Starting phenix.real_space_refine on Sun Jun 29 06:50:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tca_25807/06_2025/7tca_25807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tca_25807/06_2025/7tca_25807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tca_25807/06_2025/7tca_25807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tca_25807/06_2025/7tca_25807.map" model { file = "/net/cci-nas-00/data/ceres_data/7tca_25807/06_2025/7tca_25807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tca_25807/06_2025/7tca_25807.cif" } resolution = 3.85 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= 0.001 sd= 0.025 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 148 5.16 5 C 21430 2.51 5 N 5554 2.21 5 O 6573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33705 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8715 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "E" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "H" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 18.93, per 1000 atoms: 0.56 Number of scatterers: 33705 At special positions: 0 Unit cell: (153.9, 216.315, 234.27, 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 148 16.00 O 6573 8.00 N 5554 7.00 C 21430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 603 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 122 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 122 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 331 " " NAG U 1 " - " ASN C 801 " Time building additional restraints: 7.95 Conformation dependent library (CDL) restraints added in 4.2 seconds 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7898 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 71 sheets defined 21.5% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.153A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.519A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.572A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.299A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 837 through 845 removed outlier: 6.482A pdb=" N GLY A 842 " --> pdb=" O ASP A 839 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.533A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.150A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.568A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.193A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.032A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.062A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.217A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.967A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.570A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.031A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 removed outlier: 3.694A pdb=" N HIS B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.881A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 628 removed outlier: 4.087A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 4.297A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.539A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.658A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.743A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 827 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 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 913 through 918 removed outlier: 3.598A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.549A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.552A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 5.097A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.323A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 628 removed outlier: 3.670A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.695A pdb=" N ARG C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.511A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.662A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.507A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.541A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.574A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.651A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.529A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.610A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.741A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.573A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.745A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 185 through 191 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.900A pdb=" N CYS E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 211 through 216' Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.563A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 191 Processing helix chain 'L' and resid 211 through 216 removed outlier: 3.928A pdb=" N CYS L 215 " --> pdb=" O ALA L 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER L 216 " --> pdb=" O PRO L 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 211 through 216' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.540A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 263 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.681A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.650A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.532A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.573A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.535A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB3, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.579A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.615A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.921A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.324A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.848A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.562A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 142 through 146 removed outlier: 3.711A pdb=" N HIS B 146 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.499A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.734A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.836A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.651A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.803A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.534A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.896A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.552A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.823A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.505A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AE3, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.737A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.190A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.558A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.940A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.494A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.913A pdb=" N VAL D 12 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 33 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.913A pdb=" N VAL D 12 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 115 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.713A pdb=" N GLY D 152 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR D 189 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 194 " --> pdb=" O HIS D 177 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS D 177 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.713A pdb=" N GLY D 152 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR D 189 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 190 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 182 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 164 through 167 removed outlier: 3.564A pdb=" N VAL D 211 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 220 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS D 213 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 218 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.894A pdb=" N PHE E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN E 39 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.894A pdb=" N PHE E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 98 " --> pdb=" O MET E 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.503A pdb=" N SER E 141 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.503A pdb=" N SER E 141 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.764A pdb=" N TRP E 152 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 153 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER E 196 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 199 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 206 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.309A pdb=" N GLY H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.959A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 133 through 137 removed outlier: 3.551A pdb=" N CYS H 153 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.045A pdb=" N TYR H 207 " --> pdb=" O VAL H 224 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.526A pdb=" N GLY L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.616A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.616A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.513A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR L 181 " --> pdb=" O GLU L 164 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU L 164 " --> pdb=" O TYR L 181 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.513A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.259A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS L 153 " --> pdb=" O SER L 196 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 3012 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: 16.93 Time building geometry restraints manager: 9.61 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: 10699 1.34 - 1.47: 8696 1.47 - 1.59: 14917 1.59 - 1.71: 1 1.71 - 1.84: 186 Bond restraints: 34499 Sorted by residual: bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 34494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 46829 3.62 - 7.23: 133 7.23 - 10.85: 12 10.85 - 14.47: 1 14.47 - 18.08: 3 Bond angle restraints: 46978 Sorted by residual: angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 132.29 -17.89 2.30e+00 1.89e-01 6.05e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 131.75 -17.35 2.30e+00 1.89e-01 5.69e+01 angle pdb=" C LEU C 390 " pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta sigma weight residual 122.44 113.50 8.94 1.45e+00 4.76e-01 3.80e+01 angle pdb=" N THR A 76 " pdb=" CA THR A 76 " pdb=" C THR A 76 " ideal model delta sigma weight residual 114.56 108.65 5.91 1.27e+00 6.20e-01 2.17e+01 angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 125.00 106.92 18.08 4.10e+00 5.95e-02 1.94e+01 ... (remaining 46973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.37: 20156 25.37 - 50.75: 957 50.75 - 76.12: 118 76.12 - 101.49: 32 101.49 - 126.87: 6 Dihedral angle restraints: 21269 sinusoidal: 8943 harmonic: 12326 Sorted by residual: dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual -180.00 -126.83 -53.17 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 1.31 -87.31 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 172.75 -79.75 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 21266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 5410 0.123 - 0.246: 49 0.246 - 0.369: 4 0.369 - 0.492: 1 0.492 - 0.615: 2 Chirality restraints: 5466 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 5463 not shown) Planarity restraints: 6028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.112 5.00e-02 4.00e+02 1.70e-01 4.65e+01 pdb=" N PRO C 527 " 0.295 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.102 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.050 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN A 717 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " 0.049 2.00e-02 2.50e+03 4.54e-02 2.57e+01 pdb=" CG ASN B 717 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.052 2.00e-02 2.50e+03 ... (remaining 6025 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 871 2.69 - 3.24: 33208 3.24 - 3.79: 50915 3.79 - 4.35: 64785 4.35 - 4.90: 106320 Nonbonded interactions: 256099 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.132 3.040 nonbonded pdb=" O THR C 208 " pdb=" NH2 ARG C 214 " model vdw 2.191 3.120 nonbonded pdb=" O THR B 208 " pdb=" NH1 ARG B 214 " model vdw 2.202 3.120 nonbonded pdb=" OE1 GLN D 184 " pdb=" OG SER D 190 " model vdw 2.205 3.040 nonbonded pdb=" O CYS C 15 " pdb=" N ASN C 17 " model vdw 2.206 3.120 ... (remaining 256094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 676 or resid 689 through 1145 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 14 through 213 or resid 215 through 676 or resid 689 throu \ gh 1145 or resid 1301 through 1309)) selection = (chain 'C' and (resid 14 through 213 or resid 215 through 676 or resid 689 throu \ gh 1145 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 group one per residue 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: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.440 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 79.180 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 34601 Z= 0.155 Angle : 0.694 21.174 47236 Z= 0.331 Chirality : 0.048 0.615 5466 Planarity : 0.005 0.170 5988 Dihedral : 14.116 126.868 13227 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.03 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.02 % 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: -0.96 (0.13), residues: 4222 helix: 1.69 (0.21), residues: 728 sheet: -0.13 (0.17), residues: 958 loop : -1.62 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 258 HIS 0.004 0.000 HIS H 35 PHE 0.032 0.001 PHE A 238 TYR 0.017 0.001 TYR L 38 ARG 0.006 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00848 ( 40) link_NAG-ASN : angle 5.07728 ( 120) link_BETA1-4 : bond 0.00607 ( 14) link_BETA1-4 : angle 2.07473 ( 42) hydrogen bonds : bond 0.23435 ( 1071) hydrogen bonds : angle 8.50243 ( 3012) SS BOND : bond 0.00393 ( 48) SS BOND : angle 1.93180 ( 96) covalent geometry : bond 0.00317 (34499) covalent geometry : angle 0.63809 (46978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8642 (t80) cc_final: 0.8226 (t80) REVERT: C 177 MET cc_start: 0.6535 (mpp) cc_final: 0.6226 (mmm) REVERT: C 988 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8607 (mp0) REVERT: E 170 LYS cc_start: 0.7497 (pttt) cc_final: 0.7272 (mttt) REVERT: L 94 MET cc_start: 0.9008 (mmp) cc_final: 0.8530 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.5269 time to fit residues: 107.7008 Evaluate side-chains 77 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 0.0010 chunk 319 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 382 optimal weight: 20.0000 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 784 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 762 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.057453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.036267 restraints weight = 329058.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.036266 restraints weight = 198433.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.036296 restraints weight = 134417.821| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 34601 Z= 0.145 Angle : 0.663 18.940 47236 Z= 0.328 Chirality : 0.045 0.322 5466 Planarity : 0.005 0.171 5988 Dihedral : 8.675 117.163 5747 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.25 % Favored : 92.37 % Rotamer: Outliers : 0.30 % Allowed : 6.57 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.87 (0.13), residues: 4222 helix: 1.78 (0.21), residues: 728 sheet: -0.10 (0.17), residues: 985 loop : -1.58 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 633 HIS 0.007 0.001 HIS C 146 PHE 0.018 0.001 PHE A 400 TYR 0.022 0.001 TYR L 51 ARG 0.007 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 40) link_NAG-ASN : angle 3.54629 ( 120) link_BETA1-4 : bond 0.00338 ( 14) link_BETA1-4 : angle 1.52057 ( 42) hydrogen bonds : bond 0.04624 ( 1071) hydrogen bonds : angle 6.44565 ( 3012) SS BOND : bond 0.00325 ( 48) SS BOND : angle 1.56235 ( 96) covalent geometry : bond 0.00315 (34499) covalent geometry : angle 0.63473 (46978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8735 (t80) cc_final: 0.8495 (t80) REVERT: A 633 TRP cc_start: 0.8179 (p90) cc_final: 0.7816 (p90) REVERT: A 1050 MET cc_start: 0.8904 (ptp) cc_final: 0.8256 (mtm) REVERT: B 177 MET cc_start: 0.6810 (mpp) cc_final: 0.6605 (mpp) REVERT: C 118 LEU cc_start: 0.9439 (mm) cc_final: 0.8923 (mp) REVERT: C 177 MET cc_start: 0.6836 (mpp) cc_final: 0.6487 (mmm) REVERT: C 740 MET cc_start: 0.8897 (tpp) cc_final: 0.8644 (tpt) REVERT: C 759 PHE cc_start: 0.8864 (m-80) cc_final: 0.8574 (m-80) REVERT: C 900 MET cc_start: 0.9415 (mmm) cc_final: 0.9118 (mmp) REVERT: C 988 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9123 (mp0) REVERT: C 1050 MET cc_start: 0.8478 (pmm) cc_final: 0.8009 (pmm) REVERT: L 94 MET cc_start: 0.8786 (mmp) cc_final: 0.8333 (mmm) outliers start: 11 outliers final: 4 residues processed: 86 average time/residue: 0.5011 time to fit residues: 73.0876 Evaluate side-chains 71 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 822 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 77 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 335 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 147 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1106 GLN B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1088 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.055607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035352 restraints weight = 339543.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.036301 restraints weight = 193202.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036914 restraints weight = 135998.843| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 34601 Z= 0.199 Angle : 0.659 19.181 47236 Z= 0.327 Chirality : 0.044 0.307 5466 Planarity : 0.005 0.171 5988 Dihedral : 8.057 116.122 5747 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.75 % Favored : 91.85 % Rotamer: Outliers : 0.60 % Allowed : 9.82 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.88 (0.13), residues: 4222 helix: 1.69 (0.21), residues: 724 sheet: -0.16 (0.17), residues: 990 loop : -1.53 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.007 0.001 HIS C 146 PHE 0.022 0.002 PHE E 143 TYR 0.026 0.001 TYR B 269 ARG 0.006 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 40) link_NAG-ASN : angle 3.19746 ( 120) link_BETA1-4 : bond 0.00167 ( 14) link_BETA1-4 : angle 1.59549 ( 42) hydrogen bonds : bond 0.04168 ( 1071) hydrogen bonds : angle 5.98020 ( 3012) SS BOND : bond 0.00328 ( 48) SS BOND : angle 1.39828 ( 96) covalent geometry : bond 0.00422 (34499) covalent geometry : angle 0.63556 (46978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8659 (t80) cc_final: 0.8319 (t80) REVERT: A 633 TRP cc_start: 0.8417 (p90) cc_final: 0.8058 (p90) REVERT: A 697 MET cc_start: 0.8758 (pmm) cc_final: 0.8332 (pmm) REVERT: A 780 GLU cc_start: 0.9403 (tp30) cc_final: 0.9086 (tp30) REVERT: A 869 MET cc_start: 0.9363 (mtp) cc_final: 0.9064 (ptp) REVERT: B 697 MET cc_start: 0.9133 (mmp) cc_final: 0.8873 (mmp) REVERT: B 717 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8428 (m-40) REVERT: B 869 MET cc_start: 0.9383 (ptp) cc_final: 0.9169 (ptp) REVERT: C 177 MET cc_start: 0.6876 (mpp) cc_final: 0.6590 (mmm) REVERT: C 697 MET cc_start: 0.9154 (mmm) cc_final: 0.8669 (mmm) REVERT: C 740 MET cc_start: 0.9168 (tpp) cc_final: 0.8764 (tpt) REVERT: C 742 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9130 (tp) REVERT: C 900 MET cc_start: 0.9482 (mmm) cc_final: 0.9213 (mmp) REVERT: C 988 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9002 (mp0) REVERT: C 1050 MET cc_start: 0.8643 (pmm) cc_final: 0.8189 (pmm) REVERT: L 94 MET cc_start: 0.8757 (mmp) cc_final: 0.8324 (mmm) outliers start: 22 outliers final: 10 residues processed: 89 average time/residue: 0.5288 time to fit residues: 79.5584 Evaluate side-chains 75 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 400 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 241 optimal weight: 0.0010 chunk 370 optimal weight: 9.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.055955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035669 restraints weight = 335119.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036635 restraints weight = 188747.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037266 restraints weight = 132557.688| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 34601 Z= 0.119 Angle : 0.599 18.185 47236 Z= 0.294 Chirality : 0.044 0.304 5466 Planarity : 0.004 0.168 5988 Dihedral : 7.574 115.977 5747 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.87 % Favored : 92.73 % Rotamer: Outliers : 0.79 % Allowed : 11.51 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.77 (0.13), residues: 4222 helix: 1.96 (0.21), residues: 720 sheet: -0.11 (0.17), residues: 977 loop : -1.50 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.005 0.001 HIS B 625 PHE 0.020 0.001 PHE A 400 TYR 0.015 0.001 TYR D 109 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 40) link_NAG-ASN : angle 3.04624 ( 120) link_BETA1-4 : bond 0.00330 ( 14) link_BETA1-4 : angle 1.42369 ( 42) hydrogen bonds : bond 0.03525 ( 1071) hydrogen bonds : angle 5.63060 ( 3012) SS BOND : bond 0.00282 ( 48) SS BOND : angle 1.30553 ( 96) covalent geometry : bond 0.00260 (34499) covalent geometry : angle 0.57634 (46978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8632 (t80) cc_final: 0.8268 (t80) REVERT: A 633 TRP cc_start: 0.8358 (p90) cc_final: 0.8104 (p90) REVERT: A 697 MET cc_start: 0.8788 (pmm) cc_final: 0.8506 (pmm) REVERT: A 773 GLU cc_start: 0.9371 (tp30) cc_final: 0.8685 (tp30) REVERT: A 780 GLU cc_start: 0.9369 (tp30) cc_final: 0.9014 (tp30) REVERT: A 1050 MET cc_start: 0.8869 (ptp) cc_final: 0.8441 (mtm) REVERT: B 697 MET cc_start: 0.9059 (mmp) cc_final: 0.8788 (mmp) REVERT: B 869 MET cc_start: 0.9350 (ptp) cc_final: 0.9077 (ptp) REVERT: B 965 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8951 (tp-100) REVERT: C 177 MET cc_start: 0.6837 (mpp) cc_final: 0.6542 (mmm) REVERT: C 740 MET cc_start: 0.9130 (tpp) cc_final: 0.8709 (tpt) REVERT: C 742 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9085 (tp) REVERT: C 900 MET cc_start: 0.9463 (mmm) cc_final: 0.9130 (mmp) REVERT: C 988 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8972 (mp0) REVERT: C 1050 MET cc_start: 0.8572 (pmm) cc_final: 0.8238 (pmm) REVERT: L 94 MET cc_start: 0.8693 (mmp) cc_final: 0.8249 (mmm) outliers start: 29 outliers final: 10 residues processed: 93 average time/residue: 0.4736 time to fit residues: 76.8482 Evaluate side-chains 75 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 34 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 161 optimal weight: 0.0000 chunk 265 optimal weight: 30.0000 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3671 r_free = 0.3671 target = 0.055453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.035290 restraints weight = 338550.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.036231 restraints weight = 193304.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036843 restraints weight = 136306.194| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34601 Z= 0.155 Angle : 0.615 18.259 47236 Z= 0.301 Chirality : 0.043 0.289 5466 Planarity : 0.004 0.168 5988 Dihedral : 7.374 115.008 5747 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.67 % Favored : 91.97 % Rotamer: Outliers : 0.90 % Allowed : 12.74 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.78 (0.13), residues: 4222 helix: 1.94 (0.21), residues: 716 sheet: -0.14 (0.17), residues: 982 loop : -1.49 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 152 HIS 0.004 0.001 HIS B 625 PHE 0.015 0.001 PHE A 400 TYR 0.015 0.001 TYR B 269 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 40) link_NAG-ASN : angle 2.98695 ( 120) link_BETA1-4 : bond 0.00185 ( 14) link_BETA1-4 : angle 1.46728 ( 42) hydrogen bonds : bond 0.03503 ( 1071) hydrogen bonds : angle 5.54779 ( 3012) SS BOND : bond 0.00327 ( 48) SS BOND : angle 1.27739 ( 96) covalent geometry : bond 0.00333 (34499) covalent geometry : angle 0.59321 (46978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8603 (t80) cc_final: 0.8223 (t80) REVERT: A 633 TRP cc_start: 0.8386 (p90) cc_final: 0.8145 (p90) REVERT: A 697 MET cc_start: 0.8811 (pmm) cc_final: 0.8601 (pmm) REVERT: A 773 GLU cc_start: 0.9380 (tp30) cc_final: 0.8701 (tp30) REVERT: A 780 GLU cc_start: 0.9386 (tp30) cc_final: 0.9050 (tp30) REVERT: A 869 MET cc_start: 0.9338 (mtp) cc_final: 0.9035 (ptp) REVERT: A 1050 MET cc_start: 0.8933 (ptp) cc_final: 0.8365 (mtm) REVERT: B 414 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.6540 (pm20) REVERT: B 697 MET cc_start: 0.9070 (mmp) cc_final: 0.8810 (mmp) REVERT: C 177 MET cc_start: 0.6903 (mpp) cc_final: 0.6669 (mmm) REVERT: C 697 MET cc_start: 0.9067 (mmm) cc_final: 0.8864 (mmm) REVERT: C 740 MET cc_start: 0.9167 (tpp) cc_final: 0.8734 (tpt) REVERT: C 742 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9116 (tp) REVERT: C 759 PHE cc_start: 0.8976 (m-80) cc_final: 0.8756 (m-80) REVERT: C 900 MET cc_start: 0.9481 (mmm) cc_final: 0.9208 (mmp) REVERT: C 988 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8996 (mp0) REVERT: C 1050 MET cc_start: 0.8687 (pmm) cc_final: 0.8267 (pmm) REVERT: L 94 MET cc_start: 0.8594 (mmp) cc_final: 0.8020 (mmm) outliers start: 33 outliers final: 20 residues processed: 97 average time/residue: 0.4357 time to fit residues: 76.5736 Evaluate side-chains 85 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 153 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 397 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 342 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.055637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035427 restraints weight = 336539.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036388 restraints weight = 189875.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.037009 restraints weight = 133153.486| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 34601 Z= 0.115 Angle : 0.594 17.908 47236 Z= 0.290 Chirality : 0.043 0.289 5466 Planarity : 0.004 0.167 5988 Dihedral : 7.093 114.663 5747 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.99 % Favored : 92.66 % Rotamer: Outliers : 1.17 % Allowed : 13.23 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.72 (0.13), residues: 4222 helix: 2.01 (0.21), residues: 720 sheet: -0.04 (0.17), residues: 969 loop : -1.47 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.004 0.001 HIS H 35 PHE 0.021 0.001 PHE A 400 TYR 0.017 0.001 TYR C 160 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 40) link_NAG-ASN : angle 2.89939 ( 120) link_BETA1-4 : bond 0.00362 ( 14) link_BETA1-4 : angle 1.43254 ( 42) hydrogen bonds : bond 0.03258 ( 1071) hydrogen bonds : angle 5.33559 ( 3012) SS BOND : bond 0.00312 ( 48) SS BOND : angle 1.30153 ( 96) covalent geometry : bond 0.00255 (34499) covalent geometry : angle 0.57232 (46978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 68 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8624 (t80) cc_final: 0.8241 (t80) REVERT: A 697 MET cc_start: 0.8838 (pmm) cc_final: 0.8629 (pmm) REVERT: A 773 GLU cc_start: 0.9395 (tp30) cc_final: 0.8697 (tp30) REVERT: A 780 GLU cc_start: 0.9400 (tp30) cc_final: 0.9040 (tp30) REVERT: A 869 MET cc_start: 0.9333 (mtp) cc_final: 0.8765 (ptp) REVERT: A 1031 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8474 (mm-30) REVERT: A 1050 MET cc_start: 0.8935 (ptp) cc_final: 0.8376 (mtm) REVERT: B 414 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6467 (pm20) REVERT: B 697 MET cc_start: 0.9066 (mmp) cc_final: 0.8777 (mmp) REVERT: C 177 MET cc_start: 0.6893 (mpp) cc_final: 0.6687 (mmm) REVERT: C 740 MET cc_start: 0.9176 (tpp) cc_final: 0.8733 (tpt) REVERT: C 742 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9091 (tp) REVERT: C 759 PHE cc_start: 0.8945 (m-80) cc_final: 0.8595 (m-80) REVERT: C 900 MET cc_start: 0.9496 (mmm) cc_final: 0.9162 (mmp) REVERT: C 988 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8991 (mp0) REVERT: C 1050 MET cc_start: 0.8608 (pmm) cc_final: 0.8261 (pmm) REVERT: L 94 MET cc_start: 0.8516 (mmp) cc_final: 0.7968 (mmm) outliers start: 43 outliers final: 21 residues processed: 109 average time/residue: 0.4246 time to fit residues: 82.7389 Evaluate side-chains 87 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 368 optimal weight: 10.0000 chunk 339 optimal weight: 0.0170 chunk 74 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 375 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 282 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 342 optimal weight: 50.0000 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.055269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035114 restraints weight = 340454.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.036055 restraints weight = 194637.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036668 restraints weight = 137735.698| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34601 Z= 0.151 Angle : 0.618 18.014 47236 Z= 0.302 Chirality : 0.044 0.281 5466 Planarity : 0.004 0.168 5988 Dihedral : 7.036 113.630 5747 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.65 % Favored : 91.99 % Rotamer: Outliers : 1.12 % Allowed : 13.99 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.72 (0.13), residues: 4222 helix: 2.01 (0.21), residues: 715 sheet: -0.10 (0.17), residues: 964 loop : -1.44 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.001 PHE A 400 TYR 0.014 0.001 TYR D 109 ARG 0.008 0.000 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 40) link_NAG-ASN : angle 2.97511 ( 120) link_BETA1-4 : bond 0.00246 ( 14) link_BETA1-4 : angle 1.42020 ( 42) hydrogen bonds : bond 0.03305 ( 1071) hydrogen bonds : angle 5.32017 ( 3012) SS BOND : bond 0.00302 ( 48) SS BOND : angle 1.63627 ( 96) covalent geometry : bond 0.00328 (34499) covalent geometry : angle 0.59476 (46978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 64 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8494 (t80) cc_final: 0.8088 (t80) REVERT: A 697 MET cc_start: 0.8906 (pmm) cc_final: 0.8640 (pmm) REVERT: A 773 GLU cc_start: 0.9395 (tp30) cc_final: 0.8690 (tp30) REVERT: A 780 GLU cc_start: 0.9388 (tp30) cc_final: 0.9054 (tp30) REVERT: A 1031 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8495 (mm-30) REVERT: A 1050 MET cc_start: 0.8958 (ptp) cc_final: 0.8390 (mtm) REVERT: B 414 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: B 697 MET cc_start: 0.9087 (mmp) cc_final: 0.8807 (mmp) REVERT: C 740 MET cc_start: 0.9197 (tpp) cc_final: 0.8751 (tpt) REVERT: C 742 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9124 (tp) REVERT: C 759 PHE cc_start: 0.8975 (m-80) cc_final: 0.8637 (m-80) REVERT: C 900 MET cc_start: 0.9488 (mmm) cc_final: 0.9207 (mmp) REVERT: C 988 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9016 (mp0) REVERT: C 1050 MET cc_start: 0.8717 (pmm) cc_final: 0.8284 (pmm) REVERT: H 113 MET cc_start: 0.4708 (tpt) cc_final: 0.4451 (tpt) REVERT: L 94 MET cc_start: 0.8498 (mmp) cc_final: 0.7917 (mmm) outliers start: 41 outliers final: 27 residues processed: 104 average time/residue: 0.4174 time to fit residues: 78.7309 Evaluate side-chains 92 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 372 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 199 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.054249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.034081 restraints weight = 341434.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.034952 restraints weight = 199275.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035509 restraints weight = 143099.188| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 34601 Z= 0.262 Angle : 0.706 18.458 47236 Z= 0.348 Chirality : 0.045 0.274 5466 Planarity : 0.005 0.169 5988 Dihedral : 7.326 113.041 5747 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.67 % Favored : 90.95 % Rotamer: Outliers : 1.15 % Allowed : 14.62 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.95 (0.13), residues: 4222 helix: 1.56 (0.20), residues: 727 sheet: -0.31 (0.17), residues: 945 loop : -1.48 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.006 0.001 HIS B 207 PHE 0.016 0.002 PHE A 400 TYR 0.021 0.002 TYR B 269 ARG 0.008 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 40) link_NAG-ASN : angle 2.99859 ( 120) link_BETA1-4 : bond 0.00270 ( 14) link_BETA1-4 : angle 1.59946 ( 42) hydrogen bonds : bond 0.03735 ( 1071) hydrogen bonds : angle 5.60320 ( 3012) SS BOND : bond 0.00409 ( 48) SS BOND : angle 1.53129 ( 96) covalent geometry : bond 0.00551 (34499) covalent geometry : angle 0.68607 (46978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 62 time to evaluate : 3.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8474 (t80) cc_final: 0.8096 (t80) REVERT: A 697 MET cc_start: 0.8905 (pmm) cc_final: 0.8651 (pmm) REVERT: A 869 MET cc_start: 0.9388 (mtp) cc_final: 0.9115 (ptp) REVERT: B 414 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: B 697 MET cc_start: 0.9020 (mmp) cc_final: 0.8776 (mmp) REVERT: C 740 MET cc_start: 0.9260 (tpp) cc_final: 0.8839 (tpp) REVERT: C 742 ILE cc_start: 0.9623 (OUTLIER) cc_final: 0.9185 (tp) REVERT: C 900 MET cc_start: 0.9474 (mmm) cc_final: 0.9215 (mmp) REVERT: C 1029 MET cc_start: 0.9625 (tpp) cc_final: 0.9396 (tpp) REVERT: C 1050 MET cc_start: 0.8936 (pmm) cc_final: 0.8210 (pmm) REVERT: H 113 MET cc_start: 0.5369 (tpt) cc_final: 0.5017 (tpt) REVERT: L 94 MET cc_start: 0.8466 (mmp) cc_final: 0.7752 (mmp) outliers start: 42 outliers final: 30 residues processed: 104 average time/residue: 0.4258 time to fit residues: 79.7701 Evaluate side-chains 89 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 247 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 326 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 347 optimal weight: 40.0000 chunk 390 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.055791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034601 restraints weight = 291190.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035444 restraints weight = 190619.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035958 restraints weight = 144272.214| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 34601 Z= 0.169 Angle : 0.644 18.205 47236 Z= 0.315 Chirality : 0.044 0.281 5466 Planarity : 0.005 0.168 5988 Dihedral : 7.146 113.426 5747 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.67 % Favored : 91.97 % Rotamer: Outliers : 1.17 % Allowed : 14.86 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.88 (0.13), residues: 4222 helix: 1.76 (0.20), residues: 726 sheet: -0.33 (0.17), residues: 964 loop : -1.46 (0.13), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.005 0.001 HIS H 35 PHE 0.016 0.001 PHE A 400 TYR 0.014 0.001 TYR D 109 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 40) link_NAG-ASN : angle 2.81624 ( 120) link_BETA1-4 : bond 0.00176 ( 14) link_BETA1-4 : angle 1.41774 ( 42) hydrogen bonds : bond 0.03427 ( 1071) hydrogen bonds : angle 5.42747 ( 3012) SS BOND : bond 0.00340 ( 48) SS BOND : angle 1.41054 ( 96) covalent geometry : bond 0.00365 (34499) covalent geometry : angle 0.62548 (46978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8501 (t80) cc_final: 0.8145 (t80) REVERT: A 697 MET cc_start: 0.8907 (pmm) cc_final: 0.8661 (pmm) REVERT: A 773 GLU cc_start: 0.9375 (tp30) cc_final: 0.8719 (tp30) REVERT: A 869 MET cc_start: 0.9348 (mtp) cc_final: 0.9076 (ptp) REVERT: A 1031 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8550 (mm-30) REVERT: A 1050 MET cc_start: 0.8933 (ptp) cc_final: 0.8478 (mtp) REVERT: B 414 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: B 697 MET cc_start: 0.9109 (mmp) cc_final: 0.8854 (mmp) REVERT: B 900 MET cc_start: 0.9383 (mmm) cc_final: 0.8838 (mmm) REVERT: C 740 MET cc_start: 0.9237 (tpp) cc_final: 0.8770 (tpt) REVERT: C 742 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9130 (tp) REVERT: C 900 MET cc_start: 0.9509 (mmm) cc_final: 0.9172 (mmp) REVERT: C 1050 MET cc_start: 0.8854 (pmm) cc_final: 0.8308 (pmm) REVERT: D 113 MET cc_start: 0.8120 (tmm) cc_final: 0.7506 (tmm) REVERT: H 113 MET cc_start: 0.5417 (tpt) cc_final: 0.5028 (tpt) outliers start: 43 outliers final: 31 residues processed: 102 average time/residue: 0.4273 time to fit residues: 78.7921 Evaluate side-chains 92 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 337 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 27 optimal weight: 0.0070 chunk 182 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 370 optimal weight: 8.9990 chunk 356 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.054886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034883 restraints weight = 339823.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035820 restraints weight = 193255.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036410 restraints weight = 136272.196| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 34601 Z= 0.121 Angle : 0.623 18.090 47236 Z= 0.302 Chirality : 0.044 0.279 5466 Planarity : 0.004 0.168 5988 Dihedral : 6.915 112.854 5747 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.37 % Favored : 92.25 % Rotamer: Outliers : 1.01 % Allowed : 15.19 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.78 (0.13), residues: 4222 helix: 1.92 (0.21), residues: 724 sheet: -0.27 (0.17), residues: 976 loop : -1.42 (0.13), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 167 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.001 PHE A 400 TYR 0.015 0.001 TYR D 109 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 40) link_NAG-ASN : angle 2.72848 ( 120) link_BETA1-4 : bond 0.00350 ( 14) link_BETA1-4 : angle 1.44663 ( 42) hydrogen bonds : bond 0.03251 ( 1071) hydrogen bonds : angle 5.24583 ( 3012) SS BOND : bond 0.00325 ( 48) SS BOND : angle 1.36131 ( 96) covalent geometry : bond 0.00269 (34499) covalent geometry : angle 0.60453 (46978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 4.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8487 (t80) cc_final: 0.8163 (t80) REVERT: A 492 LEU cc_start: 0.9455 (mp) cc_final: 0.9043 (mt) REVERT: A 697 MET cc_start: 0.8983 (pmm) cc_final: 0.8669 (pmm) REVERT: A 773 GLU cc_start: 0.9389 (tp30) cc_final: 0.8694 (tp30) REVERT: A 869 MET cc_start: 0.9312 (mtp) cc_final: 0.8798 (ptp) REVERT: A 1031 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: A 1050 MET cc_start: 0.8869 (ptp) cc_final: 0.8420 (mtm) REVERT: B 414 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: B 697 MET cc_start: 0.9125 (mmp) cc_final: 0.8837 (mmp) REVERT: C 432 CYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7035 (p) REVERT: C 740 MET cc_start: 0.9189 (tpp) cc_final: 0.8736 (tpt) REVERT: C 742 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 759 PHE cc_start: 0.9005 (m-80) cc_final: 0.8694 (m-80) REVERT: C 869 MET cc_start: 0.9688 (mpp) cc_final: 0.9325 (pmm) REVERT: C 1050 MET cc_start: 0.8764 (pmm) cc_final: 0.8308 (pmm) REVERT: D 113 MET cc_start: 0.8173 (tmm) cc_final: 0.7692 (tmm) REVERT: H 113 MET cc_start: 0.5527 (tpt) cc_final: 0.5109 (tpt) outliers start: 37 outliers final: 32 residues processed: 94 average time/residue: 0.5306 time to fit residues: 92.2040 Evaluate side-chains 94 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 140 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 335 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 302 optimal weight: 20.0000 chunk 304 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 353 optimal weight: 40.0000 chunk 290 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.055098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.035111 restraints weight = 336240.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036038 restraints weight = 191224.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.036640 restraints weight = 133910.377| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 34601 Z= 0.104 Angle : 0.603 17.841 47236 Z= 0.292 Chirality : 0.044 0.278 5466 Planarity : 0.004 0.168 5988 Dihedral : 6.642 111.357 5747 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.77 % Favored : 92.85 % Rotamer: Outliers : 1.04 % Allowed : 15.16 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.70 (0.13), residues: 4222 helix: 1.98 (0.21), residues: 724 sheet: -0.21 (0.16), residues: 1000 loop : -1.38 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 167 HIS 0.005 0.001 HIS C 245 PHE 0.018 0.001 PHE A 400 TYR 0.015 0.001 TYR D 109 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 40) link_NAG-ASN : angle 2.58682 ( 120) link_BETA1-4 : bond 0.00300 ( 14) link_BETA1-4 : angle 1.41999 ( 42) hydrogen bonds : bond 0.03030 ( 1071) hydrogen bonds : angle 5.04332 ( 3012) SS BOND : bond 0.00317 ( 48) SS BOND : angle 1.27510 ( 96) covalent geometry : bond 0.00234 (34499) covalent geometry : angle 0.58565 (46978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14097.29 seconds wall clock time: 249 minutes 41.15 seconds (14981.15 seconds total)