Starting phenix.real_space_refine on Sat Aug 23 23:05:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxy_29548/08_2025/8fxy_29548_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxy_29548/08_2025/8fxy_29548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxy_29548/08_2025/8fxy_29548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxy_29548/08_2025/8fxy_29548.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxy_29548/08_2025/8fxy_29548_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxy_29548/08_2025/8fxy_29548_trim.cif" } resolution = 3.34 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 9456 2.51 5 N 2496 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15042 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "D" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "E" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "F" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "G" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "I" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "J" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "K" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "L" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.82, per 1000 atoms: 0.25 Number of scatterers: 15042 At special positions: 0 Unit cell: (177.1, 163.9, 62.7, 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 138 16.00 O 2952 8.00 N 2496 7.00 C 9456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS K 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS B 4 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS D 4 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 184 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS F 4 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 184 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 85 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 109 " - pdb=" SG CYS I 4 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 184 " distance=2.04 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 85 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 104 " - pdb=" SG CYS I 136 " distance=2.03 Simple disulfide: pdb=" SG CYS I 109 " - pdb=" SG CYS K 4 " distance=2.03 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 184 " distance=2.04 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 85 " distance=2.03 Simple disulfide: pdb=" SG CYS K 35 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 104 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 184 " distance=2.04 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 85 " 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 NAG-ASN " NAG A 201 " - " ASN A 28 " " NAG A 203 " - " ASN A 58 " " NAG B 201 " - " ASN B 28 " " NAG B 203 " - " ASN B 58 " " NAG D 201 " - " ASN D 28 " " NAG D 203 " - " ASN D 58 " " NAG F 201 " - " ASN F 28 " " NAG F 203 " - " ASN F 58 " " NAG I 201 " - " ASN I 28 " " NAG I 203 " - " ASN I 58 " " NAG K 201 " - " ASN K 28 " " NAG K 203 " - " ASN K 58 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 661.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 5.9% alpha, 55.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'H' and resid 24 through 26 No H-bonds generated for 'chain 'H' and resid 24 through 26' Processing helix chain 'H' and resid 54 through 58 Processing helix chain 'H' and resid 76 through 80 removed outlier: 4.224A pdb=" N LYS H 80 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 76 through 80 removed outlier: 4.134A pdb=" N LYS C 80 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 54 through 58 Processing helix chain 'E' and resid 76 through 80 removed outlier: 4.058A pdb=" N LYS E 80 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 54 through 58 Processing helix chain 'G' and resid 76 through 80 removed outlier: 4.094A pdb=" N LYS G 80 " --> pdb=" O ILE G 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 170 Processing helix chain 'J' and resid 24 through 26 No H-bonds generated for 'chain 'J' and resid 24 through 26' Processing helix chain 'J' and resid 54 through 58 Processing helix chain 'J' and resid 76 through 80 removed outlier: 4.181A pdb=" N LYS J 80 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 170 removed outlier: 3.547A pdb=" N ARG K 170 " --> pdb=" O TYR K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 26 No H-bonds generated for 'chain 'L' and resid 24 through 26' Processing helix chain 'L' and resid 54 through 58 Processing helix chain 'L' and resid 76 through 80 removed outlier: 4.251A pdb=" N LYS L 80 " --> pdb=" O ILE L 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.784A pdb=" N ASP A 194 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 73 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N SER A 172 " --> pdb=" O HIS H 99 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS H 99 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY A 174 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG H 97 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 89 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS H 99 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 3 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 106 " --> pdb=" O ILE H 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.784A pdb=" N ASP A 194 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 73 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N SER A 172 " --> pdb=" O HIS H 99 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS H 99 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY A 174 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG H 97 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 89 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS H 99 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU H 28 " --> pdb=" O TYR H 44 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR H 44 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL H 30 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU H 42 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP H 32 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU H 42 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.681A pdb=" N MET A 62 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 97 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 98 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR A 131 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 100 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASN A 133 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 102 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 132 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.681A pdb=" N MET A 62 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 97 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 98 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR A 131 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 100 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASN A 133 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 102 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.731A pdb=" N ASP B 194 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 73 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N SER B 172 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N HIS C 99 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY B 174 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 97 " --> pdb=" O HIS C 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS C 89 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 99 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 106 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.731A pdb=" N ASP B 194 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 73 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N SER B 172 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N HIS C 99 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY B 174 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 97 " --> pdb=" O HIS C 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS C 89 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 99 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 28 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR C 44 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 30 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU C 42 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 32 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 42 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 40 removed outlier: 6.910A pdb=" N ILE B 98 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 131 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 100 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN B 133 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 102 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 132 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 40 removed outlier: 6.910A pdb=" N ILE B 98 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 131 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 100 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN B 133 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 102 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 14 Processing sheet with id=AB2, first strand: chain 'D' and resid 194 through 195 removed outlier: 3.698A pdb=" N ASP D 194 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 73 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N SER D 172 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS E 99 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY D 174 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG E 97 " --> pdb=" O HIS E 89 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS E 89 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS E 99 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 106 " --> pdb=" O ILE E 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 194 through 195 removed outlier: 3.698A pdb=" N ASP D 194 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 73 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N SER D 172 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS E 99 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY D 174 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG E 97 " --> pdb=" O HIS E 89 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS E 89 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS E 99 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 28 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TYR E 44 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL E 30 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU E 42 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP E 32 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU E 42 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.671A pdb=" N MET D 62 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN D 97 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 98 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR D 131 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 100 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN D 133 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE D 102 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE D 132 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.671A pdb=" N MET D 62 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN D 97 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 98 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR D 131 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 100 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN D 133 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE D 102 " --> pdb=" O ASN D 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AB7, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.720A pdb=" N ASP F 194 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 73 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N SER F 172 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS G 99 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY F 174 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG G 97 " --> pdb=" O HIS G 89 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS G 89 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS G 99 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 106 " --> pdb=" O ILE G 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.720A pdb=" N ASP F 194 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 73 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N SER F 172 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS G 99 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY F 174 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG G 97 " --> pdb=" O HIS G 89 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS G 89 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS G 99 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU G 28 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR G 44 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL G 30 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU G 42 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP G 32 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU G 42 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 36 through 40 removed outlier: 3.549A pdb=" N MET F 62 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN F 97 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE F 98 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR F 131 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 100 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN F 133 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE F 102 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE F 132 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 36 through 40 removed outlier: 3.549A pdb=" N MET F 62 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN F 97 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE F 98 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR F 131 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 100 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN F 133 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE F 102 " --> pdb=" O ASN F 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 11 through 14 Processing sheet with id=AC3, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.628A pdb=" N ASP I 194 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU I 73 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N SER I 172 " --> pdb=" O HIS J 99 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HIS J 99 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY I 174 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG J 97 " --> pdb=" O HIS J 89 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS J 89 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS J 99 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU J 1 " --> pdb=" O ASN J 102 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER J 106 " --> pdb=" O ILE J 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.628A pdb=" N ASP I 194 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU I 73 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N SER I 172 " --> pdb=" O HIS J 99 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HIS J 99 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY I 174 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG J 97 " --> pdb=" O HIS J 89 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS J 89 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS J 99 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU J 28 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR J 44 " --> pdb=" O LEU J 28 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL J 30 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU J 42 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP J 32 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU J 42 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 36 through 40 removed outlier: 3.782A pdb=" N MET I 62 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN I 97 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE I 98 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR I 131 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL I 100 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN I 133 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE I 102 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE I 132 " --> pdb=" O LYS I 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 36 through 40 removed outlier: 3.782A pdb=" N MET I 62 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN I 97 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE I 98 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR I 131 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL I 100 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN I 133 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE I 102 " --> pdb=" O ASN I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 11 through 14 Processing sheet with id=AC8, first strand: chain 'K' and resid 194 through 195 removed outlier: 3.744A pdb=" N ASP K 194 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 73 " --> pdb=" O ASP K 194 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER K 172 " --> pdb=" O HIS L 99 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS L 99 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLY K 174 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG L 97 " --> pdb=" O HIS L 89 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS L 89 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS L 99 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER L 106 " --> pdb=" O ILE L 3 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 194 through 195 removed outlier: 3.744A pdb=" N ASP K 194 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 73 " --> pdb=" O ASP K 194 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER K 172 " --> pdb=" O HIS L 99 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS L 99 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLY K 174 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG L 97 " --> pdb=" O HIS L 89 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS L 89 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS L 99 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU L 28 " --> pdb=" O TYR L 44 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR L 44 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL L 30 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU L 42 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP L 32 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU L 42 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 36 through 40 removed outlier: 3.569A pdb=" N MET K 62 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN K 97 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE K 98 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N THR K 131 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL K 100 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN K 133 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE K 102 " --> pdb=" O ASN K 133 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE K 132 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 36 through 40 removed outlier: 3.569A pdb=" N MET K 62 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN K 97 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE K 98 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N THR K 131 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL K 100 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN K 133 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE K 102 " --> pdb=" O ASN K 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 11 through 14 709 hydrogen bonds defined for protein. 1782 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: 3.05 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4872 1.35 - 1.47: 3749 1.47 - 1.59: 6523 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 15354 Sorted by residual: bond pdb=" C1 NAG F 201 " pdb=" O5 NAG F 201 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C1 NAG D 201 " pdb=" O5 NAG D 201 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG B 201 " pdb=" O5 NAG B 201 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C1 NAG K 201 " pdb=" O5 NAG K 201 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C1 NAG D 203 " pdb=" O5 NAG D 203 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 15349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 19592 1.12 - 2.24: 941 2.24 - 3.36: 177 3.36 - 4.47: 55 4.47 - 5.59: 13 Bond angle restraints: 20778 Sorted by residual: angle pdb=" N MET B 107 " pdb=" CA MET B 107 " pdb=" CB MET B 107 " ideal model delta sigma weight residual 114.17 109.61 4.56 1.14e+00 7.69e-01 1.60e+01 angle pdb=" N MET I 107 " pdb=" CA MET I 107 " pdb=" CB MET I 107 " ideal model delta sigma weight residual 114.17 109.63 4.54 1.14e+00 7.69e-01 1.59e+01 angle pdb=" N MET A 107 " pdb=" CA MET A 107 " pdb=" CB MET A 107 " ideal model delta sigma weight residual 114.17 109.63 4.54 1.14e+00 7.69e-01 1.58e+01 angle pdb=" N MET F 107 " pdb=" CA MET F 107 " pdb=" CB MET F 107 " ideal model delta sigma weight residual 114.17 109.71 4.46 1.14e+00 7.69e-01 1.53e+01 angle pdb=" N ILE F 149 " pdb=" CA ILE F 149 " pdb=" C ILE F 149 " ideal model delta sigma weight residual 106.21 110.36 -4.15 1.07e+00 8.73e-01 1.51e+01 ... (remaining 20773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 8908 17.04 - 34.08: 455 34.08 - 51.12: 115 51.12 - 68.16: 34 68.16 - 85.20: 4 Dihedral angle restraints: 9516 sinusoidal: 4092 harmonic: 5424 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -39.48 -46.52 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CB CYS E 15 " pdb=" SG CYS E 15 " pdb=" SG CYS E 85 " pdb=" CB CYS E 85 " ideal model delta sinusoidal sigma weight residual -86.00 -40.71 -45.29 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS L 15 " pdb=" SG CYS L 15 " pdb=" SG CYS L 85 " pdb=" CB CYS L 85 " ideal model delta sinusoidal sigma weight residual -86.00 -41.32 -44.68 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 9513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1501 0.028 - 0.057: 477 0.057 - 0.085: 172 0.085 - 0.113: 171 0.113 - 0.142: 25 Chirality restraints: 2346 Sorted by residual: chirality pdb=" CA ILE B 27 " pdb=" N ILE B 27 " pdb=" C ILE B 27 " pdb=" CB ILE B 27 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE D 27 " pdb=" N ILE D 27 " pdb=" C ILE D 27 " pdb=" CB ILE D 27 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE F 27 " pdb=" N ILE F 27 " pdb=" C ILE F 27 " pdb=" CB ILE F 27 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 2343 not shown) Planarity restraints: 2646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS I 4 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO I 5 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO I 5 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 5 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 13 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO G 14 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 13 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO J 14 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO J 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 14 " -0.021 5.00e-02 4.00e+02 ... (remaining 2643 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 412 2.67 - 3.23: 15106 3.23 - 3.79: 20806 3.79 - 4.34: 29970 4.34 - 4.90: 49049 Nonbonded interactions: 115343 Sorted by model distance: nonbonded pdb=" O CYS B 109 " pdb=" N THR D 2 " model vdw 2.117 3.120 nonbonded pdb=" O CYS I 109 " pdb=" N THR K 2 " model vdw 2.135 3.120 nonbonded pdb=" OG SER C 20 " pdb=" OE1 GLN C 21 " model vdw 2.156 3.040 nonbonded pdb=" OG SER E 20 " pdb=" OE1 GLN E 21 " model vdw 2.159 3.040 nonbonded pdb=" OG SER L 20 " pdb=" OE1 GLN L 21 " model vdw 2.160 3.040 ... (remaining 115338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15396 Z= 0.153 Angle : 0.601 5.592 20874 Z= 0.343 Chirality : 0.041 0.142 2346 Planarity : 0.003 0.039 2634 Dihedral : 11.057 85.195 5934 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 38.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 3.08 % Allowed : 9.02 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.09 (0.20), residues: 1812 helix: None (None), residues: 0 sheet: 0.10 (0.19), residues: 804 loop : -2.82 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 11 TYR 0.012 0.001 TYR B 53 PHE 0.009 0.001 PHE A 185 TRP 0.009 0.001 TRP H 32 HIS 0.003 0.001 HIS L 99 Details of bonding type rmsd covalent geometry : bond 0.00295 (15354) covalent geometry : angle 0.58888 (20778) SS BOND : bond 0.00387 ( 30) SS BOND : angle 1.44572 ( 60) hydrogen bonds : bond 0.12850 ( 439) hydrogen bonds : angle 6.06068 ( 1782) link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 2.38282 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 0.562 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 32 MET cc_start: 0.7124 (tmm) cc_final: 0.6643 (tmm) REVERT: A 169 MET cc_start: 0.7041 (mmp) cc_final: 0.6748 (mmp) REVERT: A 183 GLN cc_start: 0.3354 (OUTLIER) cc_final: 0.3063 (tp40) REVERT: H 90 LYS cc_start: 0.8104 (tptt) cc_final: 0.7858 (tptt) REVERT: H 101 MET cc_start: 0.7307 (tpp) cc_final: 0.6947 (tpp) REVERT: B 32 MET cc_start: 0.7225 (tmm) cc_final: 0.6747 (tmm) REVERT: B 40 SER cc_start: 0.8217 (m) cc_final: 0.8007 (p) REVERT: B 49 VAL cc_start: 0.8305 (p) cc_final: 0.8041 (t) REVERT: B 101 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8207 (m) REVERT: B 113 LYS cc_start: 0.6264 (mmtm) cc_final: 0.5247 (tttm) REVERT: B 183 GLN cc_start: 0.3602 (OUTLIER) cc_final: 0.3190 (tm-30) REVERT: D 32 MET cc_start: 0.7273 (tmm) cc_final: 0.6976 (tmm) REVERT: D 38 SER cc_start: 0.8450 (m) cc_final: 0.8236 (m) REVERT: D 73 GLU cc_start: 0.6475 (pm20) cc_final: 0.6261 (pm20) REVERT: D 103 THR cc_start: 0.7950 (m) cc_final: 0.7693 (t) REVERT: D 107 MET cc_start: 0.7058 (tpt) cc_final: 0.6806 (tpt) REVERT: D 117 ASP cc_start: 0.7748 (p0) cc_final: 0.7417 (p0) REVERT: D 126 SER cc_start: 0.8154 (t) cc_final: 0.7728 (p) REVERT: D 133 ASN cc_start: 0.8318 (m-40) cc_final: 0.8023 (m-40) REVERT: D 165 SER cc_start: 0.8334 (m) cc_final: 0.8016 (p) REVERT: D 172 SER cc_start: 0.8305 (t) cc_final: 0.7976 (p) REVERT: E 58 MET cc_start: 0.7099 (mmt) cc_final: 0.6606 (mmt) REVERT: E 101 MET cc_start: 0.7305 (tpp) cc_final: 0.6957 (tpp) REVERT: F 12 TYR cc_start: 0.7148 (m-10) cc_final: 0.6745 (m-10) REVERT: F 32 MET cc_start: 0.6851 (tmm) cc_final: 0.6407 (tmm) REVERT: F 82 SER cc_start: 0.8467 (p) cc_final: 0.8245 (p) REVERT: F 101 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8376 (m) REVERT: F 115 ASP cc_start: 0.7604 (t0) cc_final: 0.7181 (t0) REVERT: F 158 ASP cc_start: 0.7915 (m-30) cc_final: 0.7690 (m-30) REVERT: F 165 SER cc_start: 0.8464 (m) cc_final: 0.8077 (p) REVERT: G 0 MET cc_start: 0.2301 (mmt) cc_final: 0.2092 (mmt) REVERT: G 58 MET cc_start: 0.7333 (mmt) cc_final: 0.7113 (mmt) REVERT: G 64 ASP cc_start: 0.7158 (t0) cc_final: 0.6901 (t0) REVERT: I 32 MET cc_start: 0.6842 (tmm) cc_final: 0.6556 (tmm) REVERT: I 40 SER cc_start: 0.8246 (m) cc_final: 0.7928 (p) REVERT: I 49 VAL cc_start: 0.8212 (p) cc_final: 0.8011 (t) REVERT: I 101 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8208 (m) REVERT: I 113 LYS cc_start: 0.6234 (mmtm) cc_final: 0.5135 (tttp) REVERT: I 126 SER cc_start: 0.8432 (t) cc_final: 0.8174 (p) REVERT: I 140 VAL cc_start: 0.7388 (t) cc_final: 0.7015 (p) REVERT: I 165 SER cc_start: 0.8368 (m) cc_final: 0.8106 (p) REVERT: I 172 SER cc_start: 0.8291 (t) cc_final: 0.8033 (p) REVERT: I 183 GLN cc_start: 0.3214 (OUTLIER) cc_final: 0.2897 (tm-30) REVERT: J 8 ASN cc_start: 0.6835 (t0) cc_final: 0.6385 (m-40) REVERT: J 69 THR cc_start: 0.7860 (m) cc_final: 0.7655 (p) REVERT: K 20 THR cc_start: 0.8128 (t) cc_final: 0.7681 (p) REVERT: K 103 THR cc_start: 0.7959 (m) cc_final: 0.7597 (t) REVERT: K 126 SER cc_start: 0.8400 (t) cc_final: 0.7842 (p) REVERT: K 133 ASN cc_start: 0.8096 (m-40) cc_final: 0.7882 (m-40) REVERT: K 165 SER cc_start: 0.8505 (m) cc_final: 0.8225 (p) REVERT: K 172 SER cc_start: 0.8412 (t) cc_final: 0.8138 (p) outliers start: 52 outliers final: 19 residues processed: 395 average time/residue: 0.1086 time to fit residues: 66.7494 Evaluate side-chains 352 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 183 GLN Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN H 37 ASN C 37 ASN C 89 HIS ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 89 HIS F 45 ASN F 133 ASN F 183 GLN G 37 ASN J 37 ASN J 89 HIS K 183 GLN L 37 ASN L 89 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.165752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142331 restraints weight = 21497.329| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.68 r_work: 0.3658 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15396 Z= 0.209 Angle : 0.784 12.766 20874 Z= 0.400 Chirality : 0.050 0.154 2346 Planarity : 0.005 0.058 2634 Dihedral : 8.669 76.355 2416 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 4.45 % Allowed : 17.32 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.02 (0.20), residues: 1812 helix: None (None), residues: 0 sheet: 0.14 (0.19), residues: 792 loop : -2.74 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 170 TYR 0.018 0.002 TYR K 25 PHE 0.014 0.002 PHE A 185 TRP 0.009 0.002 TRP C 68 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00481 (15354) covalent geometry : angle 0.76506 (20778) SS BOND : bond 0.00668 ( 30) SS BOND : angle 2.42926 ( 60) hydrogen bonds : bond 0.04385 ( 439) hydrogen bonds : angle 5.06846 ( 1782) link_NAG-ASN : bond 0.00521 ( 12) link_NAG-ASN : angle 2.91896 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 365 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7351 (tmm) cc_final: 0.6810 (tmm) REVERT: A 169 MET cc_start: 0.6966 (mmp) cc_final: 0.6650 (mmp) REVERT: B 32 MET cc_start: 0.7467 (tmm) cc_final: 0.6743 (tmm) REVERT: B 49 VAL cc_start: 0.8243 (p) cc_final: 0.8004 (t) REVERT: B 101 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8000 (p) REVERT: B 126 SER cc_start: 0.8303 (t) cc_final: 0.8062 (p) REVERT: D 32 MET cc_start: 0.7557 (tmm) cc_final: 0.7323 (tmm) REVERT: D 85 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7409 (mt) REVERT: D 117 ASP cc_start: 0.7582 (p0) cc_final: 0.7210 (p0) REVERT: D 126 SER cc_start: 0.8132 (t) cc_final: 0.7902 (p) REVERT: D 133 ASN cc_start: 0.8232 (m-40) cc_final: 0.7977 (m-40) REVERT: D 163 ARG cc_start: 0.8103 (ptm-80) cc_final: 0.7710 (mtm110) REVERT: D 165 SER cc_start: 0.8397 (m) cc_final: 0.8159 (p) REVERT: D 172 SER cc_start: 0.8233 (t) cc_final: 0.7923 (p) REVERT: E 48 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 58 MET cc_start: 0.7275 (mmt) cc_final: 0.6733 (mmt) REVERT: E 101 MET cc_start: 0.7279 (tpp) cc_final: 0.7008 (tpp) REVERT: F 32 MET cc_start: 0.7150 (tmm) cc_final: 0.6634 (tmm) REVERT: F 117 ASP cc_start: 0.7864 (p0) cc_final: 0.7496 (p0) REVERT: F 158 ASP cc_start: 0.7955 (m-30) cc_final: 0.7654 (m-30) REVERT: F 165 SER cc_start: 0.8485 (m) cc_final: 0.8106 (p) REVERT: G 32 TRP cc_start: 0.7374 (m100) cc_final: 0.5869 (m100) REVERT: G 64 ASP cc_start: 0.7492 (t0) cc_final: 0.7185 (t0) REVERT: G 101 MET cc_start: 0.7553 (tpp) cc_final: 0.7319 (tpp) REVERT: I 20 THR cc_start: 0.7689 (t) cc_final: 0.7394 (p) REVERT: I 32 MET cc_start: 0.7182 (tmm) cc_final: 0.6419 (tmm) REVERT: I 37 MET cc_start: 0.8299 (ppp) cc_final: 0.7958 (ptm) REVERT: I 40 SER cc_start: 0.8092 (m) cc_final: 0.7830 (p) REVERT: I 101 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7978 (p) REVERT: I 113 LYS cc_start: 0.6417 (mmtm) cc_final: 0.5370 (tttp) REVERT: I 165 SER cc_start: 0.8457 (m) cc_final: 0.8183 (p) REVERT: J 8 ASN cc_start: 0.6944 (t0) cc_final: 0.6540 (m-40) REVERT: J 69 THR cc_start: 0.8069 (m) cc_final: 0.7724 (p) REVERT: K 12 TYR cc_start: 0.7133 (m-10) cc_final: 0.6514 (m-10) REVERT: K 103 THR cc_start: 0.7905 (m) cc_final: 0.7623 (t) REVERT: K 117 ASP cc_start: 0.7453 (p0) cc_final: 0.7235 (p0) REVERT: K 126 SER cc_start: 0.8390 (t) cc_final: 0.8107 (p) REVERT: K 140 VAL cc_start: 0.7250 (t) cc_final: 0.7034 (p) REVERT: K 165 SER cc_start: 0.8657 (m) cc_final: 0.8392 (p) outliers start: 75 outliers final: 38 residues processed: 412 average time/residue: 0.1072 time to fit residues: 69.7674 Evaluate side-chains 381 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 340 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 97 ASN D 79 ASN D 89 GLN D 97 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 123 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.163633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140198 restraints weight = 21854.776| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.66 r_work: 0.3647 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15396 Z= 0.208 Angle : 0.756 14.044 20874 Z= 0.389 Chirality : 0.049 0.178 2346 Planarity : 0.005 0.067 2634 Dihedral : 7.389 49.453 2394 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 4.69 % Allowed : 20.05 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.19 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.06 (0.19), residues: 786 loop : -2.76 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 44 TYR 0.019 0.002 TYR D 53 PHE 0.013 0.002 PHE A 185 TRP 0.006 0.001 TRP C 68 HIS 0.005 0.001 HIS L 99 Details of bonding type rmsd covalent geometry : bond 0.00476 (15354) covalent geometry : angle 0.73677 (20778) SS BOND : bond 0.00590 ( 30) SS BOND : angle 2.55455 ( 60) hydrogen bonds : bond 0.04227 ( 439) hydrogen bonds : angle 5.05434 ( 1782) link_NAG-ASN : bond 0.00608 ( 12) link_NAG-ASN : angle 2.63028 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 324 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7449 (tmm) cc_final: 0.6983 (tmm) REVERT: B 32 MET cc_start: 0.7557 (tmm) cc_final: 0.6824 (tmm) REVERT: B 91 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7977 (mp) REVERT: B 101 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7925 (p) REVERT: B 115 ASP cc_start: 0.7696 (t0) cc_final: 0.7454 (t0) REVERT: B 126 SER cc_start: 0.8335 (t) cc_final: 0.8121 (p) REVERT: C 101 MET cc_start: 0.7261 (tpp) cc_final: 0.7058 (tpt) REVERT: D 32 MET cc_start: 0.7672 (tmm) cc_final: 0.7414 (tmm) REVERT: D 117 ASP cc_start: 0.7248 (p0) cc_final: 0.6858 (p0) REVERT: D 126 SER cc_start: 0.8082 (t) cc_final: 0.7852 (p) REVERT: D 163 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7710 (mtm110) REVERT: D 165 SER cc_start: 0.8459 (m) cc_final: 0.8150 (p) REVERT: D 172 SER cc_start: 0.8218 (t) cc_final: 0.7940 (p) REVERT: E 58 MET cc_start: 0.7270 (mmt) cc_final: 0.6824 (mmt) REVERT: E 101 MET cc_start: 0.7282 (tpp) cc_final: 0.6995 (tpp) REVERT: F 26 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: F 32 MET cc_start: 0.7174 (tmm) cc_final: 0.6655 (tmm) REVERT: F 117 ASP cc_start: 0.7874 (p0) cc_final: 0.7495 (p0) REVERT: F 158 ASP cc_start: 0.7927 (m-30) cc_final: 0.7626 (m-30) REVERT: F 165 SER cc_start: 0.8452 (m) cc_final: 0.8067 (p) REVERT: G 64 ASP cc_start: 0.7532 (t70) cc_final: 0.7163 (t0) REVERT: I 32 MET cc_start: 0.7137 (tmm) cc_final: 0.6386 (tmm) REVERT: I 37 MET cc_start: 0.8247 (ppp) cc_final: 0.7945 (ptm) REVERT: I 101 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7975 (p) REVERT: I 113 LYS cc_start: 0.6412 (mmtm) cc_final: 0.5371 (ttmm) REVERT: I 165 SER cc_start: 0.8407 (m) cc_final: 0.8070 (p) REVERT: J 8 ASN cc_start: 0.6682 (t0) cc_final: 0.6365 (m-40) REVERT: K 12 TYR cc_start: 0.7094 (m-10) cc_final: 0.6509 (m-10) REVERT: K 32 MET cc_start: 0.7808 (tmm) cc_final: 0.7322 (tmm) REVERT: K 103 THR cc_start: 0.7998 (m) cc_final: 0.7682 (t) REVERT: K 117 ASP cc_start: 0.7451 (p0) cc_final: 0.7231 (p0) REVERT: K 126 SER cc_start: 0.8411 (t) cc_final: 0.8083 (p) REVERT: K 165 SER cc_start: 0.8650 (m) cc_final: 0.8370 (p) outliers start: 79 outliers final: 62 residues processed: 372 average time/residue: 0.1049 time to fit residues: 61.8554 Evaluate side-chains 385 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 120 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 139 optimal weight: 0.0980 chunk 178 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN D 79 ASN D 155 HIS I 89 GLN I 97 ASN L 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144616 restraints weight = 21718.045| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.68 r_work: 0.3679 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15396 Z= 0.137 Angle : 0.675 9.922 20874 Z= 0.346 Chirality : 0.047 0.147 2346 Planarity : 0.004 0.060 2634 Dihedral : 6.593 52.572 2394 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 4.45 % Allowed : 21.83 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.04 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.04 (0.19), residues: 762 loop : -2.52 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.016 0.001 TYR K 25 PHE 0.013 0.001 PHE A 185 TRP 0.006 0.001 TRP K 13 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00301 (15354) covalent geometry : angle 0.66019 (20778) SS BOND : bond 0.00491 ( 30) SS BOND : angle 1.99495 ( 60) hydrogen bonds : bond 0.03698 ( 439) hydrogen bonds : angle 4.73817 ( 1782) link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 2.43180 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 331 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7370 (tmm) cc_final: 0.7101 (tmm) REVERT: B 32 MET cc_start: 0.7566 (tmm) cc_final: 0.6791 (tmm) REVERT: B 91 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7977 (mp) REVERT: B 101 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7926 (p) REVERT: B 113 LYS cc_start: 0.6485 (mptt) cc_final: 0.5111 (tttp) REVERT: B 126 SER cc_start: 0.8292 (t) cc_final: 0.8061 (p) REVERT: D 32 MET cc_start: 0.7695 (tmm) cc_final: 0.7433 (tmm) REVERT: D 85 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7320 (mt) REVERT: D 117 ASP cc_start: 0.7204 (p0) cc_final: 0.6820 (p0) REVERT: D 163 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7777 (mtm110) REVERT: D 165 SER cc_start: 0.8459 (m) cc_final: 0.8125 (p) REVERT: D 172 SER cc_start: 0.8203 (t) cc_final: 0.7922 (p) REVERT: E 58 MET cc_start: 0.7287 (mmt) cc_final: 0.6830 (mmt) REVERT: E 101 MET cc_start: 0.7233 (tpp) cc_final: 0.6941 (tpp) REVERT: F 32 MET cc_start: 0.7205 (tmm) cc_final: 0.6816 (tmm) REVERT: F 117 ASP cc_start: 0.7822 (p0) cc_final: 0.7471 (p0) REVERT: F 158 ASP cc_start: 0.7928 (m-30) cc_final: 0.7645 (m-30) REVERT: F 163 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7758 (ptm-80) REVERT: F 165 SER cc_start: 0.8448 (m) cc_final: 0.8043 (p) REVERT: G 64 ASP cc_start: 0.7478 (t70) cc_final: 0.7069 (t0) REVERT: I 32 MET cc_start: 0.7140 (tmm) cc_final: 0.6369 (tmm) REVERT: I 101 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7965 (p) REVERT: I 113 LYS cc_start: 0.6384 (mmtm) cc_final: 0.5439 (tttp) REVERT: I 165 SER cc_start: 0.8394 (m) cc_final: 0.8052 (p) REVERT: J 8 ASN cc_start: 0.6883 (t0) cc_final: 0.6617 (m-40) REVERT: K 12 TYR cc_start: 0.6838 (m-10) cc_final: 0.6269 (m-10) REVERT: K 32 MET cc_start: 0.7886 (tmm) cc_final: 0.7369 (tmm) REVERT: K 103 THR cc_start: 0.8012 (m) cc_final: 0.7704 (t) REVERT: K 126 SER cc_start: 0.8426 (t) cc_final: 0.8077 (p) REVERT: K 140 VAL cc_start: 0.7345 (t) cc_final: 0.7099 (p) REVERT: K 165 SER cc_start: 0.8654 (m) cc_final: 0.8356 (p) outliers start: 75 outliers final: 57 residues processed: 378 average time/residue: 0.1042 time to fit residues: 62.4683 Evaluate side-chains 383 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 143 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN I 79 ASN I 89 GLN ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.165641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142196 restraints weight = 21768.449| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.68 r_work: 0.3667 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15396 Z= 0.163 Angle : 0.684 9.488 20874 Z= 0.354 Chirality : 0.047 0.150 2346 Planarity : 0.004 0.060 2634 Dihedral : 6.568 54.243 2392 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 5.99 % Allowed : 21.41 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.01 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.04 (0.19), residues: 798 loop : -2.56 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.015 0.001 TYR F 53 PHE 0.012 0.001 PHE A 185 TRP 0.013 0.001 TRP K 13 HIS 0.004 0.001 HIS I 96 Details of bonding type rmsd covalent geometry : bond 0.00366 (15354) covalent geometry : angle 0.66932 (20778) SS BOND : bond 0.00531 ( 30) SS BOND : angle 2.10347 ( 60) hydrogen bonds : bond 0.03863 ( 439) hydrogen bonds : angle 4.79620 ( 1782) link_NAG-ASN : bond 0.00494 ( 12) link_NAG-ASN : angle 2.31687 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 321 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7432 (tmm) cc_final: 0.7017 (tmm) REVERT: B 32 MET cc_start: 0.7515 (tmm) cc_final: 0.6782 (tmm) REVERT: B 91 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7993 (mp) REVERT: B 101 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 113 LYS cc_start: 0.6540 (mptt) cc_final: 0.5194 (tttp) REVERT: B 126 SER cc_start: 0.8304 (t) cc_final: 0.7994 (p) REVERT: D 32 MET cc_start: 0.7672 (tmm) cc_final: 0.7436 (tmm) REVERT: D 85 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7352 (mt) REVERT: D 117 ASP cc_start: 0.7239 (p0) cc_final: 0.6858 (p0) REVERT: D 163 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7818 (mtm110) REVERT: D 165 SER cc_start: 0.8435 (m) cc_final: 0.8075 (p) REVERT: D 172 SER cc_start: 0.8218 (t) cc_final: 0.7966 (p) REVERT: E 58 MET cc_start: 0.7317 (mmt) cc_final: 0.6876 (mmt) REVERT: E 101 MET cc_start: 0.7236 (tpp) cc_final: 0.6938 (tpp) REVERT: F 26 ASP cc_start: 0.7576 (m-30) cc_final: 0.7305 (m-30) REVERT: F 32 MET cc_start: 0.7170 (tmm) cc_final: 0.6834 (tmm) REVERT: F 106 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: F 117 ASP cc_start: 0.7821 (p0) cc_final: 0.7491 (p0) REVERT: F 131 THR cc_start: 0.8140 (m) cc_final: 0.7677 (p) REVERT: F 165 SER cc_start: 0.8465 (m) cc_final: 0.8022 (p) REVERT: G 64 ASP cc_start: 0.7487 (t70) cc_final: 0.7018 (t0) REVERT: I 32 MET cc_start: 0.7173 (tmm) cc_final: 0.6430 (tmm) REVERT: I 101 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.7901 (p) REVERT: I 113 LYS cc_start: 0.6415 (mmtm) cc_final: 0.5414 (tttp) REVERT: I 165 SER cc_start: 0.8416 (m) cc_final: 0.8055 (p) REVERT: J 8 ASN cc_start: 0.6904 (t0) cc_final: 0.6696 (m-40) REVERT: K 12 TYR cc_start: 0.6939 (m-10) cc_final: 0.6276 (m-10) REVERT: K 32 MET cc_start: 0.7892 (tmm) cc_final: 0.7386 (tmm) REVERT: K 103 THR cc_start: 0.8035 (m) cc_final: 0.7715 (t) REVERT: K 126 SER cc_start: 0.8434 (t) cc_final: 0.8081 (p) REVERT: K 140 VAL cc_start: 0.7377 (t) cc_final: 0.7128 (p) REVERT: K 165 SER cc_start: 0.8658 (m) cc_final: 0.8356 (p) outliers start: 101 outliers final: 81 residues processed: 374 average time/residue: 0.0987 time to fit residues: 59.1610 Evaluate side-chains 405 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 319 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN I 108 ASN K 97 ASN ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135461 restraints weight = 21432.611| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.73 r_work: 0.3569 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15396 Z= 0.259 Angle : 0.775 9.865 20874 Z= 0.405 Chirality : 0.050 0.224 2346 Planarity : 0.005 0.068 2634 Dihedral : 7.271 56.503 2392 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.30 % Favored : 86.70 % Rotamer: Outliers : 6.70 % Allowed : 22.00 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.19 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.13 (0.19), residues: 786 loop : -2.69 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 163 TYR 0.022 0.002 TYR A 53 PHE 0.017 0.002 PHE B 185 TRP 0.013 0.001 TRP F 13 HIS 0.006 0.001 HIS I 96 Details of bonding type rmsd covalent geometry : bond 0.00590 (15354) covalent geometry : angle 0.75814 (20778) SS BOND : bond 0.00701 ( 30) SS BOND : angle 2.44817 ( 60) hydrogen bonds : bond 0.04377 ( 439) hydrogen bonds : angle 5.01534 ( 1782) link_NAG-ASN : bond 0.00691 ( 12) link_NAG-ASN : angle 2.53101 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 337 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7511 (tmm) cc_final: 0.7107 (tmm) REVERT: A 115 ASP cc_start: 0.7643 (t0) cc_final: 0.7273 (t0) REVERT: A 117 ASP cc_start: 0.7697 (p0) cc_final: 0.7456 (p0) REVERT: B 12 TYR cc_start: 0.7075 (m-10) cc_final: 0.6658 (m-10) REVERT: B 32 MET cc_start: 0.7613 (tmm) cc_final: 0.6889 (tmm) REVERT: B 91 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8023 (mp) REVERT: B 101 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7880 (p) REVERT: B 113 LYS cc_start: 0.6601 (mptt) cc_final: 0.5162 (tttm) REVERT: B 126 SER cc_start: 0.8344 (t) cc_final: 0.7989 (p) REVERT: D 32 MET cc_start: 0.7676 (tmm) cc_final: 0.7425 (tmm) REVERT: D 85 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7332 (mt) REVERT: D 117 ASP cc_start: 0.7362 (p0) cc_final: 0.6946 (p0) REVERT: D 126 SER cc_start: 0.8104 (t) cc_final: 0.7744 (p) REVERT: D 164 ASN cc_start: 0.7880 (t0) cc_final: 0.7652 (t0) REVERT: D 165 SER cc_start: 0.8490 (m) cc_final: 0.8132 (p) REVERT: E 58 MET cc_start: 0.7391 (mmt) cc_final: 0.6979 (mmt) REVERT: E 101 MET cc_start: 0.7332 (tpp) cc_final: 0.7047 (tpp) REVERT: F 26 ASP cc_start: 0.7630 (m-30) cc_final: 0.7375 (m-30) REVERT: F 32 MET cc_start: 0.7221 (tmm) cc_final: 0.6742 (tmm) REVERT: F 117 ASP cc_start: 0.7905 (p0) cc_final: 0.7526 (p0) REVERT: F 131 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7690 (p) REVERT: F 165 SER cc_start: 0.8525 (m) cc_final: 0.8032 (p) REVERT: G 64 ASP cc_start: 0.7517 (t70) cc_final: 0.7031 (t0) REVERT: I 32 MET cc_start: 0.7207 (tmm) cc_final: 0.6616 (tmm) REVERT: I 91 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8198 (mp) REVERT: I 101 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.7940 (p) REVERT: I 113 LYS cc_start: 0.6140 (mmtm) cc_final: 0.5355 (ttmm) REVERT: I 165 SER cc_start: 0.8403 (m) cc_final: 0.8027 (p) REVERT: K 12 TYR cc_start: 0.7182 (m-10) cc_final: 0.6570 (m-10) REVERT: K 32 MET cc_start: 0.7909 (tmm) cc_final: 0.7394 (tmm) REVERT: K 126 SER cc_start: 0.8392 (t) cc_final: 0.8047 (p) REVERT: K 140 VAL cc_start: 0.7411 (t) cc_final: 0.7123 (p) REVERT: K 165 SER cc_start: 0.8660 (m) cc_final: 0.8381 (p) REVERT: L 48 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7937 (mt-10) outliers start: 113 outliers final: 95 residues processed: 399 average time/residue: 0.0996 time to fit residues: 63.9966 Evaluate side-chains 431 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 330 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 155 HIS B 89 GLN I 79 ASN I 89 GLN K 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137917 restraints weight = 21320.508| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.75 r_work: 0.3598 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15396 Z= 0.171 Angle : 0.722 11.873 20874 Z= 0.370 Chirality : 0.047 0.143 2346 Planarity : 0.005 0.064 2634 Dihedral : 6.800 59.515 2392 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 5.81 % Allowed : 24.26 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.16 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.17 (0.18), residues: 798 loop : -2.63 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 163 TYR 0.015 0.002 TYR K 25 PHE 0.014 0.001 PHE A 185 TRP 0.013 0.001 TRP D 13 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00382 (15354) covalent geometry : angle 0.70539 (20778) SS BOND : bond 0.00534 ( 30) SS BOND : angle 2.30081 ( 60) hydrogen bonds : bond 0.03841 ( 439) hydrogen bonds : angle 4.82026 ( 1782) link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 2.48221 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 331 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7481 (tmm) cc_final: 0.7100 (tmm) REVERT: A 117 ASP cc_start: 0.7588 (p0) cc_final: 0.7378 (p0) REVERT: B 32 MET cc_start: 0.7546 (tmm) cc_final: 0.6823 (tmm) REVERT: B 91 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8026 (mp) REVERT: B 101 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 113 LYS cc_start: 0.6578 (mptt) cc_final: 0.5156 (tttm) REVERT: B 126 SER cc_start: 0.8315 (t) cc_final: 0.7956 (p) REVERT: D 32 MET cc_start: 0.7598 (tmm) cc_final: 0.7367 (tmm) REVERT: D 85 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7334 (mt) REVERT: D 117 ASP cc_start: 0.7327 (p0) cc_final: 0.6931 (p0) REVERT: D 126 SER cc_start: 0.8134 (t) cc_final: 0.7794 (p) REVERT: D 163 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7798 (mtm110) REVERT: D 164 ASN cc_start: 0.7898 (t0) cc_final: 0.7637 (t0) REVERT: D 165 SER cc_start: 0.8472 (m) cc_final: 0.8084 (p) REVERT: E 58 MET cc_start: 0.7430 (mmt) cc_final: 0.6996 (mmt) REVERT: E 101 MET cc_start: 0.7372 (tpp) cc_final: 0.7081 (tpp) REVERT: F 26 ASP cc_start: 0.7632 (m-30) cc_final: 0.7362 (m-30) REVERT: F 32 MET cc_start: 0.7211 (tmm) cc_final: 0.6725 (tmm) REVERT: F 117 ASP cc_start: 0.7850 (p0) cc_final: 0.7523 (p0) REVERT: F 131 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7645 (p) REVERT: F 165 SER cc_start: 0.8472 (m) cc_final: 0.7997 (p) REVERT: G 64 ASP cc_start: 0.7498 (t70) cc_final: 0.6909 (t70) REVERT: I 32 MET cc_start: 0.7175 (tmm) cc_final: 0.6607 (tmm) REVERT: I 91 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8250 (mp) REVERT: I 101 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8022 (p) REVERT: I 113 LYS cc_start: 0.6321 (mmtm) cc_final: 0.5359 (tttp) REVERT: I 165 SER cc_start: 0.8399 (m) cc_final: 0.8031 (p) REVERT: K 12 TYR cc_start: 0.7073 (m-10) cc_final: 0.6470 (m-10) REVERT: K 32 MET cc_start: 0.7878 (tmm) cc_final: 0.7342 (tmm) REVERT: K 114 TYR cc_start: 0.8358 (t80) cc_final: 0.7914 (t80) REVERT: K 126 SER cc_start: 0.8386 (t) cc_final: 0.8020 (p) REVERT: K 140 VAL cc_start: 0.7385 (t) cc_final: 0.7120 (p) REVERT: K 165 SER cc_start: 0.8670 (m) cc_final: 0.8392 (p) outliers start: 98 outliers final: 77 residues processed: 387 average time/residue: 0.1000 time to fit residues: 62.1797 Evaluate side-chains 409 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 326 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN I 79 ASN I 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.160009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135931 restraints weight = 21431.224| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.72 r_work: 0.3570 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15396 Z= 0.235 Angle : 0.776 10.661 20874 Z= 0.400 Chirality : 0.049 0.159 2346 Planarity : 0.005 0.074 2634 Dihedral : 7.136 59.514 2392 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer: Outliers : 5.93 % Allowed : 24.32 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.25 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.17 (0.18), residues: 786 loop : -2.73 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 163 TYR 0.020 0.002 TYR A 53 PHE 0.016 0.002 PHE A 185 TRP 0.013 0.001 TRP D 13 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00536 (15354) covalent geometry : angle 0.75915 (20778) SS BOND : bond 0.00660 ( 30) SS BOND : angle 2.48015 ( 60) hydrogen bonds : bond 0.04210 ( 439) hydrogen bonds : angle 4.96960 ( 1782) link_NAG-ASN : bond 0.00632 ( 12) link_NAG-ASN : angle 2.55760 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 331 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7502 (tmm) cc_final: 0.7135 (tmm) REVERT: A 117 ASP cc_start: 0.7674 (p0) cc_final: 0.7444 (p0) REVERT: B 32 MET cc_start: 0.7569 (tmm) cc_final: 0.6869 (tmm) REVERT: B 91 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8016 (mp) REVERT: B 101 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 126 SER cc_start: 0.8321 (t) cc_final: 0.7953 (p) REVERT: D 32 MET cc_start: 0.7626 (tmm) cc_final: 0.7398 (tmm) REVERT: D 85 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7269 (mt) REVERT: D 117 ASP cc_start: 0.7427 (p0) cc_final: 0.7043 (p0) REVERT: D 126 SER cc_start: 0.8119 (t) cc_final: 0.7750 (p) REVERT: E 58 MET cc_start: 0.7461 (mmt) cc_final: 0.6940 (mmt) REVERT: E 101 MET cc_start: 0.7356 (tpp) cc_final: 0.7066 (tpp) REVERT: F 26 ASP cc_start: 0.7675 (m-30) cc_final: 0.7428 (m-30) REVERT: F 32 MET cc_start: 0.7246 (tmm) cc_final: 0.6802 (tmm) REVERT: F 117 ASP cc_start: 0.7848 (p0) cc_final: 0.7486 (p0) REVERT: F 126 SER cc_start: 0.8325 (t) cc_final: 0.8120 (p) REVERT: F 165 SER cc_start: 0.8513 (m) cc_final: 0.8008 (p) REVERT: G 64 ASP cc_start: 0.7535 (t70) cc_final: 0.6932 (t70) REVERT: I 32 MET cc_start: 0.7199 (tmm) cc_final: 0.6629 (tmm) REVERT: I 91 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7986 (mp) REVERT: I 92 ASP cc_start: 0.7299 (t0) cc_final: 0.7007 (m-30) REVERT: I 101 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.7970 (p) REVERT: I 113 LYS cc_start: 0.6138 (mmtm) cc_final: 0.5343 (ttmm) REVERT: I 165 SER cc_start: 0.8402 (m) cc_final: 0.8011 (p) REVERT: K 32 MET cc_start: 0.7870 (tmm) cc_final: 0.7340 (tmm) REVERT: K 114 TYR cc_start: 0.8342 (t80) cc_final: 0.7933 (t80) REVERT: K 126 SER cc_start: 0.8384 (t) cc_final: 0.8047 (p) REVERT: K 140 VAL cc_start: 0.7407 (t) cc_final: 0.7134 (p) REVERT: K 165 SER cc_start: 0.8670 (m) cc_final: 0.8396 (p) REVERT: L 48 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7945 (mt-10) outliers start: 100 outliers final: 88 residues processed: 387 average time/residue: 0.0956 time to fit residues: 59.2440 Evaluate side-chains 418 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 325 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 103 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 174 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 89 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.162160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138091 restraints weight = 21312.670| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.74 r_work: 0.3600 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15396 Z= 0.169 Angle : 0.726 9.859 20874 Z= 0.370 Chirality : 0.047 0.143 2346 Planarity : 0.005 0.072 2634 Dihedral : 6.692 59.520 2392 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 5.63 % Allowed : 24.79 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.22 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.18 (0.18), residues: 786 loop : -2.69 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 163 TYR 0.015 0.001 TYR F 53 PHE 0.015 0.002 PHE F 185 TRP 0.010 0.001 TRP F 13 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00379 (15354) covalent geometry : angle 0.71220 (20778) SS BOND : bond 0.00513 ( 30) SS BOND : angle 2.07482 ( 60) hydrogen bonds : bond 0.03784 ( 439) hydrogen bonds : angle 4.82608 ( 1782) link_NAG-ASN : bond 0.00526 ( 12) link_NAG-ASN : angle 2.44906 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 324 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7495 (tmm) cc_final: 0.7126 (tmm) REVERT: A 117 ASP cc_start: 0.7569 (p0) cc_final: 0.7361 (p0) REVERT: B 32 MET cc_start: 0.7498 (tmm) cc_final: 0.6806 (tmm) REVERT: B 91 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8039 (mp) REVERT: B 101 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7849 (p) REVERT: B 126 SER cc_start: 0.8315 (t) cc_final: 0.7899 (p) REVERT: D 32 MET cc_start: 0.7631 (tmm) cc_final: 0.7420 (tmm) REVERT: D 85 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7344 (mt) REVERT: D 117 ASP cc_start: 0.7427 (p0) cc_final: 0.7050 (p0) REVERT: D 126 SER cc_start: 0.8149 (t) cc_final: 0.7779 (p) REVERT: D 164 ASN cc_start: 0.7872 (t0) cc_final: 0.7619 (t0) REVERT: D 165 SER cc_start: 0.8380 (m) cc_final: 0.8141 (p) REVERT: E 58 MET cc_start: 0.7489 (mmt) cc_final: 0.6943 (mmt) REVERT: E 101 MET cc_start: 0.7333 (tpp) cc_final: 0.7029 (tpp) REVERT: F 26 ASP cc_start: 0.7656 (m-30) cc_final: 0.7388 (m-30) REVERT: F 32 MET cc_start: 0.7215 (tmm) cc_final: 0.6836 (tmm) REVERT: F 117 ASP cc_start: 0.7819 (p0) cc_final: 0.7514 (p0) REVERT: F 131 THR cc_start: 0.8117 (m) cc_final: 0.7643 (p) REVERT: F 165 SER cc_start: 0.8476 (m) cc_final: 0.8007 (p) REVERT: G 64 ASP cc_start: 0.7555 (t70) cc_final: 0.6968 (t70) REVERT: I 32 MET cc_start: 0.7166 (tmm) cc_final: 0.6600 (tmm) REVERT: I 91 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8242 (mp) REVERT: I 101 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8017 (p) REVERT: I 113 LYS cc_start: 0.6307 (mmtm) cc_final: 0.5261 (ttmm) REVERT: I 165 SER cc_start: 0.8406 (m) cc_final: 0.7999 (p) REVERT: K 32 MET cc_start: 0.7898 (tmm) cc_final: 0.7345 (tmm) REVERT: K 73 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7289 (mt-10) REVERT: K 114 TYR cc_start: 0.8342 (t80) cc_final: 0.7930 (t80) REVERT: K 126 SER cc_start: 0.8383 (t) cc_final: 0.8038 (p) REVERT: K 140 VAL cc_start: 0.7400 (t) cc_final: 0.7136 (p) REVERT: K 165 SER cc_start: 0.8671 (m) cc_final: 0.8387 (p) REVERT: L 48 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7907 (mt-10) outliers start: 95 outliers final: 81 residues processed: 380 average time/residue: 0.0934 time to fit residues: 56.7971 Evaluate side-chains 404 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 318 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 0.0870 chunk 77 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 108 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN I 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140318 restraints weight = 21547.080| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.77 r_work: 0.3623 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15396 Z= 0.132 Angle : 0.686 9.890 20874 Z= 0.347 Chirality : 0.046 0.141 2346 Planarity : 0.005 0.065 2634 Dihedral : 6.131 57.883 2390 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 4.80 % Allowed : 25.74 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.18 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.20 (0.18), residues: 798 loop : -2.63 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 163 TYR 0.014 0.001 TYR K 25 PHE 0.013 0.001 PHE K 185 TRP 0.008 0.001 TRP F 13 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00288 (15354) covalent geometry : angle 0.67443 (20778) SS BOND : bond 0.00413 ( 30) SS BOND : angle 1.85142 ( 60) hydrogen bonds : bond 0.03478 ( 439) hydrogen bonds : angle 4.63925 ( 1782) link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 2.18193 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 314 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7554 (tmm) cc_final: 0.7219 (tmm) REVERT: B 32 MET cc_start: 0.7509 (tmm) cc_final: 0.6845 (tmm) REVERT: B 101 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 126 SER cc_start: 0.8306 (t) cc_final: 0.7887 (p) REVERT: D 32 MET cc_start: 0.7712 (tmm) cc_final: 0.7506 (tmm) REVERT: D 85 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7282 (mt) REVERT: D 117 ASP cc_start: 0.7416 (p0) cc_final: 0.7077 (p0) REVERT: D 165 SER cc_start: 0.8398 (m) cc_final: 0.8137 (p) REVERT: E 58 MET cc_start: 0.7501 (mmt) cc_final: 0.6923 (mmt) REVERT: E 101 MET cc_start: 0.7288 (tpp) cc_final: 0.6961 (tpp) REVERT: F 26 ASP cc_start: 0.7635 (m-30) cc_final: 0.7282 (m-30) REVERT: F 32 MET cc_start: 0.7298 (tmm) cc_final: 0.6937 (tmm) REVERT: F 117 ASP cc_start: 0.7769 (p0) cc_final: 0.7485 (p0) REVERT: F 131 THR cc_start: 0.8087 (m) cc_final: 0.7600 (p) REVERT: F 165 SER cc_start: 0.8460 (m) cc_final: 0.7976 (p) REVERT: G 64 ASP cc_start: 0.7580 (t70) cc_final: 0.6973 (t70) REVERT: I 32 MET cc_start: 0.7167 (tmm) cc_final: 0.6631 (tmm) REVERT: I 91 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8099 (mp) REVERT: I 92 ASP cc_start: 0.7287 (t0) cc_final: 0.6994 (m-30) REVERT: I 101 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7980 (p) REVERT: I 107 MET cc_start: 0.4553 (ptt) cc_final: 0.4187 (ptp) REVERT: I 113 LYS cc_start: 0.6195 (mmtm) cc_final: 0.5253 (tttp) REVERT: I 165 SER cc_start: 0.8405 (m) cc_final: 0.7991 (p) REVERT: K 32 MET cc_start: 0.7956 (tmm) cc_final: 0.7387 (tmm) REVERT: K 73 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7341 (mt-10) REVERT: K 103 THR cc_start: 0.8076 (m) cc_final: 0.7814 (t) REVERT: K 126 SER cc_start: 0.8335 (t) cc_final: 0.8000 (p) REVERT: K 140 VAL cc_start: 0.7408 (t) cc_final: 0.7147 (p) REVERT: K 165 SER cc_start: 0.8647 (m) cc_final: 0.8371 (p) outliers start: 81 outliers final: 64 residues processed: 362 average time/residue: 0.0876 time to fit residues: 51.2908 Evaluate side-chains 374 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 306 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 12 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN H 76 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN I 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141052 restraints weight = 21247.972| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.74 r_work: 0.3631 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15396 Z= 0.131 Angle : 0.687 10.298 20874 Z= 0.347 Chirality : 0.046 0.150 2346 Planarity : 0.004 0.063 2634 Dihedral : 5.955 56.936 2387 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 4.57 % Allowed : 26.04 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 aren not related in a simple way. whole: -2.14 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.19 (0.18), residues: 798 loop : -2.59 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 163 TYR 0.014 0.001 TYR K 25 PHE 0.013 0.001 PHE K 185 TRP 0.024 0.001 TRP B 13 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00286 (15354) covalent geometry : angle 0.67565 (20778) SS BOND : bond 0.00401 ( 30) SS BOND : angle 1.82242 ( 60) hydrogen bonds : bond 0.03469 ( 439) hydrogen bonds : angle 4.54863 ( 1782) link_NAG-ASN : bond 0.00445 ( 12) link_NAG-ASN : angle 2.18947 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.99 seconds wall clock time: 52 minutes 17.43 seconds (3137.43 seconds total)