.8104 (mm110) cc_final: 0.7766 (mm-40) REVERT: A 763 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8840 (mp) REVERT: A 980 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6568 (mt) REVERT: B 574 ASP cc_start: 0.8346 (t0) cc_final: 0.8001 (t0) REVERT: C 106 PHE cc_start: 0.6151 (m-80) cc_final: 0.5893 (m-80) REVERT: C 192 PHE cc_start: 0.7663 (m-80) cc_final: 0.7281 (m-10) REVERT: C 196 ASN cc_start: 0.7604 (t0) cc_final: 0.7360 (t0) REVERT: C 271 GLN cc_start: 0.8223 (tt0) cc_final: 0.7943 (mt0) REVERT: C 402 ILE cc_start: -0.0198 (OUTLIER) cc_final: -0.0522 (mp) REVERT: C 969 LYS cc_start: 0.8496 (mttm) cc_final: 0.8045 (mmtp) REVERT: C 1092 GLU cc_start: 0.8021 (tp30) cc_final: 0.7753 (tt0) REVERT: C 1144 GLU cc_start: 0.8467 (mp0) cc_final: 0.8257 (mp0) outliers start: 74 outliers final: 55 residues processed: 254 average time/residue: 0.1784 time to fit residues: 78.1077 Evaluate side-chains 254 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 64 optimal weight: 0.4980 chunk 143 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 336 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 762 GLN A 957 GLN B 196 ASN B 207 HIS B 957 GLN C 762 GLN C 949 GLN C 957 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.233924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.178885 restraints weight = 39631.272| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.05 r_work: 0.3353 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30846 Z= 0.122 Angle : 0.579 17.588 42069 Z= 0.286 Chirality : 0.046 0.301 4830 Planarity : 0.004 0.045 5364 Dihedral : 4.234 20.640 4077 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.83 % Allowed : 12.82 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3741 helix: 1.59 (0.21), residues: 630 sheet: -0.08 (0.17), residues: 885 loop : -0.60 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.022 0.001 TYR B1067 PHE 0.028 0.001 PHE B 759 TRP 0.010 0.001 TRP C 64 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (30771) covalent geometry : angle 0.54446 / 0.28 (41886) SS BOND : bond 0.00366 / 0.25 ( 42) SS BOND : angle 1.39276 / 1.01 ( 84) hydrogen bonds : bond 0.03720 / 2.38 ( 1067) hydrogen bonds : angle 5.89044 / 4.09 ( 2961) link_BETA1-4 : bond 0.00624 / 0.29 ( 3) link_BETA1-4 : angle 1.51892 / 0.87 ( 9) link_NAG-ASN : bond 0.00721 / 0.52 ( 30) link_NAG-ASN : angle 4.09141 / 3.22 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6475 (mmt90) cc_final: 0.5990 (mmp-170) REVERT: A 429 PHE cc_start: 0.2519 (OUTLIER) cc_final: 0.0445 (p90) REVERT: A 580 GLN cc_start: 0.8012 (mm110) cc_final: 0.7667 (mm-40) REVERT: A 980 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6532 (mt) REVERT: B 574 ASP cc_start: 0.8275 (t0) cc_final: 0.7928 (t0) REVERT: B 965 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8449 (mm-40) REVERT: C 192 PHE cc_start: 0.7557 (m-80) cc_final: 0.7262 (m-80) REVERT: C 271 GLN cc_start: 0.8228 (tt0) cc_final: 0.7962 (mt0) REVERT: C 314 GLN cc_start: 0.8276 (tt0) cc_final: 0.8034 (tm-30) REVERT: C 402 ILE cc_start: -0.0116 (OUTLIER) cc_final: -0.0378 (mp) REVERT: C 969 LYS cc_start: 0.8453 (mttm) cc_final: 0.7984 (mmtp) REVERT: C 1092 GLU cc_start: 0.7933 (tp30) cc_final: 0.7724 (tt0) outliers start: 60 outliers final: 40 residues processed: 252 average time/residue: 0.1774 time to fit residues: 76.9569 Evaluate side-chains 241 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 136 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 336 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 219 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 957 GLN B 207 HIS B 957 GLN C 762 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.234156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.181651 restraints weight = 39459.420| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.04 r_work: 0.3368 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30846 Z= 0.117 Angle : 0.573 17.165 42069 Z= 0.280 Chirality : 0.045 0.265 4830 Planarity : 0.004 0.044 5364 Dihedral : 4.132 19.970 4077 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.83 % Allowed : 13.06 % Favored : 85.10 % 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 (0.14), residues: 3741 helix: 1.76 (0.21), residues: 627 sheet: -0.03 (0.17), residues: 885 loop : -0.56 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 102 TYR 0.020 0.001 TYR C1067 PHE 0.020 0.001 PHE B 759 TRP 0.009 0.001 TRP C 64 HIS 0.004 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (30771) covalent geometry : angle 0.54033 / 0.27 (41886) SS BOND : bond 0.00379 / 0.26 ( 42) SS BOND : angle 1.30999 / 0.95 ( 84) hydrogen bonds : bond 0.03629 / 2.32 ( 1067) hydrogen bonds : angle 5.73679 / 3.98 ( 2961) link_BETA1-4 : bond 0.00523 / 0.24 ( 3) link_BETA1-4 : angle 1.49367 / 0.86 ( 9) link_NAG-ASN : bond 0.00682 / 0.50 ( 30) link_NAG-ASN : angle 3.99652 / 3.15 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6454 (mmt90) cc_final: 0.5945 (mmp-170) REVERT: A 429 PHE cc_start: 0.2451 (OUTLIER) cc_final: 0.0445 (p90) REVERT: A 580 GLN cc_start: 0.7944 (mm110) cc_final: 0.7609 (mm-40) REVERT: A 980 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6468 (mt) REVERT: A 1106 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8491 (pt0) REVERT: B 574 ASP cc_start: 0.8201 (t0) cc_final: 0.7853 (t0) REVERT: B 965 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8406 (mm-40) REVERT: C 192 PHE cc_start: 0.7583 (m-80) cc_final: 0.7289 (m-80) REVERT: C 314 GLN cc_start: 0.8291 (tt0) cc_final: 0.8030 (tm-30) REVERT: C 402 ILE cc_start: 0.0195 (OUTLIER) cc_final: -0.0112 (mp) REVERT: C 934 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7493 (mm) REVERT: C 969 LYS cc_start: 0.8443 (mttm) cc_final: 0.7970 (mmtp) outliers start: 60 outliers final: 44 residues processed: 248 average time/residue: 0.1753 time to fit residues: 74.6426 Evaluate side-chains 249 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 43 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 241 optimal weight: 40.0000 chunk 273 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 957 GLN B 207 HIS B 245 HIS B 949 GLN B 957 GLN C 762 GLN C 949 GLN C 957 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.231821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.177605 restraints weight = 39715.049| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.92 r_work: 0.3323 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30846 Z= 0.206 Angle : 0.619 17.228 42069 Z= 0.305 Chirality : 0.047 0.285 4830 Planarity : 0.004 0.046 5364 Dihedral : 4.299 20.003 4077 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.01 % Allowed : 13.25 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 3741 helix: 1.58 (0.21), residues: 612 sheet: -0.07 (0.17), residues: 903 loop : -0.72 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.022 0.001 TYR C1067 PHE 0.016 0.001 PHE A 238 TRP 0.013 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (30771) covalent geometry : angle 0.58724 / 0.30 (41886) SS BOND : bond 0.00682 / 0.46 ( 42) SS BOND : angle 1.47311 / 1.04 ( 84) hydrogen bonds : bond 0.03975 / 2.56 ( 1067) hydrogen bonds : angle 5.89479 / 4.09 ( 2961) link_BETA1-4 : bond 0.00483 / 0.22 ( 3) link_BETA1-4 : angle 1.48856 / 0.86 ( 9) link_NAG-ASN : bond 0.00610 / 0.46 ( 30) link_NAG-ASN : angle 4.07652 / 3.19 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7887 (mm110) cc_final: 0.7522 (mm-40) REVERT: A 980 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6526 (mt) REVERT: B 574 ASP cc_start: 0.8222 (t0) cc_final: 0.7843 (t0) REVERT: B 965 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8448 (mm-40) REVERT: C 177 MET cc_start: 0.5318 (tpp) cc_final: 0.4723 (tpp) REVERT: C 271 GLN cc_start: 0.8227 (tt0) cc_final: 0.7986 (mt0) REVERT: C 314 GLN cc_start: 0.8368 (tt0) cc_final: 0.8109 (tm-30) REVERT: C 402 ILE cc_start: 0.0111 (OUTLIER) cc_final: -0.0184 (mp) REVERT: C 934 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7719 (mm) REVERT: C 969 LYS cc_start: 0.8434 (mttm) cc_final: 0.7946 (mmtp) REVERT: C 980 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6651 (mt) REVERT: C 1004 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8714 (tt) outliers start: 66 outliers final: 50 residues processed: 251 average time/residue: 0.1732 time to fit residues: 75.1174 Evaluate side-chains 252 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 68 optimal weight: 0.7980 chunk 347 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 333 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 345 optimal weight: 30.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 957 GLN B 99 ASN B 207 HIS B 949 GLN B 957 GLN C 949 GLN C 957 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.231987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164216 restraints weight = 39379.315| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 4.20 r_work: 0.3244 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30846 Z= 0.128 Angle : 0.579 16.718 42069 Z= 0.284 Chirality : 0.045 0.269 4830 Planarity : 0.004 0.047 5364 Dihedral : 4.166 20.099 4077 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.77 % Allowed : 13.58 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3741 helix: 1.77 (0.20), residues: 627 sheet: -0.01 (0.17), residues: 903 loop : -0.66 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.020 0.001 TYR B1067 PHE 0.019 0.001 PHE A 238 TRP 0.010 0.001 TRP C 64 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (30771) covalent geometry : angle 0.54622 / 0.28 (41886) SS BOND : bond 0.00399 / 0.28 ( 42) SS BOND : angle 1.42180 / 1.01 ( 84) hydrogen bonds : bond 0.03652 / 2.34 ( 1067) hydrogen bonds : angle 5.71519 / 3.96 ( 2961) link_BETA1-4 : bond 0.00510 / 0.23 ( 3) link_BETA1-4 : angle 1.48888 / 0.86 ( 9) link_NAG-ASN : bond 0.00657 / 0.48 ( 30) link_NAG-ASN : angle 3.94626 / 3.09 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7643 (mm110) cc_final: 0.7247 (mm-40) REVERT: A 762 GLN cc_start: 0.8184 (mt0) cc_final: 0.7923 (mt0) REVERT: A 980 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6443 (mt) REVERT: A 1106 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: B 574 ASP cc_start: 0.8004 (t0) cc_final: 0.7603 (t0) REVERT: B 965 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8368 (mm-40) REVERT: C 177 MET cc_start: 0.5271 (tpp) cc_final: 0.4987 (tpp) REVERT: C 192 PHE cc_start: 0.7403 (m-80) cc_final: 0.6974 (m-10) REVERT: C 314 GLN cc_start: 0.8363 (tt0) cc_final: 0.7933 (tm-30) REVERT: C 934 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7337 (mm) REVERT: C 969 LYS cc_start: 0.8323 (mttm) cc_final: 0.7794 (mmtp) REVERT: C 1004 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8515 (tt) REVERT: C 1092 GLU cc_start: 0.8041 (tp30) cc_final: 0.7764 (pt0) outliers start: 58 outliers final: 47 residues processed: 250 average time/residue: 0.1624 time to fit residues: 70.7572 Evaluate side-chains 258 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 176 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 256 optimal weight: 0.4980 chunk 373 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 349 optimal weight: 30.0000 chunk 347 optimal weight: 30.0000 chunk 80 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 207 HIS B 949 GLN B 957 GLN C 957 GLN C1142 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.233122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167426 restraints weight = 39475.977| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.98 r_work: 0.3245 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30846 Z= 0.133 Angle : 0.582 16.473 42069 Z= 0.283 Chirality : 0.046 0.272 4830 Planarity : 0.004 0.047 5364 Dihedral : 4.128 19.830 4077 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.59 % Allowed : 13.83 % Favored : 84.58 % 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 (0.14), residues: 3741 helix: 1.80 (0.20), residues: 627 sheet: -0.01 (0.17), residues: 903 loop : -0.64 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.020 0.001 TYR C1067 PHE 0.019 0.001 PHE A 238 TRP 0.011 0.001 TRP C 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (30771) covalent geometry : angle 0.55073 / 0.28 (41886) SS BOND : bond 0.00409 / 0.29 ( 42) SS BOND : angle 1.33562 / 0.95 ( 84) hydrogen bonds : bond 0.03614 / 2.32 ( 1067) hydrogen bonds : angle 5.65170 / 3.91 ( 2961) link_BETA1-4 : bond 0.00519 / 0.24 ( 3) link_BETA1-4 : angle 1.45127 / 0.83 ( 9) link_NAG-ASN : bond 0.00643 / 0.47 ( 30) link_NAG-ASN : angle 3.88478 / 3.05 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7574 (mm110) cc_final: 0.7184 (mm-40) REVERT: A 762 GLN cc_start: 0.8322 (mt0) cc_final: 0.8116 (mt0) REVERT: A 969 LYS cc_start: 0.8453 (mmtp) cc_final: 0.7733 (pttm) REVERT: A 980 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6359 (mt) REVERT: B 574 ASP cc_start: 0.8227 (t0) cc_final: 0.7827 (t0) REVERT: B 965 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8468 (mm-40) REVERT: C 177 MET cc_start: 0.5411 (tpp) cc_final: 0.5117 (tpp) REVERT: C 192 PHE cc_start: 0.7615 (m-80) cc_final: 0.7220 (m-10) REVERT: C 314 GLN cc_start: 0.8544 (tt0) cc_final: 0.8067 (tm-30) REVERT: C 934 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7323 (mm) REVERT: C 969 LYS cc_start: 0.8289 (mttm) cc_final: 0.7750 (mmtp) REVERT: C 1004 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8584 (tt) REVERT: C 1092 GLU cc_start: 0.8271 (tp30) cc_final: 0.7769 (pt0) outliers start: 52 outliers final: 46 residues processed: 244 average time/residue: 0.1711 time to fit residues: 72.4127 Evaluate side-chains 256 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain Q residue 12 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 5 optimal weight: 9.9990 chunk 348 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 281 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 322 optimal weight: 40.0000 chunk 96 optimal weight: 0.9980 chunk 328 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 207 HIS B 949 GLN B 957 GLN C 762 GLN C 957 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.233162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178372 restraints weight = 39823.914| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.03 r_work: 0.3340 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30846 Z= 0.146 Angle : 0.592 16.222 42069 Z= 0.287 Chirality : 0.046 0.278 4830 Planarity : 0.004 0.049 5364 Dihedral : 4.130 19.654 4077 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.65 % Allowed : 14.04 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 3741 helix: 1.74 (0.21), residues: 612 sheet: -0.02 (0.17), residues: 903 loop : -0.66 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.001 PHE A 238 TRP 0.011 0.001 TRP C 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (30771) covalent geometry : angle 0.56082 / 0.28 (41886) SS BOND : bond 0.00454 / 0.32 ( 42) SS BOND : angle 1.54001 / 1.15 ( 84) hydrogen bonds : bond 0.03673 / 2.35 ( 1067) hydrogen bonds : angle 5.64840 / 3.91 ( 2961) link_BETA1-4 : bond 0.00500 / 0.23 ( 3) link_BETA1-4 : angle 1.45102 / 0.83 ( 9) link_NAG-ASN : bond 0.00622 / 0.46 ( 30) link_NAG-ASN : angle 3.85318 / 3.02 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9201.31 seconds wall clock time: 158 minutes 13.27 seconds (9493.27 seconds total)