Starting phenix.real_space_refine on Thu Jun 26 02:44:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz8_26882/06_2025/7uz8_26882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz8_26882/06_2025/7uz8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz8_26882/06_2025/7uz8_26882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz8_26882/06_2025/7uz8_26882.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz8_26882/06_2025/7uz8_26882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz8_26882/06_2025/7uz8_26882.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 1.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 27 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 dihedrals: 27 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 19.37, per 1000 atoms: 0.64 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: 6.92 Conformation dependent library (CDL) restraints added in 3.5 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: 4.66 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: 13.73 Time building geometry restraints manager: 8.13 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 - 23.12: 17687 23.12 - 46.25: 879 46.25 - 69.37: 94 69.37 - 92.50: 33 92.50 - 115.62: 51 Dihedral angle restraints: 18744 sinusoidal: 7677 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 18741 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: 0.01 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: 45.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.360 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 71.530 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 14.869 115.619 11502 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.002 TRP C 64 HIS 0.005 0.001 HIS C 207 PHE 0.025 0.001 PHE C 906 TYR 0.039 0.001 TYR A 756 ARG 0.008 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00739 ( 30) link_NAG-ASN : angle 4.53051 ( 90) link_BETA1-4 : bond 0.00549 ( 3) link_BETA1-4 : angle 1.61959 ( 9) hydrogen bonds : bond 0.20561 ( 1067) hydrogen bonds : angle 8.85868 ( 2961) SS BOND : bond 0.00484 ( 42) SS BOND : angle 1.42002 ( 84) covalent geometry : bond 0.00435 (30771) covalent geometry : angle 0.61587 (41886) *********************** 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 : 3.995 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: 0.7129 (t0) cc_final: 0.6875 (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: 0.4573 time to fit residues: 190.0687 Evaluate side-chains 192 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 7.737 ------------------------------------------------------------------------------- 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 316 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 151 optimal weight: 0.0970 chunk 293 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 340 optimal weight: 40.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 949 GLN Q 105 GLN 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 = 0.233082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.177470 restraints weight = 39501.249| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.87 r_work: 0.3329 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30846 Z= 0.222 Angle : 0.665 19.597 42069 Z= 0.332 Chirality : 0.049 0.313 4830 Planarity : 0.005 0.056 5364 Dihedral : 10.400 109.970 4772 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.82 % Allowed : 6.38 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 3741 helix: 1.40 (0.21), residues: 609 sheet: -0.11 (0.17), residues: 867 loop : -0.67 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.006 0.001 HIS B 207 PHE 0.023 0.002 PHE B 906 TYR 0.025 0.002 TYR C1067 ARG 0.007 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 30) link_NAG-ASN : angle 4.46095 ( 90) link_BETA1-4 : bond 0.00456 ( 3) link_BETA1-4 : angle 1.62389 ( 9) hydrogen bonds : bond 0.04853 ( 1067) hydrogen bonds : angle 6.88078 ( 2961) SS BOND : bond 0.00688 ( 42) SS BOND : angle 1.48611 ( 84) covalent geometry : bond 0.00529 (30771) covalent geometry : angle 0.63012 (41886) *********************** 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 252 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7482 (t80) cc_final: 0.7204 (t80) REVERT: A 740 MET cc_start: 0.7280 (ttt) cc_final: 0.7001 (ttm) REVERT: A 1092 GLU cc_start: 0.7987 (tp30) cc_final: 0.7748 (tt0) REVERT: B 84 LEU cc_start: 0.6793 (mt) cc_final: 0.6532 (mp) REVERT: B 99 ASN cc_start: 0.8297 (m-40) cc_final: 0.8082 (m-40) REVERT: B 102 ARG cc_start: 0.6227 (mmm160) cc_final: 0.5888 (mmm160) REVERT: B 106 PHE cc_start: 0.5562 (m-80) cc_final: 0.5352 (m-80) REVERT: B 574 ASP cc_start: 0.8274 (t0) cc_final: 0.8053 (t0) REVERT: C 196 ASN cc_start: 0.7420 (t0) cc_final: 0.7111 (t0) REVERT: C 271 GLN cc_start: 0.8212 (tt0) cc_final: 0.7854 (mt0) REVERT: C 574 ASP cc_start: 0.8115 (t0) cc_final: 0.7643 (t0) REVERT: C 969 LYS cc_start: 0.8480 (mttm) cc_final: 0.7966 (mmtp) REVERT: C 1144 GLU cc_start: 0.8360 (mp0) cc_final: 0.8129 (mp0) outliers start: 27 outliers final: 19 residues processed: 237 average time/residue: 0.5170 time to fit residues: 214.9239 Evaluate side-chains 222 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 289 VAL 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 645 THR Chi-restraints excluded: chain B residue 732 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 289 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 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 335 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 357 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN A 957 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 245 HIS C 755 GLN C 762 GLN C1002 GLN L 105 GLN N 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.235160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.181051 restraints weight = 39717.771| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.08 r_work: 0.3376 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1248 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= 0.128 Angle : 0.589 18.557 42069 Z= 0.288 Chirality : 0.045 0.272 4830 Planarity : 0.004 0.048 5364 Dihedral : 8.031 112.683 4770 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.50 % Allowed : 8.82 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 3741 helix: 1.73 (0.21), residues: 615 sheet: -0.02 (0.17), residues: 840 loop : -0.61 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.002 0.000 HIS B1101 PHE 0.018 0.001 PHE A 192 TYR 0.022 0.001 TYR C1067 ARG 0.007 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 30) link_NAG-ASN : angle 4.25828 ( 90) link_BETA1-4 : bond 0.00439 ( 3) link_BETA1-4 : angle 1.73500 ( 9) hydrogen bonds : bond 0.04024 ( 1067) hydrogen bonds : angle 6.22411 ( 2961) SS BOND : bond 0.00401 ( 42) SS BOND : angle 1.34721 ( 84) covalent geometry : bond 0.00289 (30771) covalent geometry : angle 0.55270 (41886) *********************** 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 278 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6265 (mmt90) cc_final: 0.5603 (mmm160) REVERT: B 574 ASP cc_start: 0.8295 (t0) cc_final: 0.7986 (t0) REVERT: C 196 ASN cc_start: 0.7357 (t0) cc_final: 0.7105 (t0) REVERT: C 314 GLN cc_start: 0.8275 (tt0) cc_final: 0.7952 (tm-30) REVERT: C 574 ASP cc_start: 0.8120 (t0) cc_final: 0.7668 (t0) REVERT: C 969 LYS cc_start: 0.8440 (mttm) cc_final: 0.7963 (mmtp) outliers start: 49 outliers final: 30 residues processed: 262 average time/residue: 0.3687 time to fit residues: 165.8502 Evaluate side-chains 232 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 3.247 ------------------------------------------------------------------------------- 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 588 THR 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 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 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER 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 551 VAL 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 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 201 optimal weight: 2.9990 chunk 39 optimal weight: 50.0000 chunk 266 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 277 optimal weight: 0.0000 chunk 36 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 949 GLN B 957 GLN C 762 GLN C 949 GLN C 957 GLN P 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.230655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172919 restraints weight = 39723.990| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.90 r_work: 0.3262 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 30846 Z= 0.276 Angle : 0.684 18.677 42069 Z= 0.339 Chirality : 0.049 0.309 4830 Planarity : 0.005 0.048 5364 Dihedral : 7.543 106.997 4770 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.14 % Allowed : 11.14 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 3741 helix: 1.28 (0.21), residues: 597 sheet: -0.11 (0.16), residues: 906 loop : -0.76 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.007 0.001 HIS B 207 PHE 0.019 0.002 PHE B 106 TYR 0.026 0.002 TYR C1067 ARG 0.008 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 30) link_NAG-ASN : angle 4.49724 ( 90) link_BETA1-4 : bond 0.00527 ( 3) link_BETA1-4 : angle 1.75397 ( 9) hydrogen bonds : bond 0.04493 ( 1067) hydrogen bonds : angle 6.39412 ( 2961) SS BOND : bond 0.00937 ( 42) SS BOND : angle 1.83049 ( 84) covalent geometry : bond 0.00668 (30771) covalent geometry : angle 0.64732 (41886) *********************** 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 277 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6584 (mmt90) cc_final: 0.6378 (mmt180) REVERT: A 208 THR cc_start: 0.7851 (m) cc_final: 0.7632 (p) REVERT: A 763 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 980 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6538 (mt) REVERT: B 574 ASP cc_start: 0.8308 (t0) cc_final: 0.7974 (t0) REVERT: C 196 ASN cc_start: 0.7554 (t0) cc_final: 0.7306 (t0) REVERT: C 271 GLN cc_start: 0.8248 (tt0) cc_final: 0.7870 (mt0) REVERT: C 969 LYS cc_start: 0.8413 (mttm) cc_final: 0.7916 (mmtp) REVERT: C 1092 GLU cc_start: 0.8005 (tp30) cc_final: 0.7710 (tt0) outliers start: 70 outliers final: 54 residues processed: 253 average time/residue: 0.3772 time to fit residues: 163.7210 Evaluate side-chains 249 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 226 LEU 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 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 763 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL 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 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 588 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 734 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 B residue 1136 THR 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 534 VAL 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 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 264 optimal weight: 0.3980 chunk 85 optimal weight: 0.0770 chunk 8 optimal weight: 20.0000 chunk 293 optimal weight: 5.9990 chunk 236 optimal weight: 50.0000 chunk 266 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 207 HIS B 245 HIS B 957 GLN C 762 GLN C 949 GLN C 957 GLN C1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.233254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.178230 restraints weight = 39582.073| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.00 r_work: 0.3344 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1724 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= 0.139 Angle : 0.591 18.131 42069 Z= 0.289 Chirality : 0.046 0.291 4830 Planarity : 0.004 0.045 5364 Dihedral : 7.220 99.365 4770 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.80 % Allowed : 12.42 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 3741 helix: 1.54 (0.20), residues: 633 sheet: -0.16 (0.17), residues: 885 loop : -0.62 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.003 0.000 HIS B 207 PHE 0.021 0.001 PHE A 238 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 30) link_NAG-ASN : angle 4.32593 ( 90) link_BETA1-4 : bond 0.00550 ( 3) link_BETA1-4 : angle 1.74241 ( 9) hydrogen bonds : bond 0.03822 ( 1067) hydrogen bonds : angle 6.01337 ( 2961) SS BOND : bond 0.00472 ( 42) SS BOND : angle 1.48545 ( 84) covalent geometry : bond 0.00322 (30771) covalent geometry : angle 0.55323 (41886) *********************** 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 272 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 4.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6491 (mmt90) cc_final: 0.6007 (mmp-170) REVERT: A 201 PHE cc_start: 0.8046 (t80) cc_final: 0.7597 (t80) REVERT: A 580 GLN cc_start: 0.7996 (mm110) cc_final: 0.7657 (mm-40) REVERT: A 762 GLN cc_start: 0.8355 (mt0) cc_final: 0.8142 (mt0) REVERT: A 1106 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8527 (pt0) REVERT: B 177 MET cc_start: 0.6666 (mmt) cc_final: 0.6405 (tpp) REVERT: B 574 ASP cc_start: 0.8310 (t0) cc_final: 0.7961 (t0) REVERT: B 965 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8481 (mm-40) REVERT: C 106 PHE cc_start: 0.6124 (m-80) cc_final: 0.5910 (m-80) REVERT: C 192 PHE cc_start: 0.7563 (m-80) cc_final: 0.7275 (m-80) REVERT: C 196 ASN cc_start: 0.7628 (t0) cc_final: 0.7380 (t0) REVERT: C 271 GLN cc_start: 0.8227 (tt0) cc_final: 0.7941 (mt0) REVERT: C 314 GLN cc_start: 0.8273 (tt0) cc_final: 0.8030 (tm-30) REVERT: C 402 ILE cc_start: -0.0239 (OUTLIER) cc_final: -0.0525 (mp) REVERT: C 574 ASP cc_start: 0.8148 (t70) cc_final: 0.7702 (t0) REVERT: C 969 LYS cc_start: 0.8460 (mttm) cc_final: 0.7994 (mmtp) REVERT: C 980 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6629 (mt) REVERT: C 1092 GLU cc_start: 0.7913 (tp30) cc_final: 0.7712 (tt0) outliers start: 59 outliers final: 43 residues processed: 254 average time/residue: 0.5296 time to fit residues: 239.2618 Evaluate side-chains 248 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 6.136 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 369 TYR 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 723 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1094 VAL 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 159 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 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 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 661 GLU Chi-restraints excluded: chain C residue 858 LEU 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 L residue 40 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 91 optimal weight: 0.9990 chunk 367 optimal weight: 30.0000 chunk 201 optimal weight: 1.9990 chunk 246 optimal weight: 30.0000 chunk 317 optimal weight: 40.0000 chunk 362 optimal weight: 0.6980 chunk 330 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 chunk 316 optimal weight: 0.6980 chunk 363 optimal weight: 6.9990 chunk 101 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 957 GLN B 207 HIS B 957 GLN C 762 GLN C 957 GLN ** 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 = 0.4635 r_free = 0.4635 target = 0.232052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159790 restraints weight = 39543.583| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 4.27 r_work: 0.3256 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30846 Z= 0.122 Angle : 0.574 17.707 42069 Z= 0.280 Chirality : 0.045 0.261 4830 Planarity : 0.004 0.043 5364 Dihedral : 6.989 96.187 4770 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.01 % Allowed : 12.79 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3741 helix: 1.75 (0.21), residues: 630 sheet: -0.07 (0.17), residues: 885 loop : -0.57 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.002 0.000 HIS C 207 PHE 0.015 0.001 PHE B 106 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 30) link_NAG-ASN : angle 4.21519 ( 90) link_BETA1-4 : bond 0.00519 ( 3) link_BETA1-4 : angle 1.69466 ( 9) hydrogen bonds : bond 0.03634 ( 1067) hydrogen bonds : angle 5.80394 ( 2961) SS BOND : bond 0.00562 ( 42) SS BOND : angle 1.19534 ( 84) covalent geometry : bond 0.00280 (30771) covalent geometry : angle 0.53812 (41886) *********************** 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 280 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6443 (mmt90) cc_final: 0.5774 (mmp-170) REVERT: A 201 PHE cc_start: 0.7453 (t80) cc_final: 0.6977 (t80) REVERT: A 580 GLN cc_start: 0.7592 (mm110) cc_final: 0.7214 (mm-40) REVERT: A 762 GLN cc_start: 0.8397 (mt0) cc_final: 0.8175 (mt0) REVERT: A 868 GLU cc_start: 0.8297 (tt0) cc_final: 0.8084 (tm-30) REVERT: A 969 LYS cc_start: 0.8526 (mmtp) cc_final: 0.7709 (pttm) REVERT: A 980 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6336 (mt) REVERT: A 1106 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8504 (pt0) REVERT: B 177 MET cc_start: 0.6690 (mmt) cc_final: 0.6339 (tpp) REVERT: B 574 ASP cc_start: 0.8284 (t0) cc_final: 0.7908 (t0) REVERT: B 1005 GLN cc_start: 0.8135 (mt0) cc_final: 0.7900 (mm-40) REVERT: B 1092 GLU cc_start: 0.8217 (tp30) cc_final: 0.7743 (pt0) REVERT: C 314 GLN cc_start: 0.8507 (tt0) cc_final: 0.8044 (tm-30) REVERT: C 969 LYS cc_start: 0.8335 (mttm) cc_final: 0.7787 (mmtp) REVERT: C 980 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6458 (mt) REVERT: C 1092 GLU cc_start: 0.8211 (tp30) cc_final: 0.7870 (tt0) outliers start: 66 outliers final: 52 residues processed: 259 average time/residue: 0.3967 time to fit residues: 176.3231 Evaluate side-chains 258 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 3.428 ------------------------------------------------------------------------------- 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 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 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 723 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL 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 312 ILE 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 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 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 159 VAL Chi-restraints excluded: chain C residue 226 LEU 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 980 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 319 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 191 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 957 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 957 GLN C 762 GLN C 949 GLN C 957 GLN C1142 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.231417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.172226 restraints weight = 39678.155| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.79 r_work: 0.3290 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30846 Z= 0.211 Angle : 0.624 17.819 42069 Z= 0.307 Chirality : 0.047 0.281 4830 Planarity : 0.004 0.043 5364 Dihedral : 7.128 96.549 4770 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.41 % Allowed : 13.03 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 3741 helix: 1.53 (0.21), residues: 612 sheet: -0.03 (0.16), residues: 912 loop : -0.69 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 PHE 0.015 0.001 PHE A1121 TYR 0.022 0.001 TYR C1067 ARG 0.008 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 30) link_NAG-ASN : angle 4.31363 ( 90) link_BETA1-4 : bond 0.00503 ( 3) link_BETA1-4 : angle 1.67333 ( 9) hydrogen bonds : bond 0.03960 ( 1067) hydrogen bonds : angle 5.93158 ( 2961) SS BOND : bond 0.00720 ( 42) SS BOND : angle 1.37487 ( 84) covalent geometry : bond 0.00508 (30771) covalent geometry : angle 0.58900 (41886) *********************** 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 281 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 202 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7884 (mm110) cc_final: 0.7539 (mm-40) REVERT: A 762 GLN cc_start: 0.8395 (mt0) cc_final: 0.8132 (mt0) REVERT: A 980 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6485 (mt) REVERT: B 177 MET cc_start: 0.6673 (mmt) cc_final: 0.6347 (tpp) REVERT: B 574 ASP cc_start: 0.8183 (t0) cc_final: 0.7820 (t0) REVERT: C 314 GLN cc_start: 0.8377 (tt0) cc_final: 0.8045 (tm-30) REVERT: C 969 LYS cc_start: 0.8434 (mttm) cc_final: 0.7944 (mmtp) REVERT: C 980 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6493 (mt) REVERT: C 1004 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8666 (tt) outliers start: 79 outliers final: 62 residues processed: 258 average time/residue: 0.3604 time to fit residues: 161.8798 Evaluate side-chains 259 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 3.794 ------------------------------------------------------------------------------- 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 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 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 749 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL 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 207 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 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 749 CYS Chi-restraints excluded: chain B residue 791 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 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 858 LEU 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 L residue 14 THR Chi-restraints excluded: chain L residue 40 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 259 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 374 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 297 optimal weight: 0.5980 chunk 313 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 957 GLN C 949 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.232959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176567 restraints weight = 39789.169| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.80 r_work: 0.3315 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30846 Z= 0.154 Angle : 0.599 17.519 42069 Z= 0.293 Chirality : 0.046 0.269 4830 Planarity : 0.004 0.045 5364 Dihedral : 7.021 94.425 4770 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.17 % Allowed : 13.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3741 helix: 1.67 (0.21), residues: 609 sheet: -0.04 (0.17), residues: 897 loop : -0.65 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.018 0.001 HIS B 207 PHE 0.015 0.001 PHE B 106 TYR 0.021 0.001 TYR C1067 ARG 0.006 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 30) link_NAG-ASN : angle 4.24783 ( 90) link_BETA1-4 : bond 0.00504 ( 3) link_BETA1-4 : angle 1.67487 ( 9) hydrogen bonds : bond 0.03765 ( 1067) hydrogen bonds : angle 5.81643 ( 2961) SS BOND : bond 0.00506 ( 42) SS BOND : angle 1.40671 ( 84) covalent geometry : bond 0.00363 (30771) covalent geometry : angle 0.56308 (41886) *********************** 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 277 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 206 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7926 (mm110) cc_final: 0.7583 (mm-40) REVERT: A 762 GLN cc_start: 0.8537 (mt0) cc_final: 0.8326 (mt0) REVERT: A 868 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8152 (mp0) REVERT: A 969 LYS cc_start: 0.8681 (mmtp) cc_final: 0.7908 (pttm) REVERT: A 980 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6548 (mt) REVERT: B 177 MET cc_start: 0.6633 (mmt) cc_final: 0.6323 (tpp) REVERT: B 574 ASP cc_start: 0.8403 (t0) cc_final: 0.8042 (t0) REVERT: C 177 MET cc_start: 0.5293 (tpp) cc_final: 0.5031 (tpp) REVERT: C 314 GLN cc_start: 0.8525 (tt0) cc_final: 0.8176 (tm-30) REVERT: C 969 LYS cc_start: 0.8443 (mttm) cc_final: 0.7953 (mmtp) REVERT: C 980 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6590 (mt) REVERT: C 1004 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8767 (tt) outliers start: 71 outliers final: 60 residues processed: 255 average time/residue: 0.3536 time to fit residues: 157.7784 Evaluate side-chains 265 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 202 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 226 LEU 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 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 723 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL 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 207 HIS 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 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 791 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 661 GLU Chi-restraints excluded: chain C residue 858 LEU 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 L residue 40 THR Chi-restraints excluded: chain M residue 39 MET 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 183 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 312 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 207 HIS B 957 GLN C 949 GLN C 957 GLN C1142 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 = 0.4624 r_free = 0.4624 target = 0.232676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.177098 restraints weight = 39719.893| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.94 r_work: 0.3304 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30846 Z= 0.160 Angle : 0.600 17.378 42069 Z= 0.292 Chirality : 0.046 0.277 4830 Planarity : 0.004 0.045 5364 Dihedral : 6.956 92.477 4770 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.26 % Allowed : 13.64 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3741 helix: 1.79 (0.21), residues: 591 sheet: -0.06 (0.16), residues: 903 loop : -0.67 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.029 0.001 HIS B 207 PHE 0.015 0.001 PHE B 192 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 30) link_NAG-ASN : angle 4.22921 ( 90) link_BETA1-4 : bond 0.00495 ( 3) link_BETA1-4 : angle 1.64926 ( 9) hydrogen bonds : bond 0.03773 ( 1067) hydrogen bonds : angle 5.78357 ( 2961) SS BOND : bond 0.00513 ( 42) SS BOND : angle 1.35162 ( 84) covalent geometry : bond 0.00379 (30771) covalent geometry : angle 0.56453 (41886) *********************** 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 284 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7905 (mm110) cc_final: 0.7552 (mm-40) REVERT: A 969 LYS cc_start: 0.8630 (mmtp) cc_final: 0.7840 (pttm) REVERT: A 980 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6460 (mt) REVERT: B 177 MET cc_start: 0.6660 (mmt) cc_final: 0.6307 (tpp) REVERT: B 574 ASP cc_start: 0.8199 (t0) cc_final: 0.7843 (t0) REVERT: C 177 MET cc_start: 0.5368 (tpp) cc_final: 0.4819 (tpp) REVERT: C 314 GLN cc_start: 0.8321 (tt0) cc_final: 0.8054 (tm-30) REVERT: C 969 LYS cc_start: 0.8423 (mttm) cc_final: 0.7938 (mmtp) REVERT: C 980 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6508 (mt) REVERT: C 1004 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8705 (tt) outliers start: 74 outliers final: 63 residues processed: 260 average time/residue: 0.3662 time to fit residues: 164.7174 Evaluate side-chains 269 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 226 LEU 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 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 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL 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 551 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 696 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 791 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 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU 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 H residue 39 MET Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 39 MET 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 373 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 345 optimal weight: 20.0000 chunk 137 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 248 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 957 GLN B 207 HIS B 957 GLN C 957 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.232352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.176233 restraints weight = 39497.066| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.73 r_work: 0.3378 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30846 Z= 0.123 Angle : 0.584 16.979 42069 Z= 0.282 Chirality : 0.045 0.270 4830 Planarity : 0.004 0.045 5364 Dihedral : 6.686 86.389 4770 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.89 % Allowed : 14.13 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3741 helix: 1.91 (0.21), residues: 609 sheet: 0.04 (0.17), residues: 882 loop : -0.62 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.008 0.001 HIS B 207 PHE 0.025 0.001 PHE A 238 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 30) link_NAG-ASN : angle 4.14094 ( 90) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 1.64141 ( 9) hydrogen bonds : bond 0.03580 ( 1067) hydrogen bonds : angle 5.60560 ( 2961) SS BOND : bond 0.00374 ( 42) SS BOND : angle 1.44560 ( 84) covalent geometry : bond 0.00285 (30771) covalent geometry : angle 0.54867 (41886) ********************** 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 277 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7951 (mm110) cc_final: 0.7644 (mm-40) REVERT: A 969 LYS cc_start: 0.8669 (mmtp) cc_final: 0.7919 (pttm) REVERT: A 980 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6671 (mt) REVERT: B 177 MET cc_start: 0.6622 (mmt) cc_final: 0.6225 (tpp) REVERT: B 574 ASP cc_start: 0.8141 (t0) cc_final: 0.7789 (t0) REVERT: C 170 TYR cc_start: 0.6935 (t80) cc_final: 0.6680 (t80) REVERT: C 177 MET cc_start: 0.5327 (tpp) cc_final: 0.5048 (tpp) REVERT: C 934 ILE cc_start: 0.7659 (mm) cc_final: 0.7426 (mm) REVERT: C 969 LYS cc_start: 0.8441 (mttm) cc_final: 0.7995 (mmtp) REVERT: C 980 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6571 (mt) REVERT: C 1004 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8656 (tt) outliers start: 62 outliers final: 54 residues processed: 255 average time/residue: 0.3688 time to fit residues: 163.7832 Evaluate side-chains 266 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 3.242 ------------------------------------------------------------------------------- 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 369 TYR 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 749 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL 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 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 791 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 226 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU 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 H residue 39 MET Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 39 MET 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 112 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 367 optimal weight: 20.0000 chunk 142 optimal weight: 40.0000 chunk 48 optimal weight: 6.9990 chunk 114 optimal weight: 40.0000 chunk 255 optimal weight: 0.0970 chunk 230 optimal weight: 0.9990 chunk 293 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 207 HIS B 949 GLN B 957 GLN C 762 GLN C 949 GLN C 957 GLN C1142 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** 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 = 0.4619 r_free = 0.4619 target = 0.232058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178089 restraints weight = 39676.219| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.96 r_work: 0.3319 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30846 Z= 0.186 Angle : 0.619 17.107 42069 Z= 0.300 Chirality : 0.047 0.289 4830 Planarity : 0.004 0.045 5364 Dihedral : 6.807 88.510 4770 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.05 % Allowed : 14.22 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3741 helix: 1.73 (0.21), residues: 591 sheet: -0.04 (0.17), residues: 903 loop : -0.67 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.004 0.001 HIS B 207 PHE 0.015 0.001 PHE C1121 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 30) link_NAG-ASN : angle 4.21371 ( 90) link_BETA1-4 : bond 0.00455 ( 3) link_BETA1-4 : angle 1.60964 ( 9) hydrogen bonds : bond 0.03841 ( 1067) hydrogen bonds : angle 5.73334 ( 2961) SS BOND : bond 0.00616 ( 42) SS BOND : angle 1.50032 ( 84) covalent geometry : bond 0.00446 (30771) covalent geometry : angle 0.58405 (41886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24426.58 seconds wall clock time: 430 minutes 32.35 seconds (25832.35 seconds total)