Starting phenix.real_space_refine on Mon Jun 23 04:21:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws4_32743/06_2025/7ws4_32743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws4_32743/06_2025/7ws4_32743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws4_32743/06_2025/7ws4_32743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws4_32743/06_2025/7ws4_32743.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws4_32743/06_2025/7ws4_32743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws4_32743/06_2025/7ws4_32743.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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 118 5.16 5 C 16958 2.51 5 N 4371 2.21 5 O 5119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26566 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8081 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8092 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8088 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 16.75, per 1000 atoms: 0.63 Number of scatterers: 26566 At special positions: 0 Unit cell: (138.944, 137.28, 211.328, 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 118 16.00 O 5119 8.00 N 4371 7.00 C 16958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG D 1 " - " ASN C 801 " " NAG E 1 " - " ASN C1074 " " NAG F 1 " - " ASN C1098 " " NAG G 1 " - " ASN C1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.2 seconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 51 sheets defined 23.9% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.240A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.038A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.138A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.145A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.553A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.566A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.506A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.076A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.963A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.536A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.536A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (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: 3.627A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.041A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.187A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.504A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.587A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.012A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.117A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.898A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.616A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.103A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.566A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.051A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.409A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.933A pdb=" N ASP I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.144A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.276A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.999A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.769A 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 removed outlier: 4.107A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.799A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.960A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.623A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.778A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.427A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.674A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.778A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.457A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.374A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.875A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.972A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.721A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 13.102A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.620A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.584A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.656A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.557A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.948A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.776A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.032A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 135 through 141 removed outlier: 8.043A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 12.109A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.419A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.219A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.424A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.573A pdb=" N LEU H 105 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 84 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.830A pdb=" N THR I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.678A pdb=" N ASP I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 50 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 117 " --> pdb=" O TYR I 94 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 2937 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.50 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8377 1.34 - 1.46: 6218 1.46 - 1.58: 12435 1.58 - 1.70: 0 1.70 - 1.83: 148 Bond restraints: 27178 Sorted by residual: bond pdb=" N VAL B 534 " pdb=" CA VAL B 534 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.02e+01 bond pdb=" N VAL B 595 " pdb=" CA VAL B 595 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" C ALA B 264 " pdb=" N TYR B 265 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.43e-02 4.89e+03 8.68e+00 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.29e-02 6.01e+03 8.23e+00 bond pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.65e+00 ... (remaining 27173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 35712 1.52 - 3.03: 1059 3.03 - 4.55: 167 4.55 - 6.06: 33 6.06 - 7.58: 3 Bond angle restraints: 36974 Sorted by residual: angle pdb=" CA ASN B 532 " pdb=" C ASN B 532 " pdb=" O ASN B 532 " ideal model delta sigma weight residual 121.55 117.81 3.74 1.06e+00 8.90e-01 1.25e+01 angle pdb=" CA LYS B 537 " pdb=" C LYS B 537 " pdb=" O LYS B 537 " ideal model delta sigma weight residual 121.38 117.67 3.71 1.06e+00 8.90e-01 1.23e+01 angle pdb=" CA CYS B 538 " pdb=" C CYS B 538 " pdb=" O CYS B 538 " ideal model delta sigma weight residual 122.41 118.22 4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" C TYR B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta sigma weight residual 122.94 128.07 -5.13 1.50e+00 4.44e-01 1.17e+01 angle pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" C THR C 19 " ideal model delta sigma weight residual 113.89 108.56 5.33 1.58e+00 4.01e-01 1.14e+01 ... (remaining 36969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 15249 17.88 - 35.77: 1161 35.77 - 53.65: 210 53.65 - 71.53: 62 71.53 - 89.42: 33 Dihedral angle restraints: 16715 sinusoidal: 7027 harmonic: 9688 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 0.86 -86.86 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 177.59 -84.59 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.11 -60.89 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 16712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3988 0.094 - 0.188: 296 0.188 - 0.281: 5 0.281 - 0.375: 0 0.375 - 0.469: 1 Chirality restraints: 4290 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CG LEU H 33 " pdb=" CB LEU H 33 " pdb=" CD1 LEU H 33 " pdb=" CD2 LEU H 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4287 not shown) Planarity restraints: 4754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO C 987 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.019 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN C 709 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 986 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.028 5.00e-02 4.00e+02 ... (remaining 4751 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 483 2.67 - 3.23: 24936 3.23 - 3.78: 40318 3.78 - 4.34: 53877 4.34 - 4.90: 89970 Nonbonded interactions: 209584 Sorted by model distance: nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS C 378 " pdb=" OH TYR C 380 " model vdw 2.222 3.120 nonbonded pdb=" O THR C 747 " pdb=" OG SER C 750 " model vdw 2.224 3.040 ... (remaining 209579 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 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 318 or (resid 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 1147 or resid 1301 \ through 1303)) selection = (chain 'B' and (resid 14 through 500 or (resid 501 and (name N or name CA or nam \ e C or name O or name CB )) or resid 502 through 518 or (resid 519 through 520 a \ nd (name N or name CA or name C or name O or name CB )) or resid 521 through 527 \ or (resid 528 through 529 and (name N or name CA or name C or name O or name CB \ )) or resid 530 through 1147 or resid 1301 through 1303)) selection = (chain 'C' and (resid 14 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 318 or (resid 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or resid 502 through 11 \ 47 or resid 1301 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 99.100 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: 1.060 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 62.270 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.140 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27259 Z= 0.211 Angle : 0.633 12.710 37172 Z= 0.346 Chirality : 0.047 0.469 4290 Planarity : 0.004 0.053 4730 Dihedral : 13.510 89.415 10349 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3269 helix: 1.91 (0.21), residues: 658 sheet: 0.43 (0.18), residues: 759 loop : -0.80 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 47 HIS 0.003 0.001 HIS C 954 PHE 0.026 0.001 PHE A 906 TYR 0.033 0.001 TYR A 453 ARG 0.004 0.000 ARG I 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 24) link_NAG-ASN : angle 2.84576 ( 72) link_BETA1-4 : bond 0.00356 ( 14) link_BETA1-4 : angle 0.84190 ( 42) hydrogen bonds : bond 0.12069 ( 1067) hydrogen bonds : angle 6.62521 ( 2937) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.22849 ( 84) covalent geometry : bond 0.00389 (27178) covalent geometry : angle 0.61900 (36974) Misc. bond : bond 0.06899 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8294 (m-80) cc_final: 0.7806 (m-80) REVERT: A 515 PHE cc_start: 0.7253 (m-80) cc_final: 0.6657 (m-80) REVERT: B 436 TRP cc_start: 0.7364 (p90) cc_final: 0.6827 (p90) REVERT: C 53 ASP cc_start: 0.7938 (t70) cc_final: 0.7561 (t70) REVERT: C 780 GLU cc_start: 0.8246 (tt0) cc_final: 0.8042 (tt0) REVERT: H 87 TYR cc_start: 0.7462 (m-10) cc_final: 0.7170 (m-10) REVERT: I 74 ASN cc_start: 0.8272 (m-40) cc_final: 0.7558 (m-40) REVERT: I 80 TYR cc_start: 0.7961 (m-80) cc_final: 0.7695 (m-80) REVERT: I 119 VAL cc_start: 0.6722 (m) cc_final: 0.5938 (m) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3596 time to fit residues: 96.8749 Evaluate side-chains 120 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 0.1980 chunk 250 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 300 optimal weight: 0.5980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 804 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.094688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061831 restraints weight = 80856.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063950 restraints weight = 41344.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065337 restraints weight = 27854.587| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27259 Z= 0.192 Angle : 0.587 10.902 37172 Z= 0.299 Chirality : 0.045 0.446 4290 Planarity : 0.004 0.048 4730 Dihedral : 6.898 59.611 4366 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.38 % Allowed : 5.44 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3269 helix: 1.99 (0.21), residues: 662 sheet: 0.27 (0.18), residues: 764 loop : -0.85 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.005 0.001 HIS H 38 PHE 0.019 0.001 PHE A 906 TYR 0.025 0.001 TYR A 453 ARG 0.005 0.000 ARG I 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 24) link_NAG-ASN : angle 2.53828 ( 72) link_BETA1-4 : bond 0.00376 ( 14) link_BETA1-4 : angle 0.92151 ( 42) hydrogen bonds : bond 0.04864 ( 1067) hydrogen bonds : angle 5.44995 ( 2937) SS BOND : bond 0.00340 ( 42) SS BOND : angle 1.31509 ( 84) covalent geometry : bond 0.00454 (27178) covalent geometry : angle 0.57328 (36974) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 3.183 Fit side-chains revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8259 (m-80) cc_final: 0.7945 (m-80) REVERT: B 342 PHE cc_start: 0.8745 (m-10) cc_final: 0.8025 (m-10) REVERT: B 436 TRP cc_start: 0.7517 (p90) cc_final: 0.7083 (p90) REVERT: C 53 ASP cc_start: 0.8025 (t70) cc_final: 0.7764 (t70) REVERT: H 24 ARG cc_start: 0.8467 (mmm160) cc_final: 0.8256 (mmm160) REVERT: H 46 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7479 (tp) REVERT: H 95 PRO cc_start: 0.6182 (Cg_exo) cc_final: 0.5875 (Cg_endo) REVERT: I 119 VAL cc_start: 0.5410 (OUTLIER) cc_final: 0.4925 (t) outliers start: 11 outliers final: 6 residues processed: 137 average time/residue: 0.4156 time to fit residues: 93.2488 Evaluate side-chains 122 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 75 optimal weight: 3.9990 chunk 282 optimal weight: 0.9980 chunk 284 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 92 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 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 = 0.3683 r_free = 0.3683 target = 0.090656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057669 restraints weight = 81126.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.059854 restraints weight = 40400.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.061276 restraints weight = 26769.955| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27259 Z= 0.128 Angle : 0.535 10.958 37172 Z= 0.271 Chirality : 0.044 0.424 4290 Planarity : 0.004 0.048 4730 Dihedral : 6.448 59.890 4366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.72 % Allowed : 7.85 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3269 helix: 2.12 (0.21), residues: 664 sheet: 0.38 (0.18), residues: 770 loop : -0.84 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.005 0.001 HIS H 38 PHE 0.019 0.001 PHE C 562 TYR 0.025 0.001 TYR H 49 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 24) link_NAG-ASN : angle 2.35081 ( 72) link_BETA1-4 : bond 0.00301 ( 14) link_BETA1-4 : angle 0.90974 ( 42) hydrogen bonds : bond 0.04359 ( 1067) hydrogen bonds : angle 5.18543 ( 2937) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.13165 ( 84) covalent geometry : bond 0.00296 (27178) covalent geometry : angle 0.52273 (36974) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 3.935 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7622 (m-10) cc_final: 0.7263 (m-80) REVERT: A 571 ASP cc_start: 0.8319 (t0) cc_final: 0.7871 (t0) REVERT: B 342 PHE cc_start: 0.8689 (m-10) cc_final: 0.7981 (m-10) REVERT: B 436 TRP cc_start: 0.7462 (p90) cc_final: 0.7034 (p90) REVERT: C 53 ASP cc_start: 0.8038 (t70) cc_final: 0.7758 (t70) REVERT: H 24 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8140 (mmm160) REVERT: H 95 PRO cc_start: 0.6289 (Cg_exo) cc_final: 0.5999 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7825 (m-80) cc_final: 0.7313 (m-80) REVERT: I 104 ILE cc_start: 0.7729 (pt) cc_final: 0.6840 (mt) outliers start: 21 outliers final: 8 residues processed: 150 average time/residue: 0.5294 time to fit residues: 135.2546 Evaluate side-chains 129 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 14 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A 935 GLN A1083 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 125 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 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 = 0.3734 r_free = 0.3734 target = 0.092037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.059963 restraints weight = 80910.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.062025 restraints weight = 41965.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063412 restraints weight = 28621.194| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27259 Z= 0.233 Angle : 0.599 10.998 37172 Z= 0.304 Chirality : 0.046 0.417 4290 Planarity : 0.004 0.049 4730 Dihedral : 6.291 58.775 4366 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.89 % Allowed : 9.94 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3269 helix: 1.98 (0.21), residues: 663 sheet: 0.10 (0.18), residues: 756 loop : -0.87 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.005 0.001 HIS C1058 PHE 0.031 0.002 PHE H 71 TYR 0.029 0.001 TYR B 265 ARG 0.004 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 24) link_NAG-ASN : angle 2.49830 ( 72) link_BETA1-4 : bond 0.00241 ( 14) link_BETA1-4 : angle 1.03379 ( 42) hydrogen bonds : bond 0.04902 ( 1067) hydrogen bonds : angle 5.23564 ( 2937) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.38941 ( 84) covalent geometry : bond 0.00548 (27178) covalent geometry : angle 0.58548 (36974) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 3.010 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6671 (m-10) REVERT: A 1083 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7439 (t-90) REVERT: B 342 PHE cc_start: 0.8690 (m-10) cc_final: 0.8007 (m-10) REVERT: B 436 TRP cc_start: 0.7686 (p90) cc_final: 0.7075 (p90) REVERT: C 53 ASP cc_start: 0.7997 (t70) cc_final: 0.7785 (t70) REVERT: C 153 MET cc_start: 0.6181 (ppp) cc_final: 0.5958 (ppp) REVERT: H 24 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8353 (mmm160) REVERT: H 95 PRO cc_start: 0.6494 (Cg_exo) cc_final: 0.6206 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7881 (m-80) cc_final: 0.7351 (m-80) REVERT: H 106 GLU cc_start: 0.8001 (pm20) cc_final: 0.7775 (pm20) REVERT: I 87 ARG cc_start: 0.8781 (mpp80) cc_final: 0.8473 (mpp80) REVERT: I 104 ILE cc_start: 0.7890 (pt) cc_final: 0.7009 (mt) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 0.3794 time to fit residues: 92.4203 Evaluate side-chains 140 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 267 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 935 GLN A 965 GLN A1083 HIS B 239 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 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 = 0.3742 r_free = 0.3742 target = 0.092093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060389 restraints weight = 80835.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062495 restraints weight = 41267.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.063899 restraints weight = 27726.096| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27259 Z= 0.164 Angle : 0.552 11.060 37172 Z= 0.279 Chirality : 0.044 0.404 4290 Planarity : 0.004 0.052 4730 Dihedral : 5.950 54.573 4366 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.00 % Allowed : 11.11 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.15), residues: 3269 helix: 2.09 (0.21), residues: 663 sheet: 0.18 (0.18), residues: 777 loop : -0.85 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.012 0.001 HIS A1083 PHE 0.027 0.001 PHE H 71 TYR 0.022 0.001 TYR B 265 ARG 0.010 0.000 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 24) link_NAG-ASN : angle 2.35082 ( 72) link_BETA1-4 : bond 0.00292 ( 14) link_BETA1-4 : angle 0.95808 ( 42) hydrogen bonds : bond 0.04531 ( 1067) hydrogen bonds : angle 5.09958 ( 2937) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.22656 ( 84) covalent geometry : bond 0.00383 (27178) covalent geometry : angle 0.53922 (36974) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 4.141 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6693 (m-10) REVERT: B 342 PHE cc_start: 0.8649 (m-10) cc_final: 0.7955 (m-10) REVERT: B 436 TRP cc_start: 0.7662 (p90) cc_final: 0.7060 (p90) REVERT: H 24 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8358 (mmm160) REVERT: H 88 CYS cc_start: 0.5682 (m) cc_final: 0.5044 (m) REVERT: H 95 PRO cc_start: 0.6537 (Cg_exo) cc_final: 0.6243 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7856 (m-80) cc_final: 0.7335 (m-80) REVERT: I 87 ARG cc_start: 0.8782 (mpp80) cc_final: 0.8481 (mpp80) REVERT: I 104 ILE cc_start: 0.7881 (pt) cc_final: 0.7020 (mt) outliers start: 29 outliers final: 18 residues processed: 155 average time/residue: 0.5400 time to fit residues: 143.2370 Evaluate side-chains 140 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 326 optimal weight: 9.9990 chunk 70 optimal weight: 0.0670 chunk 139 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 212 optimal weight: 0.3980 chunk 237 optimal weight: 3.9990 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.093367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061981 restraints weight = 82418.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.064289 restraints weight = 41077.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065816 restraints weight = 27107.995| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27259 Z= 0.183 Angle : 0.565 11.135 37172 Z= 0.286 Chirality : 0.045 0.394 4290 Planarity : 0.004 0.053 4730 Dihedral : 5.648 52.989 4366 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.10 % Allowed : 12.04 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3269 helix: 2.02 (0.20), residues: 669 sheet: 0.15 (0.18), residues: 790 loop : -0.84 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 35 HIS 0.007 0.001 HIS H 38 PHE 0.030 0.001 PHE H 71 TYR 0.024 0.001 TYR B 265 ARG 0.005 0.000 ARG H 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 24) link_NAG-ASN : angle 2.35173 ( 72) link_BETA1-4 : bond 0.00287 ( 14) link_BETA1-4 : angle 0.98739 ( 42) hydrogen bonds : bond 0.04556 ( 1067) hydrogen bonds : angle 5.07050 ( 2937) SS BOND : bond 0.00376 ( 42) SS BOND : angle 1.24300 ( 84) covalent geometry : bond 0.00431 (27178) covalent geometry : angle 0.55318 (36974) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 3.270 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6741 (m-10) REVERT: B 342 PHE cc_start: 0.8631 (m-10) cc_final: 0.7906 (m-10) REVERT: B 436 TRP cc_start: 0.7690 (p90) cc_final: 0.6957 (p90) REVERT: C 979 ASP cc_start: 0.8542 (m-30) cc_final: 0.8310 (t70) REVERT: C 988 GLU cc_start: 0.8259 (pm20) cc_final: 0.7970 (pm20) REVERT: H 24 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8399 (mmm-85) REVERT: H 35 TRP cc_start: 0.5332 (m-10) cc_final: 0.4894 (m-10) REVERT: H 88 CYS cc_start: 0.5777 (m) cc_final: 0.5365 (m) REVERT: H 95 PRO cc_start: 0.6582 (Cg_exo) cc_final: 0.6289 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7900 (m-80) cc_final: 0.7359 (m-80) REVERT: H 104 LYS cc_start: 0.8135 (tppt) cc_final: 0.7933 (tppt) REVERT: I 87 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8482 (mpp80) REVERT: I 104 ILE cc_start: 0.7912 (pt) cc_final: 0.7049 (mt) outliers start: 32 outliers final: 21 residues processed: 157 average time/residue: 0.3595 time to fit residues: 93.7535 Evaluate side-chains 147 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 271 optimal weight: 2.9990 chunk 282 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 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 = 0.3775 r_free = 0.3775 target = 0.093462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062155 restraints weight = 82236.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064456 restraints weight = 40971.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065951 restraints weight = 27082.725| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27259 Z= 0.168 Angle : 0.562 10.777 37172 Z= 0.284 Chirality : 0.044 0.389 4290 Planarity : 0.004 0.054 4730 Dihedral : 5.417 52.952 4366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.20 % Allowed : 12.15 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.15), residues: 3269 helix: 2.09 (0.21), residues: 669 sheet: 0.15 (0.18), residues: 794 loop : -0.83 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 35 HIS 0.006 0.001 HIS H 38 PHE 0.014 0.001 PHE C 562 TYR 0.022 0.001 TYR B 265 ARG 0.004 0.000 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 24) link_NAG-ASN : angle 2.30602 ( 72) link_BETA1-4 : bond 0.00309 ( 14) link_BETA1-4 : angle 0.97245 ( 42) hydrogen bonds : bond 0.04463 ( 1067) hydrogen bonds : angle 5.01906 ( 2937) SS BOND : bond 0.00297 ( 42) SS BOND : angle 1.64358 ( 84) covalent geometry : bond 0.00393 (27178) covalent geometry : angle 0.54775 (36974) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 2.725 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6799 (m-10) REVERT: B 342 PHE cc_start: 0.8640 (m-10) cc_final: 0.7905 (m-10) REVERT: B 436 TRP cc_start: 0.7668 (p90) cc_final: 0.6905 (p90) REVERT: C 979 ASP cc_start: 0.8561 (m-30) cc_final: 0.8341 (t70) REVERT: C 988 GLU cc_start: 0.8308 (pm20) cc_final: 0.8000 (pm20) REVERT: H 24 ARG cc_start: 0.8645 (mmm160) cc_final: 0.8390 (mmm-85) REVERT: H 46 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7633 (tp) REVERT: H 55 GLN cc_start: 0.8195 (tp40) cc_final: 0.7955 (tp-100) REVERT: H 95 PRO cc_start: 0.6536 (Cg_exo) cc_final: 0.6230 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7838 (m-80) cc_final: 0.7295 (m-80) REVERT: H 106 GLU cc_start: 0.8025 (pm20) cc_final: 0.7810 (pm20) REVERT: I 82 GLN cc_start: 0.8495 (tt0) cc_final: 0.8260 (tp40) REVERT: I 87 ARG cc_start: 0.8824 (mpp80) cc_final: 0.8511 (mpp80) REVERT: I 104 ILE cc_start: 0.7892 (pt) cc_final: 0.7027 (mt) outliers start: 35 outliers final: 21 residues processed: 162 average time/residue: 0.3406 time to fit residues: 92.2799 Evaluate side-chains 151 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 301 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 935 GLN B 121 ASN B 907 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** H 89 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 = 0.3736 r_free = 0.3736 target = 0.091798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060246 restraints weight = 82337.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062393 restraints weight = 42640.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063812 restraints weight = 28862.726| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27259 Z= 0.239 Angle : 0.618 11.187 37172 Z= 0.311 Chirality : 0.046 0.376 4290 Planarity : 0.004 0.052 4730 Dihedral : 5.433 52.768 4366 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.24 % Allowed : 13.01 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.15), residues: 3269 helix: 1.95 (0.21), residues: 669 sheet: -0.01 (0.18), residues: 764 loop : -0.88 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 35 HIS 0.007 0.001 HIS H 38 PHE 0.033 0.002 PHE I 29 TYR 0.027 0.001 TYR B 265 ARG 0.005 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 24) link_NAG-ASN : angle 2.43130 ( 72) link_BETA1-4 : bond 0.00275 ( 14) link_BETA1-4 : angle 1.03865 ( 42) hydrogen bonds : bond 0.04882 ( 1067) hydrogen bonds : angle 5.13257 ( 2937) SS BOND : bond 0.00320 ( 42) SS BOND : angle 1.80976 ( 84) covalent geometry : bond 0.00562 (27178) covalent geometry : angle 0.60277 (36974) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 2.805 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6952 (m-10) REVERT: B 342 PHE cc_start: 0.8690 (m-10) cc_final: 0.7997 (m-10) REVERT: B 436 TRP cc_start: 0.7698 (p90) cc_final: 0.6963 (p90) REVERT: B 1005 GLN cc_start: 0.8860 (tp40) cc_final: 0.8438 (tm-30) REVERT: C 478 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7305 (pptt) REVERT: C 988 GLU cc_start: 0.8368 (pm20) cc_final: 0.8039 (pm20) REVERT: H 24 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8537 (mmm160) REVERT: H 95 PRO cc_start: 0.6627 (Cg_exo) cc_final: 0.6326 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7867 (m-80) cc_final: 0.7184 (m-80) REVERT: I 99 ASP cc_start: 0.8999 (t0) cc_final: 0.8661 (t0) REVERT: I 104 ILE cc_start: 0.7978 (pt) cc_final: 0.7110 (mt) outliers start: 36 outliers final: 28 residues processed: 161 average time/residue: 0.3811 time to fit residues: 100.8375 Evaluate side-chains 156 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 46 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 907 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 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 = 0.3743 r_free = 0.3743 target = 0.092224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060886 restraints weight = 82444.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063009 restraints weight = 43227.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.064397 restraints weight = 29343.564| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27259 Z= 0.178 Angle : 0.583 10.909 37172 Z= 0.295 Chirality : 0.045 0.374 4290 Planarity : 0.004 0.054 4730 Dihedral : 5.269 52.856 4366 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.00 % Allowed : 13.56 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3269 helix: 2.05 (0.21), residues: 663 sheet: 0.10 (0.18), residues: 782 loop : -0.83 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 35 HIS 0.010 0.001 HIS H 38 PHE 0.029 0.001 PHE I 29 TYR 0.022 0.001 TYR B 265 ARG 0.007 0.000 ARG I 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 24) link_NAG-ASN : angle 2.32914 ( 72) link_BETA1-4 : bond 0.00311 ( 14) link_BETA1-4 : angle 0.98324 ( 42) hydrogen bonds : bond 0.04617 ( 1067) hydrogen bonds : angle 5.04325 ( 2937) SS BOND : bond 0.00329 ( 42) SS BOND : angle 1.71577 ( 84) covalent geometry : bond 0.00419 (27178) covalent geometry : angle 0.56847 (36974) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: B 342 PHE cc_start: 0.8641 (m-10) cc_final: 0.7919 (m-10) REVERT: B 436 TRP cc_start: 0.7673 (p90) cc_final: 0.6920 (p90) REVERT: B 1005 GLN cc_start: 0.8863 (tp40) cc_final: 0.8403 (tm-30) REVERT: C 478 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7309 (pptt) REVERT: C 988 GLU cc_start: 0.8331 (pm20) cc_final: 0.8028 (pm20) REVERT: H 24 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8519 (mmm160) REVERT: H 95 PRO cc_start: 0.6586 (Cg_exo) cc_final: 0.6278 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7831 (m-80) cc_final: 0.7174 (m-80) REVERT: I 3 GLN cc_start: 0.7440 (mp10) cc_final: 0.7239 (mp10) REVERT: I 74 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8245 (t0) REVERT: I 99 ASP cc_start: 0.8972 (t0) cc_final: 0.8638 (t0) REVERT: I 104 ILE cc_start: 0.7929 (pt) cc_final: 0.7033 (mt) outliers start: 29 outliers final: 22 residues processed: 158 average time/residue: 0.3756 time to fit residues: 97.5269 Evaluate side-chains 154 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 227 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 328 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.093115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.062511 restraints weight = 81576.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065388 restraints weight = 44128.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065615 restraints weight = 26265.414| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27259 Z= 0.129 Angle : 0.557 10.995 37172 Z= 0.282 Chirality : 0.044 0.373 4290 Planarity : 0.004 0.055 4730 Dihedral : 5.008 53.346 4366 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.93 % Allowed : 13.76 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3269 helix: 2.20 (0.21), residues: 658 sheet: 0.23 (0.18), residues: 774 loop : -0.79 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 35 HIS 0.010 0.001 HIS H 38 PHE 0.030 0.001 PHE I 29 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.000 ARG I 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 24) link_NAG-ASN : angle 2.21145 ( 72) link_BETA1-4 : bond 0.00349 ( 14) link_BETA1-4 : angle 0.93196 ( 42) hydrogen bonds : bond 0.04234 ( 1067) hydrogen bonds : angle 4.93389 ( 2937) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.51191 ( 84) covalent geometry : bond 0.00301 (27178) covalent geometry : angle 0.54463 (36974) Misc. bond : bond 0.00012 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 2.744 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6902 (m-10) REVERT: A 571 ASP cc_start: 0.8138 (t0) cc_final: 0.7670 (t0) REVERT: B 342 PHE cc_start: 0.8573 (m-10) cc_final: 0.7706 (m-10) REVERT: B 434 ILE cc_start: 0.6278 (tp) cc_final: 0.6035 (tp) REVERT: B 436 TRP cc_start: 0.7678 (p90) cc_final: 0.6781 (p90) REVERT: B 763 LEU cc_start: 0.8972 (mt) cc_final: 0.8768 (mp) REVERT: B 1005 GLN cc_start: 0.8768 (tp40) cc_final: 0.8534 (tm-30) REVERT: C 478 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7192 (pptt) REVERT: C 988 GLU cc_start: 0.8405 (pm20) cc_final: 0.8066 (pm20) REVERT: H 24 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8539 (mmm160) REVERT: H 95 PRO cc_start: 0.6398 (Cg_exo) cc_final: 0.6082 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7865 (m-80) cc_final: 0.7161 (m-80) REVERT: I 3 GLN cc_start: 0.7518 (mp10) cc_final: 0.7307 (mp10) REVERT: I 74 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8205 (t0) REVERT: I 99 ASP cc_start: 0.8907 (t0) cc_final: 0.8606 (t0) REVERT: I 104 ILE cc_start: 0.7732 (pt) cc_final: 0.6876 (mt) outliers start: 27 outliers final: 21 residues processed: 154 average time/residue: 0.3899 time to fit residues: 101.4472 Evaluate side-chains 148 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 134 optimal weight: 8.9990 chunk 329 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 43 optimal weight: 0.0670 chunk 106 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 323 optimal weight: 0.0980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** I 13 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 = 0.3802 r_free = 0.3802 target = 0.094536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.064576 restraints weight = 82699.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.068164 restraints weight = 41814.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068468 restraints weight = 22629.246| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27259 Z= 0.104 Angle : 0.544 11.137 37172 Z= 0.274 Chirality : 0.044 0.371 4290 Planarity : 0.004 0.056 4730 Dihedral : 4.736 53.594 4366 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.72 % Allowed : 13.83 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3269 helix: 2.32 (0.21), residues: 653 sheet: 0.32 (0.18), residues: 767 loop : -0.72 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 35 HIS 0.011 0.001 HIS H 38 PHE 0.029 0.001 PHE I 29 TYR 0.020 0.001 TYR A1067 ARG 0.011 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 24) link_NAG-ASN : angle 2.09256 ( 72) link_BETA1-4 : bond 0.00380 ( 14) link_BETA1-4 : angle 0.89836 ( 42) hydrogen bonds : bond 0.03863 ( 1067) hydrogen bonds : angle 4.84212 ( 2937) SS BOND : bond 0.00215 ( 42) SS BOND : angle 1.31458 ( 84) covalent geometry : bond 0.00235 (27178) covalent geometry : angle 0.53322 (36974) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10149.77 seconds wall clock time: 183 minutes 13.43 seconds (10993.43 seconds total)