Starting phenix.real_space_refine on Thu Mar 5 23:43:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bnm_12229/03_2026/7bnm_12229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bnm_12229/03_2026/7bnm_12229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bnm_12229/03_2026/7bnm_12229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bnm_12229/03_2026/7bnm_12229.map" model { file = "/net/cci-nas-00/data/ceres_data/7bnm_12229/03_2026/7bnm_12229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bnm_12229/03_2026/7bnm_12229.cif" } resolution = 3.6 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= 0.004 sd= 0.050 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 114 5.16 5 C 16521 2.51 5 N 4251 2.21 5 O 5085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25971 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8363 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 54, 'TRANS': 1014} Chain breaks: 5 Chain: "B" Number of atoms: 8363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8363 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 54, 'TRANS': 1014} Chain breaks: 5 Chain: "C" Number of atoms: 8363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8363 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 54, 'TRANS': 1014} Chain breaks: 5 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "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: "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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "3" 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: "7" 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: "9" 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: "BA" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.93, per 1000 atoms: 0.23 Number of scatterers: 25971 At special positions: 0 Unit cell: (162.35, 153.85, 178.5, 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 114 16.00 O 5085 8.00 N 4251 7.00 C 16521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 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 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 3 1 " - " NAG 3 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 9 1 " - " NAG 9 2 " " NAG D 1 " - " NAG D 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG Y 1 " - " NAG Y 2 " " NAG i 1 " - " NAG i 2 " " NAG m 1 " - " NAG m 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG t 1 " - " NAG t 2 " " NAGBA 1 " - " NAGBA 2 " NAG-ASN " NAG 3 1 " - " ASN C 717 " " NAG 7 1 " - " ASN C1098 " " NAG 9 1 " - " ASN C1134 " " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 331 " " NAG A1206 " - " ASN A 343 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 709 " " NAG A1210 " - " ASN A 801 " " NAG A1211 " - " ASN A1074 " " NAG B1201 " - " ASN B 282 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 234 " " NAG B1205 " - " ASN B 331 " " NAG B1206 " - " ASN B 343 " " NAG B1207 " - " ASN B 616 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 709 " " NAG B1210 " - " ASN B 801 " " NAG B1211 " - " ASN B1074 " " NAG C1201 " - " ASN C 282 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 234 " " NAG C1205 " - " ASN C 331 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 616 " " NAG C1208 " - " ASN C 657 " " NAG C1209 " - " ASN C 709 " " NAG C1210 " - " ASN C 801 " " NAG C1211 " - " ASN C1074 " " NAG D 1 " - " ASN A 17 " " NAG N 1 " - " ASN A 717 " " NAG R 1 " - " ASN A1098 " " NAG T 1 " - " ASN A1134 " " NAG V 1 " - " ASN A 61 " " NAG Y 1 " - " ASN B 17 " " NAG i 1 " - " ASN B 717 " " NAG m 1 " - " ASN B1098 " " NAG o 1 " - " ASN B1134 " " NAG q 1 " - " ASN B 61 " " NAG t 1 " - " ASN C 17 " " NAGBA 1 " - " ASN C 61 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 46 sheets defined 23.3% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.553A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.125A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.693A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.596A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.712A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.503A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.064A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.669A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.180A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.728A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.608A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.529A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.022A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.126A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.692A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.596A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.712A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.503A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.063A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.670A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.179A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.728A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.608A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.529A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.021A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.126A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.693A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.596A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.712A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.502A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.064A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.669A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.181A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.728A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.608A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.530A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.392A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.275A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.664A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.885A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.558A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.538A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.790A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.136A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 removed outlier: 4.051A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.570A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.265A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.977A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.392A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.275A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.664A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.885A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.558A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.538A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) 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 551 through 554 removed outlier: 5.789A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.136A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.264A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.977A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.392A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.275A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.664A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.885A pdb=" N THR C 645 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.558A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.538A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.790A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.136A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.570A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.264A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.977A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2679 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: 5.47 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8173 1.34 - 1.46: 6000 1.46 - 1.58: 12239 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 26556 Sorted by residual: bond pdb=" N ILE A 358 " pdb=" CA ILE A 358 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ILE B 358 " pdb=" CA ILE B 358 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE C 358 " pdb=" CA ILE C 358 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.01e-02 9.80e+03 9.84e+00 bond pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.01e-02 9.80e+03 9.69e+00 ... (remaining 26551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 34738 2.01 - 4.01: 1271 4.01 - 6.02: 112 6.02 - 8.03: 10 8.03 - 10.03: 7 Bond angle restraints: 36138 Sorted by residual: angle pdb=" C TYR A 369 " pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " ideal model delta sigma weight residual 109.03 119.06 -10.03 1.62e+00 3.81e-01 3.84e+01 angle pdb=" CA ALA A 363 " pdb=" C ALA A 363 " pdb=" N ASP A 364 " ideal model delta sigma weight residual 115.96 109.52 6.44 1.31e+00 5.83e-01 2.42e+01 angle pdb=" CA TYR A 369 " pdb=" C TYR A 369 " pdb=" O TYR A 369 " ideal model delta sigma weight residual 119.24 113.84 5.40 1.13e+00 7.83e-01 2.28e+01 angle pdb=" O ALA A 363 " pdb=" C ALA A 363 " pdb=" N ASP A 364 " ideal model delta sigma weight residual 122.84 128.49 -5.65 1.20e+00 6.94e-01 2.22e+01 angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 113.20 108.43 4.77 1.21e+00 6.83e-01 1.55e+01 ... (remaining 36133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 15431 17.03 - 34.06: 926 34.06 - 51.08: 203 51.08 - 68.11: 51 68.11 - 85.14: 27 Dihedral angle restraints: 16638 sinusoidal: 7308 harmonic: 9330 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.14 49.14 1 1.00e+01 1.00e-02 3.32e+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 -135.14 49.14 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.12 49.12 1 1.00e+01 1.00e-02 3.32e+01 ... (remaining 16635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3674 0.079 - 0.159: 543 0.159 - 0.238: 36 0.238 - 0.318: 14 0.318 - 0.397: 2 Chirality restraints: 4269 Sorted by residual: chirality pdb=" CA LEU A 368 " pdb=" N LEU A 368 " pdb=" C LEU A 368 " pdb=" CB LEU A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR A 369 " pdb=" N TYR A 369 " pdb=" C TYR A 369 " pdb=" CB TYR A 369 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4266 not shown) Planarity restraints: 4650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1201 " 0.031 2.00e-02 2.50e+03 2.57e-02 8.23e+00 pdb=" C7 NAG C1201 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG C1201 " 0.024 2.00e-02 2.50e+03 pdb=" N2 NAG C1201 " -0.041 2.00e-02 2.50e+03 pdb=" O7 NAG C1201 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1201 " 0.031 2.00e-02 2.50e+03 2.56e-02 8.19e+00 pdb=" C7 NAG A1201 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG A1201 " 0.024 2.00e-02 2.50e+03 pdb=" N2 NAG A1201 " -0.041 2.00e-02 2.50e+03 pdb=" O7 NAG A1201 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1201 " -0.031 2.00e-02 2.50e+03 2.53e-02 8.02e+00 pdb=" C7 NAG B1201 " 0.008 2.00e-02 2.50e+03 pdb=" C8 NAG B1201 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B1201 " 0.040 2.00e-02 2.50e+03 pdb=" O7 NAG B1201 " 0.006 2.00e-02 2.50e+03 ... (remaining 4647 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3790 2.75 - 3.29: 24868 3.29 - 3.83: 40682 3.83 - 4.36: 46553 4.36 - 4.90: 80466 Nonbonded interactions: 196359 Sorted by model distance: nonbonded pdb=" OG SER B1097 " pdb=" O HIS B1101 " model vdw 2.213 3.040 nonbonded pdb=" OG SER A1097 " pdb=" O HIS A1101 " model vdw 2.213 3.040 nonbonded pdb=" OG SER C1097 " pdb=" O HIS C1101 " model vdw 2.213 3.040 nonbonded pdb=" O GLN B 804 " pdb=" OG SER B 816 " model vdw 2.221 3.040 nonbonded pdb=" O GLN C 804 " pdb=" OG SER C 816 " model vdw 2.221 3.040 ... (remaining 196354 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: 0.02 Found NCS groups: ncs_group { reference = chain '3' selection = chain '7' selection = chain '9' selection = chain 'BA' selection = chain 'D' selection = chain 'N' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'i' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 't' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.940 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.250 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.008 0.055 26661 Z= 0.376 Angle : 0.862 10.356 36411 Z= 0.468 Chirality : 0.056 0.397 4269 Planarity : 0.005 0.053 4602 Dihedral : 12.004 85.139 10512 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.61 % Allowed : 1.96 % Favored : 97.43 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3171 helix: 0.78 (0.21), residues: 603 sheet: -0.88 (0.19), residues: 639 loop : -2.36 (0.12), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 21 TYR 0.037 0.002 TYR A 369 PHE 0.035 0.003 PHE C 906 TRP 0.017 0.002 TRP C 353 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00815 (26556) covalent geometry : angle 0.83514 (36138) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.46356 ( 84) hydrogen bonds : bond 0.12916 ( 972) hydrogen bonds : angle 6.91857 ( 2679) link_BETA1-4 : bond 0.00301 ( 15) link_BETA1-4 : angle 1.42303 ( 45) link_NAG-ASN : bond 0.00663 ( 48) link_NAG-ASN : angle 3.31779 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5639 (pmm) cc_final: 0.4052 (pmm) REVERT: A 285 ILE cc_start: 0.8941 (mt) cc_final: 0.8741 (mt) REVERT: A 398 ASP cc_start: 0.8753 (m-30) cc_final: 0.8471 (m-30) REVERT: B 177 MET cc_start: 0.5344 (pmm) cc_final: 0.3386 (pmm) REVERT: B 957 GLN cc_start: 0.8571 (tp40) cc_final: 0.8148 (tp40) REVERT: B 985 ASP cc_start: 0.7496 (p0) cc_final: 0.7146 (p0) REVERT: C 177 MET cc_start: 0.5619 (pmm) cc_final: 0.3814 (pmm) REVERT: C 285 ILE cc_start: 0.9003 (mt) cc_final: 0.8536 (mt) REVERT: C 398 ASP cc_start: 0.8719 (m-30) cc_final: 0.8403 (m-30) outliers start: 17 outliers final: 6 residues processed: 279 average time/residue: 0.1892 time to fit residues: 81.2698 Evaluate side-chains 146 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 102 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 164 ASN A 474 GLN A 563 GLN A 641 ASN A 901 GLN A1071 GLN B 146 HIS B 164 ASN B 474 GLN B 563 GLN B 641 ASN B 901 GLN B1071 GLN C 146 HIS C 164 ASN C 474 GLN C 563 GLN C 641 ASN C 901 GLN C1071 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.110318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071265 restraints weight = 75789.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073907 restraints weight = 36960.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075595 restraints weight = 23910.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076605 restraints weight = 18398.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077240 restraints weight = 15758.822| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26661 Z= 0.143 Angle : 0.647 11.425 36411 Z= 0.332 Chirality : 0.045 0.200 4269 Planarity : 0.005 0.048 4602 Dihedral : 7.123 59.214 4777 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.96 % Allowed : 7.03 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3171 helix: 1.52 (0.21), residues: 639 sheet: -0.67 (0.20), residues: 660 loop : -1.97 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 214 TYR 0.024 0.002 TYR A1138 PHE 0.020 0.002 PHE C 400 TRP 0.009 0.001 TRP C1102 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00318 (26556) covalent geometry : angle 0.62899 (36138) SS BOND : bond 0.00193 ( 42) SS BOND : angle 1.34491 ( 84) hydrogen bonds : bond 0.06194 ( 972) hydrogen bonds : angle 5.51209 ( 2679) link_BETA1-4 : bond 0.00261 ( 15) link_BETA1-4 : angle 1.13735 ( 45) link_NAG-ASN : bond 0.00262 ( 48) link_NAG-ASN : angle 2.25935 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5267 (pmm) cc_final: 0.3661 (pmm) REVERT: A 226 LEU cc_start: 0.7762 (tp) cc_final: 0.7546 (tt) REVERT: A 780 GLU cc_start: 0.8688 (tp30) cc_final: 0.8438 (tp30) REVERT: A 957 GLN cc_start: 0.8590 (tp40) cc_final: 0.8223 (tp40) REVERT: B 177 MET cc_start: 0.4877 (pmm) cc_final: 0.3070 (pmm) REVERT: B 456 PHE cc_start: 0.9100 (m-80) cc_final: 0.8809 (t80) REVERT: B 780 GLU cc_start: 0.8511 (tp30) cc_final: 0.8275 (tp30) REVERT: B 957 GLN cc_start: 0.8477 (tp40) cc_final: 0.8092 (tp40) REVERT: C 177 MET cc_start: 0.5173 (pmm) cc_final: 0.3503 (pmm) REVERT: C 780 GLU cc_start: 0.8636 (tp30) cc_final: 0.8263 (tp30) REVERT: C 957 GLN cc_start: 0.8555 (tp40) cc_final: 0.8312 (tp40) outliers start: 27 outliers final: 11 residues processed: 190 average time/residue: 0.1635 time to fit residues: 51.0563 Evaluate side-chains 133 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 142 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 120 optimal weight: 0.0470 chunk 213 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 310 optimal weight: 0.6980 chunk 131 optimal weight: 0.0020 overall best weight: 0.7490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 644 GLN A 901 GLN A 965 GLN B 360 ASN B 978 ASN C 360 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 901 GLN C 926 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.110510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071480 restraints weight = 75543.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074113 restraints weight = 37015.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075804 restraints weight = 23998.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076803 restraints weight = 18426.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077398 restraints weight = 15781.079| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26661 Z= 0.130 Angle : 0.591 9.493 36411 Z= 0.304 Chirality : 0.044 0.189 4269 Planarity : 0.004 0.046 4602 Dihedral : 6.596 58.000 4773 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.64 % Allowed : 8.99 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.15), residues: 3171 helix: 1.65 (0.21), residues: 654 sheet: -0.49 (0.20), residues: 654 loop : -1.80 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.021 0.001 TYR A1067 PHE 0.029 0.001 PHE A 135 TRP 0.004 0.001 TRP C1102 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00291 (26556) covalent geometry : angle 0.57305 (36138) SS BOND : bond 0.00254 ( 42) SS BOND : angle 1.30125 ( 84) hydrogen bonds : bond 0.05670 ( 972) hydrogen bonds : angle 5.26083 ( 2679) link_BETA1-4 : bond 0.00244 ( 15) link_BETA1-4 : angle 1.14984 ( 45) link_NAG-ASN : bond 0.00241 ( 48) link_NAG-ASN : angle 2.14806 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.754 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 177 MET cc_start: 0.5299 (pmm) cc_final: 0.3615 (pmm) REVERT: A 226 LEU cc_start: 0.7643 (tp) cc_final: 0.7399 (tt) REVERT: A 421 TYR cc_start: 0.8255 (m-10) cc_final: 0.8048 (m-10) REVERT: A 957 GLN cc_start: 0.8597 (tp40) cc_final: 0.8232 (tp40) REVERT: B 177 MET cc_start: 0.4897 (pmm) cc_final: 0.4595 (pmm) REVERT: B 456 PHE cc_start: 0.9080 (m-80) cc_final: 0.8801 (t80) REVERT: B 780 GLU cc_start: 0.8608 (tp30) cc_final: 0.8022 (tp30) REVERT: B 957 GLN cc_start: 0.8492 (tp40) cc_final: 0.8115 (tp40) REVERT: B 985 ASP cc_start: 0.7958 (t0) cc_final: 0.7576 (t0) REVERT: C 177 MET cc_start: 0.5298 (pmm) cc_final: 0.3492 (pmm) REVERT: C 780 GLU cc_start: 0.8646 (tp30) cc_final: 0.8278 (tp30) REVERT: C 957 GLN cc_start: 0.8548 (tp40) cc_final: 0.8295 (tp40) outliers start: 18 outliers final: 11 residues processed: 153 average time/residue: 0.1613 time to fit residues: 40.8993 Evaluate side-chains 135 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 28 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 275 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN B 926 GLN B 965 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.110121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070834 restraints weight = 75238.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073458 restraints weight = 37280.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075128 restraints weight = 24290.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076152 restraints weight = 18674.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076751 restraints weight = 16011.496| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26661 Z= 0.143 Angle : 0.584 11.772 36411 Z= 0.294 Chirality : 0.043 0.229 4269 Planarity : 0.004 0.046 4602 Dihedral : 6.272 56.684 4773 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.00 % Allowed : 10.31 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.92 (0.15), residues: 3171 helix: 1.92 (0.22), residues: 630 sheet: -0.34 (0.20), residues: 651 loop : -1.70 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.021 0.001 TYR A1067 PHE 0.031 0.001 PHE C 135 TRP 0.005 0.001 TRP B 353 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00331 (26556) covalent geometry : angle 0.56742 (36138) SS BOND : bond 0.00222 ( 42) SS BOND : angle 1.01383 ( 84) hydrogen bonds : bond 0.05542 ( 972) hydrogen bonds : angle 5.11577 ( 2679) link_BETA1-4 : bond 0.00199 ( 15) link_BETA1-4 : angle 1.15075 ( 45) link_NAG-ASN : bond 0.00231 ( 48) link_NAG-ASN : angle 2.07200 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.741 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 177 MET cc_start: 0.5261 (pmm) cc_final: 0.3576 (pmm) REVERT: A 226 LEU cc_start: 0.7578 (tp) cc_final: 0.7315 (tt) REVERT: A 421 TYR cc_start: 0.8227 (m-10) cc_final: 0.7961 (m-10) REVERT: A 957 GLN cc_start: 0.8601 (tp40) cc_final: 0.8229 (tp40) REVERT: B 177 MET cc_start: 0.4926 (pmm) cc_final: 0.4567 (pmm) REVERT: B 456 PHE cc_start: 0.9050 (m-80) cc_final: 0.8777 (t80) REVERT: B 780 GLU cc_start: 0.8639 (tp30) cc_final: 0.8088 (tp30) REVERT: B 957 GLN cc_start: 0.8513 (tp40) cc_final: 0.8166 (tp40) REVERT: B 985 ASP cc_start: 0.7777 (t0) cc_final: 0.7358 (t0) REVERT: C 177 MET cc_start: 0.5371 (pmm) cc_final: 0.3506 (pmm) REVERT: C 780 GLU cc_start: 0.8673 (tp30) cc_final: 0.8334 (tp30) REVERT: C 957 GLN cc_start: 0.8556 (tp40) cc_final: 0.8314 (tp40) outliers start: 28 outliers final: 20 residues processed: 148 average time/residue: 0.1601 time to fit residues: 39.2455 Evaluate side-chains 143 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1027 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 131 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 chunk 262 optimal weight: 0.0060 chunk 191 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 287 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 564 GLN A 644 GLN B 360 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 564 GLN C 644 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.110852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071969 restraints weight = 75475.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074632 restraints weight = 36838.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076327 restraints weight = 23807.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077340 restraints weight = 18263.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077953 restraints weight = 15583.612| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26661 Z= 0.110 Angle : 0.545 8.855 36411 Z= 0.274 Chirality : 0.043 0.201 4269 Planarity : 0.004 0.047 4602 Dihedral : 5.952 56.179 4773 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.11 % Allowed : 10.85 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3171 helix: 2.12 (0.22), residues: 627 sheet: -0.33 (0.20), residues: 639 loop : -1.58 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.022 0.001 TYR C1138 PHE 0.015 0.001 PHE B 392 TRP 0.004 0.001 TRP B 353 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00249 (26556) covalent geometry : angle 0.53025 (36138) SS BOND : bond 0.00165 ( 42) SS BOND : angle 0.82562 ( 84) hydrogen bonds : bond 0.04977 ( 972) hydrogen bonds : angle 4.95833 ( 2679) link_BETA1-4 : bond 0.00283 ( 15) link_BETA1-4 : angle 1.13004 ( 45) link_NAG-ASN : bond 0.00197 ( 48) link_NAG-ASN : angle 1.92501 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.013 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 177 MET cc_start: 0.5196 (pmm) cc_final: 0.3503 (pmm) REVERT: A 226 LEU cc_start: 0.7459 (tp) cc_final: 0.7197 (tt) REVERT: A 421 TYR cc_start: 0.8252 (m-10) cc_final: 0.7974 (m-10) REVERT: A 957 GLN cc_start: 0.8576 (tp40) cc_final: 0.8214 (tp40) REVERT: B 177 MET cc_start: 0.4843 (pmm) cc_final: 0.4433 (pmm) REVERT: B 456 PHE cc_start: 0.9053 (m-80) cc_final: 0.8815 (t80) REVERT: B 780 GLU cc_start: 0.8613 (tp30) cc_final: 0.8123 (tp30) REVERT: B 957 GLN cc_start: 0.8484 (tp40) cc_final: 0.8163 (tp40) REVERT: B 985 ASP cc_start: 0.7476 (t0) cc_final: 0.7157 (t0) REVERT: C 177 MET cc_start: 0.5405 (pmm) cc_final: 0.3647 (pmm) REVERT: C 780 GLU cc_start: 0.8669 (tp30) cc_final: 0.8319 (tp30) REVERT: C 957 GLN cc_start: 0.8525 (tp40) cc_final: 0.8289 (tp40) outliers start: 31 outliers final: 22 residues processed: 163 average time/residue: 0.1536 time to fit residues: 41.6670 Evaluate side-chains 146 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 247 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1010 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070536 restraints weight = 75466.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073129 restraints weight = 37575.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074773 restraints weight = 24562.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075778 restraints weight = 18978.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076360 restraints weight = 16266.336| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26661 Z= 0.168 Angle : 0.593 8.904 36411 Z= 0.299 Chirality : 0.043 0.190 4269 Planarity : 0.004 0.049 4602 Dihedral : 5.988 55.581 4773 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.75 % Allowed : 11.10 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 3171 helix: 1.94 (0.22), residues: 630 sheet: -0.33 (0.20), residues: 669 loop : -1.60 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.021 0.001 TYR A1067 PHE 0.032 0.001 PHE B 135 TRP 0.006 0.001 TRP B 353 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00395 (26556) covalent geometry : angle 0.57506 (36138) SS BOND : bond 0.00199 ( 42) SS BOND : angle 1.67099 ( 84) hydrogen bonds : bond 0.05511 ( 972) hydrogen bonds : angle 5.06058 ( 2679) link_BETA1-4 : bond 0.00163 ( 15) link_BETA1-4 : angle 1.18185 ( 45) link_NAG-ASN : bond 0.00217 ( 48) link_NAG-ASN : angle 1.95588 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.874 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 177 MET cc_start: 0.5110 (pmm) cc_final: 0.3346 (pmm) REVERT: A 226 LEU cc_start: 0.7528 (tp) cc_final: 0.7257 (tt) REVERT: A 421 TYR cc_start: 0.8218 (m-10) cc_final: 0.7927 (m-10) REVERT: A 957 GLN cc_start: 0.8616 (tp40) cc_final: 0.8245 (tp40) REVERT: B 177 MET cc_start: 0.4870 (pmm) cc_final: 0.4424 (pmm) REVERT: B 456 PHE cc_start: 0.9044 (m-80) cc_final: 0.8797 (t80) REVERT: B 780 GLU cc_start: 0.8625 (tp30) cc_final: 0.8130 (tp30) REVERT: B 902 MET cc_start: 0.8801 (tpt) cc_final: 0.8597 (tpt) REVERT: B 957 GLN cc_start: 0.8534 (tp40) cc_final: 0.8222 (tp40) REVERT: B 985 ASP cc_start: 0.7560 (t0) cc_final: 0.7226 (t0) REVERT: C 177 MET cc_start: 0.5276 (pmm) cc_final: 0.3397 (pmm) REVERT: C 780 GLU cc_start: 0.8683 (tp30) cc_final: 0.8352 (tp30) REVERT: C 957 GLN cc_start: 0.8558 (tp40) cc_final: 0.8306 (tp40) outliers start: 49 outliers final: 32 residues processed: 166 average time/residue: 0.1573 time to fit residues: 43.7212 Evaluate side-chains 157 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 202 optimal weight: 0.0170 chunk 179 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 270 optimal weight: 0.1980 chunk 288 optimal weight: 0.0470 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.111039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072237 restraints weight = 76134.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074900 restraints weight = 36988.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076603 restraints weight = 23835.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077619 restraints weight = 18272.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078256 restraints weight = 15563.352| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26661 Z= 0.108 Angle : 0.571 11.742 36411 Z= 0.286 Chirality : 0.043 0.193 4269 Planarity : 0.004 0.050 4602 Dihedral : 5.841 55.663 4773 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.11 % Allowed : 11.92 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.15), residues: 3171 helix: 2.26 (0.22), residues: 612 sheet: -0.07 (0.20), residues: 669 loop : -1.51 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.020 0.001 TYR C1138 PHE 0.018 0.001 PHE B 135 TRP 0.004 0.001 TRP B 353 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00238 (26556) covalent geometry : angle 0.55282 (36138) SS BOND : bond 0.00583 ( 42) SS BOND : angle 1.85911 ( 84) hydrogen bonds : bond 0.04782 ( 972) hydrogen bonds : angle 4.92177 ( 2679) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.12436 ( 45) link_NAG-ASN : bond 0.00193 ( 48) link_NAG-ASN : angle 1.86276 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5216 (pmm) cc_final: 0.3531 (pmm) REVERT: A 389 ASP cc_start: 0.8799 (t0) cc_final: 0.8582 (p0) REVERT: A 421 TYR cc_start: 0.8213 (m-10) cc_final: 0.7909 (m-10) REVERT: A 957 GLN cc_start: 0.8554 (tp40) cc_final: 0.8164 (tp40) REVERT: B 177 MET cc_start: 0.4830 (pmm) cc_final: 0.4413 (pmm) REVERT: B 456 PHE cc_start: 0.9028 (m-80) cc_final: 0.8775 (t80) REVERT: B 697 MET cc_start: 0.8558 (ptm) cc_final: 0.8308 (ptm) REVERT: B 780 GLU cc_start: 0.8617 (tp30) cc_final: 0.8174 (tp30) REVERT: B 957 GLN cc_start: 0.8506 (tp40) cc_final: 0.8197 (tp40) REVERT: B 985 ASP cc_start: 0.7382 (t0) cc_final: 0.7119 (t0) REVERT: C 177 MET cc_start: 0.5310 (pmm) cc_final: 0.3555 (pmm) REVERT: C 780 GLU cc_start: 0.8659 (tp30) cc_final: 0.8317 (tp30) REVERT: C 957 GLN cc_start: 0.8484 (tp40) cc_final: 0.8256 (tp40) outliers start: 31 outliers final: 26 residues processed: 163 average time/residue: 0.1639 time to fit residues: 43.9677 Evaluate side-chains 152 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 93 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 196 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 143 optimal weight: 0.4980 chunk 233 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN C1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.110849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072004 restraints weight = 75510.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.074652 restraints weight = 36759.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076356 restraints weight = 23739.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.077380 restraints weight = 18104.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077916 restraints weight = 15435.945| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26661 Z= 0.118 Angle : 0.576 11.071 36411 Z= 0.289 Chirality : 0.043 0.214 4269 Planarity : 0.004 0.052 4602 Dihedral : 5.767 55.212 4773 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.43 % Allowed : 12.17 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3171 helix: 2.14 (0.22), residues: 630 sheet: -0.11 (0.20), residues: 639 loop : -1.51 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.023 0.001 TYR C 265 PHE 0.015 0.001 PHE B 135 TRP 0.005 0.001 TRP B 353 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00273 (26556) covalent geometry : angle 0.56012 (36138) SS BOND : bond 0.00599 ( 42) SS BOND : angle 1.56791 ( 84) hydrogen bonds : bond 0.04807 ( 972) hydrogen bonds : angle 4.89405 ( 2679) link_BETA1-4 : bond 0.00247 ( 15) link_BETA1-4 : angle 1.16012 ( 45) link_NAG-ASN : bond 0.00187 ( 48) link_NAG-ASN : angle 1.83679 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5196 (pmm) cc_final: 0.3449 (pmm) REVERT: A 226 LEU cc_start: 0.7506 (tp) cc_final: 0.7225 (tt) REVERT: A 421 TYR cc_start: 0.8222 (m-10) cc_final: 0.7919 (m-10) REVERT: A 957 GLN cc_start: 0.8575 (tp40) cc_final: 0.8203 (tp40) REVERT: B 177 MET cc_start: 0.4871 (pmm) cc_final: 0.4438 (pmm) REVERT: B 421 TYR cc_start: 0.8802 (m-10) cc_final: 0.8345 (m-10) REVERT: B 456 PHE cc_start: 0.9013 (m-80) cc_final: 0.8798 (t80) REVERT: B 780 GLU cc_start: 0.8629 (tp30) cc_final: 0.8202 (tp30) REVERT: B 957 GLN cc_start: 0.8512 (tp40) cc_final: 0.8196 (tp40) REVERT: B 985 ASP cc_start: 0.7362 (t0) cc_final: 0.7100 (t0) REVERT: C 177 MET cc_start: 0.5155 (pmm) cc_final: 0.3309 (pmm) REVERT: C 780 GLU cc_start: 0.8675 (tp30) cc_final: 0.8344 (tp30) REVERT: C 957 GLN cc_start: 0.8525 (tp40) cc_final: 0.8278 (tp40) outliers start: 40 outliers final: 37 residues processed: 163 average time/residue: 0.1533 time to fit residues: 41.3339 Evaluate side-chains 169 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 129 optimal weight: 7.9990 chunk 315 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.109987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070459 restraints weight = 75744.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073025 restraints weight = 37922.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074679 restraints weight = 24880.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075638 restraints weight = 19208.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076274 restraints weight = 16539.588| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.004 0.058 26661 Z= 0.156 Angle : 0.597 10.420 36411 Z= 0.299 Chirality : 0.043 0.193 4269 Planarity : 0.004 0.051 4602 Dihedral : 5.814 54.842 4773 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.39 % Allowed : 12.24 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3171 helix: 2.12 (0.22), residues: 615 sheet: -0.21 (0.20), residues: 648 loop : -1.57 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.021 0.001 TYR A1067 PHE 0.014 0.001 PHE B 392 TRP 0.008 0.001 TRP B 353 HIS 0.003 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00367 (26556) covalent geometry : angle 0.58166 (36138) SS BOND : bond 0.00436 ( 42) SS BOND : angle 1.45253 ( 84) hydrogen bonds : bond 0.05384 ( 972) hydrogen bonds : angle 4.97098 ( 2679) link_BETA1-4 : bond 0.00183 ( 15) link_BETA1-4 : angle 1.18329 ( 45) link_NAG-ASN : bond 0.00215 ( 48) link_NAG-ASN : angle 1.87787 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5212 (pmm) cc_final: 0.4753 (pmm) REVERT: A 226 LEU cc_start: 0.7432 (tp) cc_final: 0.7115 (tt) REVERT: A 421 TYR cc_start: 0.8216 (m-10) cc_final: 0.7922 (m-10) REVERT: A 957 GLN cc_start: 0.8615 (tp40) cc_final: 0.8249 (tp40) REVERT: B 177 MET cc_start: 0.5006 (pmm) cc_final: 0.4608 (pmm) REVERT: B 421 TYR cc_start: 0.8806 (m-10) cc_final: 0.8352 (m-10) REVERT: B 456 PHE cc_start: 0.9039 (m-80) cc_final: 0.8812 (t80) REVERT: B 780 GLU cc_start: 0.8623 (tp30) cc_final: 0.8174 (tp30) REVERT: B 902 MET cc_start: 0.8779 (tpt) cc_final: 0.8547 (tpt) REVERT: B 957 GLN cc_start: 0.8532 (tp40) cc_final: 0.8220 (tp40) REVERT: B 985 ASP cc_start: 0.7416 (t0) cc_final: 0.7172 (t0) REVERT: C 177 MET cc_start: 0.5348 (pmm) cc_final: 0.3466 (pmm) REVERT: C 265 TYR cc_start: 0.8401 (p90) cc_final: 0.8169 (p90) REVERT: C 421 TYR cc_start: 0.8773 (m-10) cc_final: 0.8314 (m-10) REVERT: C 780 GLU cc_start: 0.8677 (tp30) cc_final: 0.8338 (tp30) REVERT: C 957 GLN cc_start: 0.8562 (tp40) cc_final: 0.8313 (tp40) outliers start: 39 outliers final: 36 residues processed: 161 average time/residue: 0.1531 time to fit residues: 40.9267 Evaluate side-chains 160 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 111 optimal weight: 1.9990 chunk 312 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 288 optimal weight: 0.4980 chunk 153 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.110594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071392 restraints weight = 76073.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074012 restraints weight = 37536.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075684 restraints weight = 24428.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076680 restraints weight = 18818.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077316 restraints weight = 16129.428| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26661 Z= 0.123 Angle : 0.576 8.208 36411 Z= 0.288 Chirality : 0.043 0.202 4269 Planarity : 0.004 0.053 4602 Dihedral : 5.719 54.945 4773 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.28 % Allowed : 12.67 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3171 helix: 2.29 (0.22), residues: 609 sheet: -0.20 (0.20), residues: 651 loop : -1.51 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.021 0.001 TYR A1067 PHE 0.019 0.001 PHE A 392 TRP 0.006 0.001 TRP B 353 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00285 (26556) covalent geometry : angle 0.56228 (36138) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.25752 ( 84) hydrogen bonds : bond 0.04982 ( 972) hydrogen bonds : angle 4.89796 ( 2679) link_BETA1-4 : bond 0.00266 ( 15) link_BETA1-4 : angle 1.13713 ( 45) link_NAG-ASN : bond 0.00188 ( 48) link_NAG-ASN : angle 1.79641 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5371 (pmm) cc_final: 0.3609 (pmm) REVERT: A 226 LEU cc_start: 0.7352 (tp) cc_final: 0.7038 (tt) REVERT: A 389 ASP cc_start: 0.8814 (t0) cc_final: 0.8602 (p0) REVERT: A 421 TYR cc_start: 0.8228 (m-10) cc_final: 0.7935 (m-10) REVERT: A 957 GLN cc_start: 0.8574 (tp40) cc_final: 0.8216 (tp40) REVERT: B 177 MET cc_start: 0.5078 (pmm) cc_final: 0.4661 (pmm) REVERT: B 390 LEU cc_start: 0.8741 (tp) cc_final: 0.8228 (tp) REVERT: B 421 TYR cc_start: 0.8843 (m-10) cc_final: 0.8389 (m-10) REVERT: B 456 PHE cc_start: 0.9049 (m-80) cc_final: 0.8826 (t80) REVERT: B 780 GLU cc_start: 0.8611 (tp30) cc_final: 0.8182 (tp30) REVERT: B 902 MET cc_start: 0.8757 (tpt) cc_final: 0.8522 (tpt) REVERT: B 957 GLN cc_start: 0.8495 (tp40) cc_final: 0.8185 (tp40) REVERT: B 985 ASP cc_start: 0.7386 (t0) cc_final: 0.7128 (t0) REVERT: C 177 MET cc_start: 0.5328 (pmm) cc_final: 0.3474 (pmm) REVERT: C 265 TYR cc_start: 0.8360 (p90) cc_final: 0.8131 (p90) REVERT: C 421 TYR cc_start: 0.8771 (m-10) cc_final: 0.8324 (m-10) REVERT: C 780 GLU cc_start: 0.8658 (tp30) cc_final: 0.8335 (tp30) REVERT: C 957 GLN cc_start: 0.8471 (tp40) cc_final: 0.8233 (tp40) outliers start: 36 outliers final: 35 residues processed: 160 average time/residue: 0.1613 time to fit residues: 42.4301 Evaluate side-chains 161 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 288 optimal weight: 0.0670 chunk 279 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN B 901 GLN C 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.110625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071737 restraints weight = 75120.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074364 restraints weight = 36667.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076004 restraints weight = 23694.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077054 restraints weight = 18165.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.077624 restraints weight = 15500.128| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26661 Z= 0.123 Angle : 0.572 10.690 36411 Z= 0.286 Chirality : 0.042 0.206 4269 Planarity : 0.004 0.053 4602 Dihedral : 5.655 54.747 4773 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.46 % Allowed : 12.56 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.15), residues: 3171 helix: 2.28 (0.22), residues: 609 sheet: -0.17 (0.20), residues: 645 loop : -1.50 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.020 0.001 TYR A1067 PHE 0.020 0.001 PHE A 392 TRP 0.006 0.001 TRP B 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00285 (26556) covalent geometry : angle 0.55915 (36138) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.19575 ( 84) hydrogen bonds : bond 0.04918 ( 972) hydrogen bonds : angle 4.86363 ( 2679) link_BETA1-4 : bond 0.00237 ( 15) link_BETA1-4 : angle 1.15105 ( 45) link_NAG-ASN : bond 0.00186 ( 48) link_NAG-ASN : angle 1.77741 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5216.28 seconds wall clock time: 90 minutes 24.48 seconds (5424.48 seconds total)