Starting phenix.real_space_refine on Sat Feb 7 13:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc0_39918/02_2026/8zc0_39918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc0_39918/02_2026/8zc0_39918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zc0_39918/02_2026/8zc0_39918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc0_39918/02_2026/8zc0_39918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zc0_39918/02_2026/8zc0_39918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc0_39918/02_2026/8zc0_39918.map" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 144 5.16 5 C 21633 2.51 5 N 5566 2.21 5 O 6632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33975 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7793 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "B" Number of atoms: 7793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7793 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "C" Number of atoms: 7781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7781 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "G" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "N" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "Q" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.27, per 1000 atoms: 0.24 Number of scatterers: 33975 At special positions: 0 Unit cell: (176.88, 207.24, 240.24, 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 144 16.00 O 6632 8.00 N 5566 7.00 C 21633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 145 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 145 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 204 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 103 " - pdb=" SG CYS Q 108 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 154 " - pdb=" SG CYS Q 210 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 154 " - pdb=" SG CYS R 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 657 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 234 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A 331 " " NAG L 1 " - " ASN B 709 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 331 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN C 616 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 77 sheets defined 17.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 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 383 through 387 removed outlier: 3.513A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.763A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.802A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 760 through 781 removed outlier: 3.571A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) 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 890 removed outlier: 3.783A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.442A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.778A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.921A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.225A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 368 removed outlier: 4.048A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.944A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.503A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.762A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.506A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.536A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.767A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.573A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.675A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.187A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.866A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.631A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.290A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.038A pdb=" N GLU G 84 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 139 Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.787A pdb=" N ARG H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 138 removed outlier: 3.629A pdb=" N LEU M 136 " --> pdb=" O SER M 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 197 Processing helix chain 'N' and resid 132 through 138 Processing helix chain 'N' and resid 192 through 199 removed outlier: 3.699A pdb=" N TRP N 196 " --> pdb=" O THR N 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.556A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.829A pdb=" N ASP R 90 " --> pdb=" O ARG R 87 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR R 91 " --> pdb=" O SER R 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 87 through 91' Processing helix chain 'R' and resid 106 through 112 removed outlier: 3.682A pdb=" N GLN R 109 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG R 110 " --> pdb=" O SER R 107 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP R 111 " --> pdb=" O CYS R 108 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET R 112 " --> pdb=" O GLN R 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 106 through 112' Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.744A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.744A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.739A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.394A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.605A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.866A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.698A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.353A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.726A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.525A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.784A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.267A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.290A 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 Processing sheet with id=AC2, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.725A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.644A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.556A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.541A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (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 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.608A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.625A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.607A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.912A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 286 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.721A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.519A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.620A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.511A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.153A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 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 654 through 655 removed outlier: 6.445A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.951A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.538A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.908A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.754A pdb=" N THR G 108 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'G' and resid 45 through 49 removed outlier: 7.009A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 37 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 93 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY G 98 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.582A pdb=" N SER G 125 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 146 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE G 129 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 143 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.582A pdb=" N SER G 125 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 146 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE G 129 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 143 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA G 184 " --> pdb=" O SER G 176 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER G 176 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 157 through 160 Processing sheet with id=AF7, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.578A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS H 22 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 32 through 39 Processing sheet with id=AF9, first strand: chain 'H' and resid 32 through 39 removed outlier: 3.509A pdb=" N ALA H 121 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 49 through 51 removed outlier: 4.035A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'H' and resid 151 through 159 removed outlier: 3.564A pdb=" N CYS H 154 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU H 192 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP H 158 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.692A pdb=" N THR H 165 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN H 213 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS H 210 " --> pdb=" O LYS H 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AG5, first strand: chain 'M' and resid 18 through 22 removed outlier: 3.665A pdb=" N ALA M 72 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.953A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN M 39 " --> pdb=" O ASP M 86 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL M 100 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP M 93 " --> pdb=" O GLY M 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 125 through 129 removed outlier: 3.899A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP M 149 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR M 188 " --> pdb=" O GLU M 171 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU M 171 " --> pdb=" O TYR M 188 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 125 through 129 removed outlier: 3.899A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP M 149 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 157 through 160 Processing sheet with id=AH1, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.654A pdb=" N VAL N 18 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 76 " --> pdb=" O VAL N 18 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 45 through 49 removed outlier: 6.649A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA N 91 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL N 100 " --> pdb=" O ALA N 91 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 45 through 49 removed outlier: 6.649A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.755A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR N 127 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA N 141 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS N 145 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER N 187 " --> pdb=" O CYS N 145 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.755A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR N 127 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR N 183 " --> pdb=" O ASP N 149 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 45 through 46 removed outlier: 4.196A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 45 through 46 removed outlier: 4.196A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Q 37 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL Q 93 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL Q 123 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 68 through 71 Processing sheet with id=AH9, first strand: chain 'Q' and resid 150 through 155 removed outlier: 3.798A pdb=" N CYS Q 154 " --> pdb=" O SER Q 194 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER Q 194 " --> pdb=" O CYS Q 154 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 165 through 168 removed outlier: 4.271A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN Q 213 " --> pdb=" O THR Q 165 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Q 223 " --> pdb=" O CYS Q 210 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 6 through 7 removed outlier: 3.783A pdb=" N SER R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP R 73 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU R 82 " --> pdb=" O THR R 69 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR R 69 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 58 through 60 removed outlier: 3.504A pdb=" N TRP R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL R 37 " --> pdb=" O PHE R 95 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 134 through 136 removed outlier: 3.615A pdb=" N LEU R 155 " --> pdb=" O PHE R 136 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR R 190 " --> pdb=" O ASP R 158 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER R 191 " --> pdb=" O VAL R 183 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 165 through 168 removed outlier: 4.004A pdb=" N VAL R 212 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL R 221 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS R 214 " --> pdb=" O THR R 219 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR R 219 " --> pdb=" O HIS R 214 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2823 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10711 1.35 - 1.47: 9039 1.47 - 1.60: 14849 1.60 - 1.72: 0 1.72 - 1.85: 180 Bond restraints: 34779 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 ... (remaining 34774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 45898 1.86 - 3.72: 1285 3.72 - 5.58: 123 5.58 - 7.44: 43 7.44 - 9.30: 3 Bond angle restraints: 47352 Sorted by residual: angle pdb=" N ASP R 56 " pdb=" CA ASP R 56 " pdb=" C ASP R 56 " ideal model delta sigma weight residual 112.93 107.59 5.34 1.12e+00 7.97e-01 2.27e+01 angle pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" C ASN B 360 " ideal model delta sigma weight residual 112.24 117.56 -5.32 1.28e+00 6.10e-01 1.73e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.09 -4.39 1.22e+00 6.72e-01 1.29e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.06 -4.36 1.22e+00 6.72e-01 1.28e+01 angle pdb=" C LYS R 157 " pdb=" N ASP R 158 " pdb=" CA ASP R 158 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 47347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19474 18.00 - 36.00: 1612 36.00 - 54.00: 275 54.00 - 72.00: 62 72.00 - 90.00: 39 Dihedral angle restraints: 21462 sinusoidal: 9030 harmonic: 12432 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 5.35 87.65 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 10.51 82.49 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -6.84 -79.16 1 1.00e+01 1.00e-02 7.79e+01 ... (remaining 21459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 5474 0.135 - 0.270: 45 0.270 - 0.405: 2 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 5522 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.81e+02 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 5519 not shown) Planarity restraints: 6049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG L 2 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.243 2.00e-02 2.50e+03 2.07e-01 5.35e+02 pdb=" C7 NAG L 1 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.342 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 295 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.036 5.00e-02 4.00e+02 ... (remaining 6046 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5337 2.77 - 3.30: 29610 3.30 - 3.83: 54305 3.83 - 4.37: 57305 4.37 - 4.90: 104019 Nonbonded interactions: 250576 Sorted by model distance: nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.269 3.040 nonbonded pdb=" OE2 GLU H 46 " pdb=" OG SER H 63 " model vdw 2.276 3.040 nonbonded pdb=" O ASN Q 33 " pdb=" OG SER Q 99 " model vdw 2.285 3.040 ... (remaining 250571 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 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1306)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1306)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'R' } 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=0.00 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.720 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 0.048 34887 Z= 0.178 Angle : 0.700 13.226 47625 Z= 0.359 Chirality : 0.050 0.675 5522 Planarity : 0.007 0.295 6010 Dihedral : 13.628 89.999 13307 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.11 % Allowed : 0.51 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.12), residues: 4193 helix: 0.19 (0.20), residues: 653 sheet: -0.35 (0.17), residues: 929 loop : -1.60 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 26 TYR 0.036 0.001 TYR N 50 PHE 0.030 0.001 PHE C 374 TRP 0.018 0.001 TRP Q 50 HIS 0.018 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00354 (34779) covalent geometry : angle 0.68661 (47352) SS BOND : bond 0.00354 ( 51) SS BOND : angle 1.23298 ( 102) hydrogen bonds : bond 0.23974 ( 979) hydrogen bonds : angle 8.77615 ( 2823) link_BETA1-4 : bond 0.00593 ( 18) link_BETA1-4 : angle 1.82737 ( 54) link_NAG-ASN : bond 0.00451 ( 39) link_NAG-ASN : angle 2.42496 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8171 (mtm) cc_final: 0.7875 (mtm) REVERT: A 1118 ASP cc_start: 0.7161 (p0) cc_final: 0.6946 (p0) REVERT: C 731 MET cc_start: 0.8998 (pmm) cc_final: 0.8714 (pmm) REVERT: N 16 GLN cc_start: 0.6009 (pp30) cc_final: 0.5805 (pt0) REVERT: Q 113 TRP cc_start: 0.5475 (p-90) cc_final: 0.5256 (p-90) REVERT: R 73 ASP cc_start: 0.5194 (m-30) cc_final: 0.4351 (m-30) REVERT: R 112 MET cc_start: 0.8392 (mmp) cc_final: 0.7960 (mmm) outliers start: 4 outliers final: 2 residues processed: 225 average time/residue: 0.1953 time to fit residues: 76.7969 Evaluate side-chains 142 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 394 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN G 32 ASN N 28 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN R 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.155681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129161 restraints weight = 81196.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130030 restraints weight = 174770.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130619 restraints weight = 119842.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130629 restraints weight = 84213.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131267 restraints weight = 70427.410| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34887 Z= 0.187 Angle : 0.596 10.543 47625 Z= 0.304 Chirality : 0.045 0.398 5522 Planarity : 0.005 0.062 6010 Dihedral : 5.904 59.677 5761 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4193 helix: 1.10 (0.21), residues: 643 sheet: -0.19 (0.17), residues: 958 loop : -1.47 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 62 TYR 0.027 0.001 TYR B1067 PHE 0.031 0.002 PHE A 275 TRP 0.012 0.001 TRP Q 50 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00424 (34779) covalent geometry : angle 0.58326 (47352) SS BOND : bond 0.00607 ( 51) SS BOND : angle 1.17049 ( 102) hydrogen bonds : bond 0.04752 ( 979) hydrogen bonds : angle 6.19954 ( 2823) link_BETA1-4 : bond 0.00535 ( 18) link_BETA1-4 : angle 1.21406 ( 54) link_NAG-ASN : bond 0.00370 ( 39) link_NAG-ASN : angle 2.28088 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9305 (m) cc_final: 0.8893 (p) REVERT: A 731 MET cc_start: 0.8927 (ppp) cc_final: 0.7990 (ppp) REVERT: A 1118 ASP cc_start: 0.7215 (p0) cc_final: 0.7008 (p0) REVERT: B 1029 MET cc_start: 0.9055 (tpp) cc_final: 0.8836 (tpp) REVERT: C 731 MET cc_start: 0.9075 (pmm) cc_final: 0.8509 (pmm) REVERT: C 987 PRO cc_start: 0.7718 (Cg_exo) cc_final: 0.6948 (Cg_endo) REVERT: G 46 LYS cc_start: 0.3072 (mppt) cc_final: 0.2671 (tptm) REVERT: M 54 GLN cc_start: 0.6432 (mp10) cc_final: 0.6217 (mp10) REVERT: N 16 GLN cc_start: 0.6443 (pp30) cc_final: 0.6032 (pt0) REVERT: N 61 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7326 (pm20) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1987 time to fit residues: 71.2055 Evaluate side-chains 129 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 314 optimal weight: 40.0000 chunk 203 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A1010 GLN A1011 GLN B 955 ASN B 965 GLN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS H 43 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.136713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117105 restraints weight = 83185.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.116979 restraints weight = 221625.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115447 restraints weight = 127100.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114470 restraints weight = 133925.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114438 restraints weight = 135082.054| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.100 34887 Z= 0.411 Angle : 0.837 12.780 47625 Z= 0.424 Chirality : 0.052 0.385 5522 Planarity : 0.006 0.067 6010 Dihedral : 6.500 59.566 5761 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.16 % Allowed : 7.37 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4193 helix: 0.57 (0.20), residues: 643 sheet: -0.65 (0.16), residues: 978 loop : -1.70 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 102 TYR 0.028 0.003 TYR B1067 PHE 0.037 0.003 PHE C 92 TRP 0.040 0.002 TRP Q 50 HIS 0.020 0.002 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00962 (34779) covalent geometry : angle 0.82201 (47352) SS BOND : bond 0.00672 ( 51) SS BOND : angle 1.91066 ( 102) hydrogen bonds : bond 0.06175 ( 979) hydrogen bonds : angle 6.36411 ( 2823) link_BETA1-4 : bond 0.00420 ( 18) link_BETA1-4 : angle 1.66454 ( 54) link_NAG-ASN : bond 0.00651 ( 39) link_NAG-ASN : angle 2.69310 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.7317 (m-30) cc_final: 0.6969 (m-30) REVERT: B 731 MET cc_start: 0.8855 (ptm) cc_final: 0.8398 (ptm) REVERT: B 867 ASP cc_start: 0.7704 (m-30) cc_final: 0.7485 (t70) REVERT: C 223 LEU cc_start: 0.8212 (mm) cc_final: 0.7999 (mm) REVERT: C 987 PRO cc_start: 0.7972 (Cg_exo) cc_final: 0.7196 (Cg_endo) REVERT: H 114 PHE cc_start: 0.3913 (m-10) cc_final: 0.3322 (m-10) REVERT: Q 81 MET cc_start: 0.4395 (tpt) cc_final: 0.3495 (ppp) outliers start: 6 outliers final: 4 residues processed: 201 average time/residue: 0.2017 time to fit residues: 68.7006 Evaluate side-chains 126 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 416 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 chunk 345 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 286 optimal weight: 0.6980 chunk 372 optimal weight: 20.0000 chunk 340 optimal weight: 0.2980 chunk 63 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS A 955 ASN B 755 GLN B1011 GLN B1088 HIS C 955 ASN C 965 GLN C1054 GLN G 16 GLN G 52 ASN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.147273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128674 restraints weight = 83383.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129119 restraints weight = 214223.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128642 restraints weight = 129493.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.128499 restraints weight = 96572.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128584 restraints weight = 85927.720| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34887 Z= 0.115 Angle : 0.574 8.407 47625 Z= 0.288 Chirality : 0.045 0.381 5522 Planarity : 0.004 0.062 6010 Dihedral : 5.657 59.904 5761 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 4193 helix: 1.37 (0.22), residues: 641 sheet: -0.45 (0.17), residues: 965 loop : -1.51 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 110 TYR 0.021 0.001 TYR B1067 PHE 0.028 0.001 PHE C 429 TRP 0.016 0.001 TRP Q 50 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00256 (34779) covalent geometry : angle 0.55980 (47352) SS BOND : bond 0.00395 ( 51) SS BOND : angle 1.45788 ( 102) hydrogen bonds : bond 0.04206 ( 979) hydrogen bonds : angle 5.51776 ( 2823) link_BETA1-4 : bond 0.00423 ( 18) link_BETA1-4 : angle 1.38508 ( 54) link_NAG-ASN : bond 0.00369 ( 39) link_NAG-ASN : angle 2.08115 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9274 (m) cc_final: 0.8928 (p) REVERT: A 592 PHE cc_start: 0.8117 (p90) cc_final: 0.7743 (p90) REVERT: A 962 LEU cc_start: 0.9398 (tp) cc_final: 0.9190 (tt) REVERT: C 223 LEU cc_start: 0.8062 (mm) cc_final: 0.7806 (mm) REVERT: C 238 PHE cc_start: 0.8380 (p90) cc_final: 0.8112 (p90) REVERT: C 987 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7157 (Cg_endo) REVERT: H 114 PHE cc_start: 0.3640 (m-10) cc_final: 0.3180 (m-10) REVERT: N 16 GLN cc_start: 0.6586 (pp30) cc_final: 0.6159 (pt0) REVERT: N 61 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7224 (pm20) REVERT: R 6 GLN cc_start: 0.7646 (pt0) cc_final: 0.7435 (pp30) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1908 time to fit residues: 74.3472 Evaluate side-chains 140 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 338 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 329 optimal weight: 9.9990 chunk 268 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 460 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN G 16 GLN H 43 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN R 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.137019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112640 restraints weight = 82415.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112935 restraints weight = 223491.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113683 restraints weight = 144655.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113370 restraints weight = 104529.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114174 restraints weight = 83902.069| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 34887 Z= 0.329 Angle : 0.747 9.790 47625 Z= 0.377 Chirality : 0.049 0.367 5522 Planarity : 0.005 0.065 6010 Dihedral : 6.069 59.058 5761 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4193 helix: 0.83 (0.21), residues: 644 sheet: -0.69 (0.16), residues: 998 loop : -1.66 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 110 TYR 0.024 0.002 TYR B1067 PHE 0.033 0.003 PHE B 238 TRP 0.023 0.002 TRP Q 50 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00770 (34779) covalent geometry : angle 0.73258 (47352) SS BOND : bond 0.00640 ( 51) SS BOND : angle 1.75717 ( 102) hydrogen bonds : bond 0.05391 ( 979) hydrogen bonds : angle 5.91475 ( 2823) link_BETA1-4 : bond 0.00342 ( 18) link_BETA1-4 : angle 1.67118 ( 54) link_NAG-ASN : bond 0.00601 ( 39) link_NAG-ASN : angle 2.38560 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.7347 (m-30) cc_final: 0.7113 (m-30) REVERT: A 869 MET cc_start: 0.8526 (mtm) cc_final: 0.8324 (mtm) REVERT: B 775 ASP cc_start: 0.8145 (t0) cc_final: 0.7821 (t70) REVERT: C 987 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7208 (Cg_endo) REVERT: N 128 LEU cc_start: 0.3620 (mp) cc_final: 0.2577 (tt) REVERT: Q 113 TRP cc_start: 0.7017 (p-90) cc_final: 0.6815 (p-90) REVERT: R 3 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6944 (tm-30) REVERT: R 6 GLN cc_start: 0.8090 (pt0) cc_final: 0.7481 (pp30) REVERT: R 76 ILE cc_start: 0.8194 (mt) cc_final: 0.7854 (mt) REVERT: R 119 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7608 (pp30) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1823 time to fit residues: 59.6453 Evaluate side-chains 129 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 281 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 347 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 chunk 389 optimal weight: 0.0970 chunk 220 optimal weight: 0.0870 chunk 318 optimal weight: 0.9990 chunk 375 optimal weight: 10.0000 chunk 391 optimal weight: 4.9990 overall best weight: 1.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS C 394 ASN C 422 ASN C 460 ASN C 505 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN G 16 GLN H 43 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.153103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126588 restraints weight = 80839.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126769 restraints weight = 181325.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127791 restraints weight = 135739.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127926 restraints weight = 86893.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129753 restraints weight = 73039.321| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34887 Z= 0.150 Angle : 0.589 8.888 47625 Z= 0.297 Chirality : 0.045 0.367 5522 Planarity : 0.004 0.061 6010 Dihedral : 5.588 59.971 5761 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4193 helix: 1.23 (0.21), residues: 643 sheet: -0.52 (0.17), residues: 969 loop : -1.51 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 110 TYR 0.020 0.001 TYR B1067 PHE 0.024 0.001 PHE C 275 TRP 0.015 0.001 TRP Q 50 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00348 (34779) covalent geometry : angle 0.57536 (47352) SS BOND : bond 0.00504 ( 51) SS BOND : angle 1.48131 ( 102) hydrogen bonds : bond 0.04328 ( 979) hydrogen bonds : angle 5.40504 ( 2823) link_BETA1-4 : bond 0.00378 ( 18) link_BETA1-4 : angle 1.42780 ( 54) link_NAG-ASN : bond 0.00321 ( 39) link_NAG-ASN : angle 2.14449 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8737 (mtp) cc_final: 0.8279 (mtt) REVERT: A 745 ASP cc_start: 0.7094 (m-30) cc_final: 0.6868 (m-30) REVERT: A 962 LEU cc_start: 0.9456 (tp) cc_final: 0.9223 (tt) REVERT: B 869 MET cc_start: 0.8639 (mmm) cc_final: 0.8347 (mmm) REVERT: C 223 LEU cc_start: 0.8010 (mm) cc_final: 0.7802 (mm) REVERT: C 394 ASN cc_start: 0.8694 (m110) cc_final: 0.8485 (m-40) REVERT: C 987 PRO cc_start: 0.8055 (Cg_exo) cc_final: 0.7617 (Cg_endo) REVERT: H 114 PHE cc_start: 0.3267 (m-10) cc_final: 0.2901 (m-10) REVERT: H 212 VAL cc_start: 0.2256 (t) cc_final: 0.2046 (t) REVERT: N 128 LEU cc_start: 0.3452 (mp) cc_final: 0.2464 (tt) REVERT: Q 113 TRP cc_start: 0.7048 (p-90) cc_final: 0.6706 (p-90) REVERT: R 3 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7124 (tm-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1972 time to fit residues: 71.1801 Evaluate side-chains 138 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 388 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 240 optimal weight: 0.5980 chunk 336 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 372 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 177 optimal weight: 0.3980 chunk 252 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B1036 GLN C 901 GLN C 955 ASN G 16 GLN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN M 6 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.140386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113064 restraints weight = 81065.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.113604 restraints weight = 175627.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114479 restraints weight = 128510.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114735 restraints weight = 83693.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115238 restraints weight = 73030.897| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34887 Z= 0.144 Angle : 0.575 8.816 47625 Z= 0.289 Chirality : 0.045 0.361 5522 Planarity : 0.004 0.062 6010 Dihedral : 5.353 59.776 5761 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4193 helix: 1.29 (0.21), residues: 649 sheet: -0.45 (0.17), residues: 960 loop : -1.48 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 26 TYR 0.019 0.001 TYR B1067 PHE 0.017 0.001 PHE Q 29 TRP 0.015 0.001 TRP Q 50 HIS 0.003 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00335 (34779) covalent geometry : angle 0.56253 (47352) SS BOND : bond 0.00384 ( 51) SS BOND : angle 1.36286 ( 102) hydrogen bonds : bond 0.04138 ( 979) hydrogen bonds : angle 5.27159 ( 2823) link_BETA1-4 : bond 0.00355 ( 18) link_BETA1-4 : angle 1.42511 ( 54) link_NAG-ASN : bond 0.00318 ( 39) link_NAG-ASN : angle 2.02916 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9333 (m) cc_final: 0.9057 (p) REVERT: A 731 MET cc_start: 0.9101 (ppp) cc_final: 0.8024 (ppp) REVERT: A 745 ASP cc_start: 0.7354 (m-30) cc_final: 0.7107 (m-30) REVERT: A 962 LEU cc_start: 0.9473 (tp) cc_final: 0.9244 (tt) REVERT: B 786 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7644 (mmtm) REVERT: C 223 LEU cc_start: 0.8076 (mm) cc_final: 0.7859 (mm) REVERT: C 394 ASN cc_start: 0.8608 (m110) cc_final: 0.8253 (m-40) REVERT: C 987 PRO cc_start: 0.7979 (Cg_exo) cc_final: 0.7160 (Cg_endo) REVERT: H 114 PHE cc_start: 0.3699 (m-10) cc_final: 0.3151 (m-10) REVERT: M 54 GLN cc_start: 0.6508 (mp10) cc_final: 0.6283 (mp10) REVERT: N 61 GLU cc_start: 0.8071 (tp30) cc_final: 0.7698 (pm20) REVERT: N 128 LEU cc_start: 0.3484 (mp) cc_final: 0.2491 (tt) REVERT: Q 113 TRP cc_start: 0.6942 (p-90) cc_final: 0.6659 (p-90) REVERT: R 90 ASP cc_start: 0.7331 (m-30) cc_final: 0.6997 (m-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1877 time to fit residues: 68.2504 Evaluate side-chains 148 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 119 optimal weight: 0.7980 chunk 241 optimal weight: 0.2980 chunk 32 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 286 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN G 16 GLN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.142259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115010 restraints weight = 80469.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114790 restraints weight = 169958.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.116030 restraints weight = 135640.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116248 restraints weight = 85679.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.116872 restraints weight = 75805.163| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34887 Z= 0.103 Angle : 0.542 9.094 47625 Z= 0.271 Chirality : 0.044 0.354 5522 Planarity : 0.004 0.063 6010 Dihedral : 4.986 59.433 5761 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4193 helix: 1.50 (0.22), residues: 655 sheet: -0.37 (0.17), residues: 964 loop : -1.42 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 26 TYR 0.018 0.001 TYR B1067 PHE 0.029 0.001 PHE C 486 TRP 0.028 0.001 TRP G 36 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00234 (34779) covalent geometry : angle 0.53016 (47352) SS BOND : bond 0.00373 ( 51) SS BOND : angle 1.19952 ( 102) hydrogen bonds : bond 0.03733 ( 979) hydrogen bonds : angle 5.00409 ( 2823) link_BETA1-4 : bond 0.00424 ( 18) link_BETA1-4 : angle 1.33109 ( 54) link_NAG-ASN : bond 0.00304 ( 39) link_NAG-ASN : angle 1.90087 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 THR cc_start: 0.9244 (m) cc_final: 0.8991 (p) REVERT: A 731 MET cc_start: 0.8975 (ppp) cc_final: 0.7974 (ppp) REVERT: A 745 ASP cc_start: 0.7329 (m-30) cc_final: 0.7114 (m-30) REVERT: A 869 MET cc_start: 0.8336 (mtm) cc_final: 0.8093 (mtm) REVERT: A 962 LEU cc_start: 0.9428 (tp) cc_final: 0.9219 (tt) REVERT: A 1051 SER cc_start: 0.9225 (m) cc_final: 0.8709 (p) REVERT: C 987 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7462 (Cg_endo) REVERT: M 54 GLN cc_start: 0.6484 (mp10) cc_final: 0.6116 (mp10) REVERT: N 61 GLU cc_start: 0.8004 (tp30) cc_final: 0.7659 (pm20) REVERT: N 128 LEU cc_start: 0.3347 (mp) cc_final: 0.2379 (tt) REVERT: R 90 ASP cc_start: 0.7011 (m-30) cc_final: 0.6655 (m-30) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1963 time to fit residues: 74.1272 Evaluate side-chains 146 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 84 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 166 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 408 optimal weight: 3.9990 chunk 341 optimal weight: 0.7980 chunk 329 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.155665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128494 restraints weight = 80726.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122132 restraints weight = 103267.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123390 restraints weight = 125309.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124425 restraints weight = 84706.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124988 restraints weight = 72077.994| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34887 Z= 0.109 Angle : 0.545 8.977 47625 Z= 0.273 Chirality : 0.044 0.355 5522 Planarity : 0.004 0.065 6010 Dihedral : 4.816 58.273 5761 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.13), residues: 4193 helix: 1.50 (0.21), residues: 661 sheet: -0.35 (0.17), residues: 967 loop : -1.36 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 110 TYR 0.016 0.001 TYR B1067 PHE 0.022 0.001 PHE C 429 TRP 0.054 0.001 TRP Q 113 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00250 (34779) covalent geometry : angle 0.53207 (47352) SS BOND : bond 0.00385 ( 51) SS BOND : angle 1.43510 ( 102) hydrogen bonds : bond 0.03677 ( 979) hydrogen bonds : angle 4.93823 ( 2823) link_BETA1-4 : bond 0.00402 ( 18) link_BETA1-4 : angle 1.31530 ( 54) link_NAG-ASN : bond 0.00298 ( 39) link_NAG-ASN : angle 1.89903 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8380 (mm) cc_final: 0.8001 (tp) REVERT: A 549 THR cc_start: 0.9136 (m) cc_final: 0.8935 (p) REVERT: A 731 MET cc_start: 0.8907 (ppp) cc_final: 0.7856 (ppp) REVERT: A 962 LEU cc_start: 0.9412 (tp) cc_final: 0.9136 (tt) REVERT: A 1051 SER cc_start: 0.9273 (m) cc_final: 0.8759 (p) REVERT: B 699 LEU cc_start: 0.8278 (mm) cc_final: 0.7945 (mm) REVERT: C 987 PRO cc_start: 0.7809 (Cg_exo) cc_final: 0.7208 (Cg_endo) REVERT: M 54 GLN cc_start: 0.6840 (mp10) cc_final: 0.6307 (mp10) REVERT: N 61 GLU cc_start: 0.8019 (tp30) cc_final: 0.7604 (pm20) REVERT: N 128 LEU cc_start: 0.3344 (mp) cc_final: 0.2219 (tt) REVERT: N 150 PHE cc_start: 0.4086 (p90) cc_final: 0.3653 (p90) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1969 time to fit residues: 71.0086 Evaluate side-chains 140 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 285 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 343 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 346 optimal weight: 1.9990 chunk 354 optimal weight: 1.9990 chunk 418 optimal weight: 0.0670 chunk 219 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 253 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1011 GLN C 955 ASN G 16 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.155034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127429 restraints weight = 81070.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.126899 restraints weight = 170900.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128500 restraints weight = 132554.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128435 restraints weight = 84133.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129247 restraints weight = 76315.021| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34887 Z= 0.130 Angle : 0.560 10.004 47625 Z= 0.279 Chirality : 0.044 0.354 5522 Planarity : 0.004 0.065 6010 Dihedral : 4.764 56.351 5761 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4193 helix: 1.43 (0.21), residues: 662 sheet: -0.37 (0.17), residues: 980 loop : -1.36 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.020 0.001 TYR B 873 PHE 0.022 0.001 PHE C 486 TRP 0.029 0.001 TRP H 117 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00303 (34779) covalent geometry : angle 0.54642 (47352) SS BOND : bond 0.00358 ( 51) SS BOND : angle 1.38500 ( 102) hydrogen bonds : bond 0.03790 ( 979) hydrogen bonds : angle 4.96660 ( 2823) link_BETA1-4 : bond 0.00337 ( 18) link_BETA1-4 : angle 1.33875 ( 54) link_NAG-ASN : bond 0.00318 ( 39) link_NAG-ASN : angle 2.02816 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8369 (mm) cc_final: 0.7981 (tp) REVERT: A 549 THR cc_start: 0.9219 (m) cc_final: 0.8946 (p) REVERT: A 731 MET cc_start: 0.8899 (ppp) cc_final: 0.7798 (ppp) REVERT: A 745 ASP cc_start: 0.7334 (m-30) cc_final: 0.7121 (m-30) REVERT: A 962 LEU cc_start: 0.9438 (tp) cc_final: 0.9212 (tt) REVERT: A 1051 SER cc_start: 0.9315 (m) cc_final: 0.8793 (p) REVERT: B 651 ILE cc_start: 0.9246 (mm) cc_final: 0.9026 (mt) REVERT: B 699 LEU cc_start: 0.8371 (mm) cc_final: 0.8057 (mm) REVERT: B 786 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7763 (mmtm) REVERT: C 987 PRO cc_start: 0.8138 (Cg_exo) cc_final: 0.7499 (Cg_endo) REVERT: M 54 GLN cc_start: 0.6585 (mp10) cc_final: 0.6140 (mp10) REVERT: N 61 GLU cc_start: 0.7937 (tp30) cc_final: 0.7611 (pm20) REVERT: N 128 LEU cc_start: 0.3313 (mp) cc_final: 0.2338 (tt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1898 time to fit residues: 68.2999 Evaluate side-chains 139 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 335 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 363 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1011 GLN C 955 ASN G 16 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 HIS ** R 3 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 = 0.4073 r_free = 0.4073 target = 0.154245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126741 restraints weight = 80681.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125398 restraints weight = 170403.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127156 restraints weight = 141438.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127012 restraints weight = 90244.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127945 restraints weight = 79594.211| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34887 Z= 0.143 Angle : 0.570 8.964 47625 Z= 0.285 Chirality : 0.045 0.353 5522 Planarity : 0.004 0.065 6010 Dihedral : 4.770 52.134 5761 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4193 helix: 1.43 (0.21), residues: 650 sheet: -0.36 (0.17), residues: 981 loop : -1.37 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 62 TYR 0.023 0.001 TYR B 873 PHE 0.026 0.001 PHE C 429 TRP 0.048 0.001 TRP Q 113 HIS 0.003 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00334 (34779) covalent geometry : angle 0.55737 (47352) SS BOND : bond 0.00348 ( 51) SS BOND : angle 1.31741 ( 102) hydrogen bonds : bond 0.03904 ( 979) hydrogen bonds : angle 4.99542 ( 2823) link_BETA1-4 : bond 0.00341 ( 18) link_BETA1-4 : angle 1.33580 ( 54) link_NAG-ASN : bond 0.00300 ( 39) link_NAG-ASN : angle 2.01545 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4386.00 seconds wall clock time: 77 minutes 31.91 seconds (4651.91 seconds total)