Starting phenix.real_space_refine on Thu Mar 5 00:02:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxx_29547/03_2026/8fxx_29547_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxx_29547/03_2026/8fxx_29547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxx_29547/03_2026/8fxx_29547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxx_29547/03_2026/8fxx_29547.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxx_29547/03_2026/8fxx_29547_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxx_29547/03_2026/8fxx_29547_neut.cif" } resolution = 3.26 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= 0.002 sd= 0.026 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 161 5.16 5 C 11032 2.51 5 N 2912 2.21 5 O 3451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17556 Number of models: 1 Model: "" Number of chains: 21 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: "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: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Modifications used: {'COO': 1} 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: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Modifications used: {'COO': 1} 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: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Modifications used: {'COO': 1} 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: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Modifications used: {'COO': 1} 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: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "M" 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: "N" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Modifications used: {'COO': 1} 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 Chain: "M" 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: 4.25, per 1000 atoms: 0.24 Number of scatterers: 17556 At special positions: 0 Unit cell: (188.1, 184.8, 63.8, 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 161 16.00 O 3451 8.00 N 2912 7.00 C 11032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS M 109 " distance=2.01 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 196 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 136 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 136 " distance=2.02 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS F 4 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 136 " distance=2.02 Simple disulfide: pdb=" SG CYS F 109 " - pdb=" SG CYS I 4 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 85 " distance=2.04 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 104 " - pdb=" SG CYS I 136 " distance=2.02 Simple disulfide: pdb=" SG CYS I 109 " - pdb=" SG CYS K 4 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS K 35 " - pdb=" SG CYS K 196 " distance=2.02 Simple disulfide: pdb=" SG CYS K 104 " - pdb=" SG CYS K 136 " distance=2.02 Simple disulfide: pdb=" SG CYS K 109 " - pdb=" SG CYS M 4 " distance=1.92 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=2.04 Simple disulfide: pdb=" SG CYS M 35 " - pdb=" SG CYS M 196 " distance=2.02 Simple disulfide: pdb=" SG CYS M 104 " - pdb=" SG CYS M 136 " distance=2.03 Simple disulfide: pdb=" SG CYS M 139 " - pdb=" SG CYS M 184 " distance=2.04 Simple disulfide: pdb=" SG CYS N 15 " - pdb=" SG CYS N 85 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 " " NAG M 201 " - " ASN M 28 " " NAG M 203 " - " ASN M 58 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 806.7 milliseconds 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 40 sheets defined 5.9% alpha, 55.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 166 through 170 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: 3.966A 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: 3.984A 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: 3.985A pdb=" N LYS G 80 " --> pdb=" O ILE G 77 " (cutoff:3.500A) 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: 3.870A pdb=" N LYS H 80 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 170 removed outlier: 3.537A pdb=" N ARG I 170 " --> pdb=" O TYR I 167 " (cutoff:3.500A) 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: 3.864A pdb=" N LYS J 80 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 170 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: 3.852A pdb=" N LYS L 80 " --> pdb=" O ILE L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 170 Processing helix chain 'N' and resid 24 through 26 No H-bonds generated for 'chain 'N' and resid 24 through 26' Processing helix chain 'N' and resid 54 through 58 Processing helix chain 'N' and resid 76 through 80 removed outlier: 3.836A pdb=" N LYS N 80 " --> pdb=" O ILE N 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.612A pdb=" N ASP A 194 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N SER A 172 " --> pdb=" O HIS H 99 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N HIS H 99 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY A 174 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG H 97 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS H 89 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS H 99 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU H 1 " --> pdb=" O ASN H 102 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 106 " --> pdb=" O ILE H 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.612A pdb=" N ASP A 194 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N SER A 172 " --> pdb=" O HIS H 99 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N HIS H 99 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY A 174 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG H 97 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS H 89 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS H 99 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU H 28 " --> pdb=" O TYR H 44 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR H 44 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL H 30 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU H 42 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP H 32 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU H 42 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.581A pdb=" N ILE A 132 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.726A pdb=" N ASP B 194 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 73 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N SER B 172 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS C 99 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 174 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 1 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 106 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.726A pdb=" N ASP B 194 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 73 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N SER B 172 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS C 99 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 174 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG C 97 " --> pdb=" O HIS C 89 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS C 89 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS C 99 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 101 " --> pdb=" O CYS C 85 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU C 28 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR C 44 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 30 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 42 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP C 32 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU C 42 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 40 removed outlier: 3.558A pdb=" N MET B 62 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN B 97 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 98 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR B 131 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 100 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASN B 133 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 102 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 132 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 36 through 40 removed outlier: 3.558A pdb=" N MET B 62 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN B 97 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 98 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR B 131 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 100 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASN B 133 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 102 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 14 Processing sheet with id=AB3, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'D' and resid 194 through 195 removed outlier: 3.822A pdb=" N ASP D 194 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 73 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N SER D 172 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS E 99 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY D 174 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU E 1 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 106 " --> pdb=" O ILE E 3 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 194 through 195 removed outlier: 3.822A pdb=" N ASP D 194 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 73 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N SER D 172 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS E 99 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY D 174 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG E 97 " --> pdb=" O HIS E 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N HIS E 89 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS E 99 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU E 28 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TYR E 44 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL E 30 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU E 42 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP E 32 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU E 42 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 36 through 40 removed outlier: 6.924A pdb=" N ILE D 98 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N THR D 131 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 100 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN D 133 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 102 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE D 132 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 36 through 40 removed outlier: 6.924A pdb=" N ILE D 98 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N THR D 131 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 100 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN D 133 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 102 " --> pdb=" O ASN D 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AB9, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.802A pdb=" N ASP F 194 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 73 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N SER F 172 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS G 99 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY F 174 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU G 1 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER G 106 " --> pdb=" O ILE G 3 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.802A pdb=" N ASP F 194 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 73 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N SER F 172 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS G 99 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY F 174 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG G 97 " --> pdb=" O HIS G 89 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS G 89 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS G 99 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU G 28 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR G 44 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G 30 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU G 42 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP G 32 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU G 42 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 36 through 40 removed outlier: 6.484A pdb=" N ILE F 132 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 36 through 40 Processing sheet with id=AC4, first strand: chain 'G' and resid 11 through 14 Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 14 Processing sheet with id=AC6, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.685A pdb=" N ASP I 194 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU I 73 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N SER I 172 " --> pdb=" O HIS J 99 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS J 99 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY I 174 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU J 1 " --> pdb=" O ASN J 102 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER J 106 " --> pdb=" O ILE J 3 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.685A pdb=" N ASP I 194 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU I 73 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N SER I 172 " --> pdb=" O HIS J 99 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS J 99 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY I 174 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG J 97 " --> pdb=" O HIS J 89 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N HIS J 89 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS J 99 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET J 101 " --> pdb=" O CYS J 85 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU J 28 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR J 44 " --> pdb=" O LEU J 28 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL J 30 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU J 42 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP J 32 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU J 42 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 36 through 40 removed outlier: 6.953A pdb=" N ILE I 98 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR I 131 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 100 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ASN I 133 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE I 102 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE I 132 " --> pdb=" O LYS I 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 36 through 40 removed outlier: 6.953A pdb=" N ILE I 98 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR I 131 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 100 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ASN I 133 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE I 102 " --> pdb=" O ASN I 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 11 through 14 Processing sheet with id=AD2, first strand: chain 'K' and resid 13 through 14 Processing sheet with id=AD3, first strand: chain 'K' and resid 194 through 195 removed outlier: 3.712A pdb=" N ASP K 194 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU K 73 " --> pdb=" O ASP K 194 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N SER K 172 " --> pdb=" O HIS L 99 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS L 99 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY K 174 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU L 1 " --> pdb=" O ASN L 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER L 106 " --> pdb=" O ILE L 3 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 194 through 195 removed outlier: 3.712A pdb=" N ASP K 194 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU K 73 " --> pdb=" O ASP K 194 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N SER K 172 " --> pdb=" O HIS L 99 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS L 99 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY K 174 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG L 97 " --> pdb=" O HIS L 89 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS L 89 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS L 99 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU L 28 " --> pdb=" O TYR L 44 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR L 44 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL L 30 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU L 42 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TRP L 32 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU L 42 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.861A pdb=" N ILE K 98 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR K 131 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL K 100 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN K 133 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE K 102 " --> pdb=" O ASN K 133 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE K 132 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.861A pdb=" N ILE K 98 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR K 131 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL K 100 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN K 133 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE K 102 " --> pdb=" O ASN K 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 11 through 14 Processing sheet with id=AD8, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AD9, first strand: chain 'M' and resid 194 through 195 removed outlier: 3.612A pdb=" N ASP M 194 " --> pdb=" O GLU M 73 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N SER M 172 " --> pdb=" O HIS N 99 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS N 99 " --> pdb=" O SER M 172 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY M 174 " --> pdb=" O ARG N 97 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG N 97 " --> pdb=" O HIS N 89 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS N 89 " --> pdb=" O ARG N 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS N 99 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU N 1 " --> pdb=" O ASN N 102 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER N 106 " --> pdb=" O ILE N 3 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 194 through 195 removed outlier: 3.612A pdb=" N ASP M 194 " --> pdb=" O GLU M 73 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N SER M 172 " --> pdb=" O HIS N 99 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS N 99 " --> pdb=" O SER M 172 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY M 174 " --> pdb=" O ARG N 97 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG N 97 " --> pdb=" O HIS N 89 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS N 89 " --> pdb=" O ARG N 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS N 99 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU N 28 " --> pdb=" O TYR N 44 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR N 44 " --> pdb=" O LEU N 28 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL N 30 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU N 42 " --> pdb=" O VAL N 30 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP N 32 " --> pdb=" O LEU N 40 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU N 42 " --> pdb=" O LYS N 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 36 through 40 removed outlier: 6.581A pdb=" N ILE M 132 " --> pdb=" O LYS M 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 36 through 40 Processing sheet with id=AE4, first strand: chain 'N' and resid 11 through 14 877 hydrogen bonds defined for protein. 2193 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: 3.00 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5682 1.34 - 1.47: 4359 1.47 - 1.59: 7634 1.59 - 1.71: 0 1.71 - 1.83: 245 Bond restraints: 17920 Sorted by residual: bond pdb=" N MET G 0 " pdb=" CA MET G 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N MET H 0 " pdb=" CA MET H 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET L 0 " pdb=" CA MET L 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET N 0 " pdb=" CA MET N 0 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET E 0 " pdb=" CA MET E 0 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 17915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 23541 1.72 - 3.43: 599 3.43 - 5.15: 93 5.15 - 6.87: 14 6.87 - 8.58: 8 Bond angle restraints: 24255 Sorted by residual: angle pdb=" C LEU D 154 " pdb=" N HIS D 155 " pdb=" CA HIS D 155 " ideal model delta sigma weight residual 121.70 130.28 -8.58 1.80e+00 3.09e-01 2.27e+01 angle pdb=" C LEU A 154 " pdb=" N HIS A 155 " pdb=" CA HIS A 155 " ideal model delta sigma weight residual 121.70 130.10 -8.40 1.80e+00 3.09e-01 2.18e+01 angle pdb=" C LEU M 154 " pdb=" N HIS M 155 " pdb=" CA HIS M 155 " ideal model delta sigma weight residual 121.70 130.08 -8.38 1.80e+00 3.09e-01 2.17e+01 angle pdb=" C LEU B 154 " pdb=" N HIS B 155 " pdb=" CA HIS B 155 " ideal model delta sigma weight residual 121.70 129.90 -8.20 1.80e+00 3.09e-01 2.07e+01 angle pdb=" C LEU F 154 " pdb=" N HIS F 155 " pdb=" CA HIS F 155 " ideal model delta sigma weight residual 121.70 129.87 -8.17 1.80e+00 3.09e-01 2.06e+01 ... (remaining 24250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 10134 15.03 - 30.06: 716 30.06 - 45.08: 156 45.08 - 60.11: 99 60.11 - 75.14: 4 Dihedral angle restraints: 11109 sinusoidal: 4781 harmonic: 6328 Sorted by residual: dihedral pdb=" CB CYS G 15 " pdb=" SG CYS G 15 " pdb=" SG CYS G 85 " pdb=" CB CYS G 85 " ideal model delta sinusoidal sigma weight residual -86.00 -29.09 -56.91 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS J 15 " pdb=" SG CYS J 15 " pdb=" SG CYS J 85 " pdb=" CB CYS J 85 " ideal model delta sinusoidal sigma weight residual -86.00 -30.36 -55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS N 15 " pdb=" SG CYS N 15 " pdb=" SG CYS N 85 " pdb=" CB CYS N 85 " ideal model delta sinusoidal sigma weight residual -86.00 -30.71 -55.29 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 11106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2173 0.054 - 0.107: 474 0.107 - 0.161: 83 0.161 - 0.214: 0 0.214 - 0.268: 7 Chirality restraints: 2737 Sorted by residual: chirality pdb=" C1 NAG F 201 " pdb=" ND2 ASN F 28 " pdb=" C2 NAG F 201 " pdb=" O5 NAG F 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG M 201 " pdb=" ND2 ASN M 28 " pdb=" C2 NAG M 201 " pdb=" O5 NAG M 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 28 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2734 not shown) Planarity restraints: 3094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS M 4 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO M 5 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO M 5 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO M 5 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 4 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 5 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS K 4 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO K 5 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO K 5 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 5 " -0.035 5.00e-02 4.00e+02 ... (remaining 3091 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 379 2.64 - 3.21: 16692 3.21 - 3.77: 23735 3.77 - 4.34: 34403 4.34 - 4.90: 57577 Nonbonded interactions: 132786 Sorted by model distance: nonbonded pdb=" NZ LYS A 80 " pdb=" O CYS A 184 " model vdw 2.081 3.120 nonbonded pdb=" NZ LYS M 80 " pdb=" O CYS M 184 " model vdw 2.081 3.120 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLU L 27 " model vdw 2.081 3.040 nonbonded pdb=" OG SER N 26 " pdb=" OE1 GLU N 27 " model vdw 2.086 3.040 nonbonded pdb=" OG SER E 20 " pdb=" OE1 GLN E 21 " model vdw 2.087 3.040 ... (remaining 132781 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' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.880 Find NCS groups from input model: 0.300 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 : 0.005 0.115 17969 Z= 0.246 Angle : 0.713 8.584 24367 Z= 0.393 Chirality : 0.047 0.268 2737 Planarity : 0.004 0.072 3080 Dihedral : 11.926 59.820 6930 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 4.02 % Allowed : 8.39 % Favored : 87.60 % 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 are not related in a simple way. whole: -2.44 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: -0.11 (0.17), residues: 875 loop : -2.95 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 11 TYR 0.020 0.002 TYR K 53 PHE 0.017 0.002 PHE M 185 TRP 0.007 0.002 TRP K 13 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00516 (17920) covalent geometry : angle 0.70224 (24255) SS BOND : bond 0.02078 ( 35) SS BOND : angle 1.64460 ( 70) hydrogen bonds : bond 0.13682 ( 552) hydrogen bonds : angle 6.33174 ( 2193) link_NAG-ASN : bond 0.00360 ( 14) link_NAG-ASN : angle 2.39828 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 465 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7533 (tmm) cc_final: 0.7201 (tmm) REVERT: A 38 SER cc_start: 0.8513 (m) cc_final: 0.8098 (p) REVERT: A 51 THR cc_start: 0.8501 (t) cc_final: 0.8281 (p) REVERT: A 55 LEU cc_start: 0.7311 (pp) cc_final: 0.6914 (pp) REVERT: A 82 SER cc_start: 0.8609 (p) cc_final: 0.8257 (t) REVERT: A 115 ASP cc_start: 0.7177 (t0) cc_final: 0.6676 (t0) REVERT: A 130 ILE cc_start: 0.8077 (mt) cc_final: 0.7736 (tt) REVERT: A 135 SER cc_start: 0.8956 (m) cc_final: 0.8257 (t) REVERT: A 159 LYS cc_start: 0.8240 (mmtm) cc_final: 0.8032 (mmtp) REVERT: A 180 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.4037 (pp20) REVERT: B 23 VAL cc_start: 0.7632 (p) cc_final: 0.7368 (m) REVERT: B 32 MET cc_start: 0.7589 (tmm) cc_final: 0.6966 (tmm) REVERT: B 38 SER cc_start: 0.8598 (m) cc_final: 0.8186 (p) REVERT: B 51 THR cc_start: 0.8531 (t) cc_final: 0.8238 (p) REVERT: B 55 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7206 (pt) REVERT: B 140 VAL cc_start: 0.7916 (t) cc_final: 0.7684 (p) REVERT: B 165 SER cc_start: 0.8294 (m) cc_final: 0.8068 (t) REVERT: B 180 GLU cc_start: 0.4737 (OUTLIER) cc_final: 0.4372 (pp20) REVERT: D 38 SER cc_start: 0.8478 (m) cc_final: 0.8191 (p) REVERT: D 55 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7168 (pt) REVERT: D 99 SER cc_start: 0.8548 (m) cc_final: 0.8338 (m) REVERT: D 107 MET cc_start: 0.6517 (tpt) cc_final: 0.6077 (mmm) REVERT: D 115 ASP cc_start: 0.7394 (t0) cc_final: 0.6907 (t0) REVERT: D 180 GLU cc_start: 0.4579 (OUTLIER) cc_final: 0.4344 (pp20) REVERT: F 19 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6810 (pt) REVERT: F 23 VAL cc_start: 0.7886 (p) cc_final: 0.7426 (m) REVERT: F 32 MET cc_start: 0.7698 (tmm) cc_final: 0.7166 (tmm) REVERT: F 38 SER cc_start: 0.8570 (m) cc_final: 0.8084 (p) REVERT: F 55 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7309 (pp) REVERT: F 82 SER cc_start: 0.8646 (p) cc_final: 0.8424 (t) REVERT: F 89 GLN cc_start: 0.7582 (tt0) cc_final: 0.7289 (tt0) REVERT: F 100 VAL cc_start: 0.8469 (p) cc_final: 0.8243 (t) REVERT: F 101 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7929 (m) REVERT: F 180 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.4237 (pp20) REVERT: G 57 TYR cc_start: 0.7232 (m-10) cc_final: 0.6974 (m-10) REVERT: G 74 ASN cc_start: 0.7931 (t0) cc_final: 0.7696 (t0) REVERT: H 0 MET cc_start: 0.5723 (mmt) cc_final: 0.5325 (mmp) REVERT: I 32 MET cc_start: 0.7528 (tmm) cc_final: 0.7053 (tmm) REVERT: I 38 SER cc_start: 0.8608 (m) cc_final: 0.8156 (p) REVERT: I 73 GLU cc_start: 0.6125 (pm20) cc_final: 0.5908 (pm20) REVERT: I 81 LEU cc_start: 0.8604 (tp) cc_final: 0.8183 (tp) REVERT: I 85 LEU cc_start: 0.7762 (mt) cc_final: 0.7442 (mt) REVERT: I 97 ASN cc_start: 0.8608 (m110) cc_final: 0.8295 (m-40) REVERT: I 133 ASN cc_start: 0.8415 (m-40) cc_final: 0.8195 (m-40) REVERT: I 135 SER cc_start: 0.8949 (m) cc_final: 0.8245 (t) REVERT: J 58 MET cc_start: 0.7155 (mmt) cc_final: 0.6921 (mmt) REVERT: J 74 ASN cc_start: 0.7915 (t0) cc_final: 0.7708 (t0) REVERT: K 23 VAL cc_start: 0.8236 (p) cc_final: 0.7980 (m) REVERT: K 38 SER cc_start: 0.8523 (m) cc_final: 0.8089 (p) REVERT: K 41 TYR cc_start: 0.8461 (t80) cc_final: 0.8151 (t80) REVERT: K 55 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6999 (pp) REVERT: K 60 THR cc_start: 0.8380 (m) cc_final: 0.8178 (t) REVERT: K 99 SER cc_start: 0.8146 (m) cc_final: 0.7786 (m) REVERT: K 129 ASP cc_start: 0.6735 (p0) cc_final: 0.6443 (p0) REVERT: K 180 GLU cc_start: 0.4471 (OUTLIER) cc_final: 0.4196 (pp20) REVERT: L 74 ASN cc_start: 0.7936 (t0) cc_final: 0.7703 (t0) REVERT: M 32 MET cc_start: 0.7545 (tmm) cc_final: 0.7113 (tmm) REVERT: M 38 SER cc_start: 0.8449 (m) cc_final: 0.8132 (p) REVERT: M 51 THR cc_start: 0.8550 (t) cc_final: 0.8327 (p) REVERT: M 59 MET cc_start: 0.7882 (ttp) cc_final: 0.7649 (ttt) REVERT: M 99 SER cc_start: 0.8067 (m) cc_final: 0.7696 (m) REVERT: M 115 ASP cc_start: 0.7342 (t0) cc_final: 0.7056 (t0) REVERT: M 135 SER cc_start: 0.8877 (m) cc_final: 0.8362 (t) REVERT: M 180 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.4237 (pp20) outliers start: 79 outliers final: 36 residues processed: 536 average time/residue: 0.1058 time to fit residues: 90.6094 Evaluate side-chains 469 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 421 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 188 ILE 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 150 ASN Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 188 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 150 ASN Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 188 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.0770 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.0470 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN B 133 ASN B 150 ASN C 8 ASN C 102 ASN D 89 GLN D 97 ASN I 45 ASN J 8 ASN J 102 ASN K 89 GLN L 8 ASN L 102 ASN M 150 ASN N 102 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.175267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151510 restraints weight = 25660.846| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.40 r_work: 0.3792 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17969 Z= 0.138 Angle : 0.755 12.982 24367 Z= 0.390 Chirality : 0.047 0.195 2737 Planarity : 0.004 0.051 3080 Dihedral : 8.578 59.960 2860 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.47 % Allowed : 15.00 % Favored : 80.53 % 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 are not related in a simple way. whole: -2.10 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.22 (0.17), residues: 868 loop : -2.79 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 7 TYR 0.021 0.001 TYR F 25 PHE 0.020 0.001 PHE K 185 TRP 0.009 0.001 TRP A 13 HIS 0.003 0.001 HIS N 99 Details of bonding type rmsd covalent geometry : bond 0.00313 (17920) covalent geometry : angle 0.73595 (24255) SS BOND : bond 0.00460 ( 35) SS BOND : angle 2.77465 ( 70) hydrogen bonds : bond 0.03588 ( 552) hydrogen bonds : angle 4.78847 ( 2193) link_NAG-ASN : bond 0.00183 ( 14) link_NAG-ASN : angle 2.29719 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 432 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8232 (tmm) cc_final: 0.7911 (tmm) REVERT: A 38 SER cc_start: 0.8585 (m) cc_final: 0.8227 (p) REVERT: A 51 THR cc_start: 0.8414 (t) cc_final: 0.8180 (p) REVERT: A 78 ASP cc_start: 0.7721 (t0) cc_final: 0.7199 (t0) REVERT: A 113 LYS cc_start: 0.5839 (mmtm) cc_final: 0.4475 (tttp) REVERT: A 133 ASN cc_start: 0.8239 (m-40) cc_final: 0.7973 (m-40) REVERT: A 135 SER cc_start: 0.8945 (m) cc_final: 0.8400 (t) REVERT: A 180 GLU cc_start: 0.4789 (OUTLIER) cc_final: 0.4413 (pp20) REVERT: A 196 CYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5877 (t) REVERT: B 23 VAL cc_start: 0.7750 (p) cc_final: 0.7528 (m) REVERT: B 32 MET cc_start: 0.8024 (tmm) cc_final: 0.7397 (tmm) REVERT: B 38 SER cc_start: 0.8668 (m) cc_final: 0.8329 (p) REVERT: B 51 THR cc_start: 0.8472 (t) cc_final: 0.8208 (p) REVERT: B 55 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6949 (pp) REVERT: B 127 SER cc_start: 0.8288 (m) cc_final: 0.8039 (p) REVERT: B 140 VAL cc_start: 0.7950 (t) cc_final: 0.7598 (p) REVERT: B 180 GLU cc_start: 0.5106 (OUTLIER) cc_final: 0.4715 (pp20) REVERT: D 115 ASP cc_start: 0.7655 (t0) cc_final: 0.7070 (t0) REVERT: D 135 SER cc_start: 0.8951 (m) cc_final: 0.8242 (t) REVERT: D 180 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.4747 (pp20) REVERT: E 0 MET cc_start: 0.5730 (mmm) cc_final: 0.5404 (mmm) REVERT: E 86 ILE cc_start: 0.8481 (mm) cc_final: 0.8279 (mt) REVERT: F 23 VAL cc_start: 0.7723 (p) cc_final: 0.7397 (m) REVERT: F 32 MET cc_start: 0.8252 (tmm) cc_final: 0.7685 (tmm) REVERT: F 38 SER cc_start: 0.8578 (m) cc_final: 0.8311 (p) REVERT: F 55 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7021 (pp) REVERT: F 100 VAL cc_start: 0.8526 (p) cc_final: 0.8252 (t) REVERT: F 107 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5961 (ttm) REVERT: F 180 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4516 (pp20) REVERT: F 187 ASP cc_start: 0.8031 (t0) cc_final: 0.7830 (t0) REVERT: G 74 ASN cc_start: 0.7906 (t0) cc_final: 0.7575 (t0) REVERT: I 32 MET cc_start: 0.8072 (tmm) cc_final: 0.7542 (tmm) REVERT: I 37 MET cc_start: 0.8586 (ptm) cc_final: 0.8276 (ptm) REVERT: I 38 SER cc_start: 0.8561 (m) cc_final: 0.8220 (p) REVERT: I 41 TYR cc_start: 0.8212 (t80) cc_final: 0.7909 (t80) REVERT: I 135 SER cc_start: 0.8863 (m) cc_final: 0.8368 (t) REVERT: J 58 MET cc_start: 0.7380 (mmt) cc_final: 0.7060 (mmt) REVERT: J 74 ASN cc_start: 0.7853 (t0) cc_final: 0.7547 (t0) REVERT: K 38 SER cc_start: 0.8664 (m) cc_final: 0.8339 (p) REVERT: K 55 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7171 (pp) REVERT: K 99 SER cc_start: 0.8119 (m) cc_final: 0.7867 (m) REVERT: K 115 ASP cc_start: 0.7820 (t0) cc_final: 0.7387 (t0) REVERT: K 180 GLU cc_start: 0.4698 (OUTLIER) cc_final: 0.4386 (pp20) REVERT: L 8 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6413 (t0) REVERT: L 74 ASN cc_start: 0.7896 (t0) cc_final: 0.7578 (t0) REVERT: M 32 MET cc_start: 0.8128 (tmm) cc_final: 0.7764 (tmm) REVERT: M 38 SER cc_start: 0.8557 (m) cc_final: 0.8321 (p) REVERT: M 115 ASP cc_start: 0.7632 (t0) cc_final: 0.7361 (t0) REVERT: M 135 SER cc_start: 0.8901 (m) cc_final: 0.8470 (t) REVERT: M 164 ASN cc_start: 0.8279 (t0) cc_final: 0.8057 (t0) REVERT: M 180 GLU cc_start: 0.5258 (OUTLIER) cc_final: 0.4935 (pp20) outliers start: 88 outliers final: 39 residues processed: 490 average time/residue: 0.1067 time to fit residues: 83.3827 Evaluate side-chains 454 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 403 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 186 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN D 89 GLN F 79 ASN I 150 ASN K 89 GLN M 133 ASN N 8 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.176571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.151687 restraints weight = 25692.950| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.50 r_work: 0.3772 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17969 Z= 0.137 Angle : 0.697 10.648 24367 Z= 0.361 Chirality : 0.046 0.190 2737 Planarity : 0.004 0.050 3080 Dihedral : 7.260 59.868 2819 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.47 % Allowed : 18.10 % Favored : 77.43 % 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 are not related in a simple way. whole: -1.90 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.40 (0.17), residues: 868 loop : -2.69 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.016 0.001 TYR K 53 PHE 0.021 0.001 PHE A 185 TRP 0.006 0.001 TRP K 13 HIS 0.003 0.001 HIS J 99 Details of bonding type rmsd covalent geometry : bond 0.00312 (17920) covalent geometry : angle 0.68069 (24255) SS BOND : bond 0.00466 ( 35) SS BOND : angle 2.35946 ( 70) hydrogen bonds : bond 0.03439 ( 552) hydrogen bonds : angle 4.65153 ( 2193) link_NAG-ASN : bond 0.00134 ( 14) link_NAG-ASN : angle 2.16311 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 409 time to evaluate : 0.552 Fit side-chains REVERT: A 11 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6420 (mpt180) REVERT: A 32 MET cc_start: 0.7755 (tmm) cc_final: 0.7484 (tmm) REVERT: A 38 SER cc_start: 0.8484 (m) cc_final: 0.8089 (p) REVERT: A 51 THR cc_start: 0.8396 (t) cc_final: 0.8155 (p) REVERT: A 55 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6977 (pp) REVERT: A 113 LYS cc_start: 0.5770 (mmtm) cc_final: 0.4637 (tttp) REVERT: A 135 SER cc_start: 0.8927 (m) cc_final: 0.8429 (t) REVERT: A 180 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.4169 (pp20) REVERT: A 196 CYS cc_start: 0.5826 (OUTLIER) cc_final: 0.5498 (t) REVERT: B 32 MET cc_start: 0.7540 (tmm) cc_final: 0.6958 (tmm) REVERT: B 38 SER cc_start: 0.8430 (m) cc_final: 0.8165 (p) REVERT: B 51 THR cc_start: 0.8419 (t) cc_final: 0.8160 (p) REVERT: B 127 SER cc_start: 0.8260 (m) cc_final: 0.8017 (p) REVERT: B 140 VAL cc_start: 0.7892 (t) cc_final: 0.7606 (p) REVERT: B 180 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.4767 (pp20) REVERT: B 196 CYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6192 (t) REVERT: C 8 ASN cc_start: 0.6803 (t0) cc_final: 0.6600 (m-40) REVERT: D 7 ARG cc_start: 0.5690 (tpt170) cc_final: 0.5456 (tpt170) REVERT: D 32 MET cc_start: 0.7573 (tmm) cc_final: 0.7109 (tmm) REVERT: D 115 ASP cc_start: 0.7434 (t0) cc_final: 0.6867 (t0) REVERT: D 180 GLU cc_start: 0.4942 (OUTLIER) cc_final: 0.4672 (pp20) REVERT: E 0 MET cc_start: 0.5735 (mmm) cc_final: 0.5350 (mmm) REVERT: F 23 VAL cc_start: 0.7683 (p) cc_final: 0.7417 (m) REVERT: F 32 MET cc_start: 0.8038 (tmm) cc_final: 0.7506 (tmm) REVERT: F 38 SER cc_start: 0.8377 (m) cc_final: 0.8095 (p) REVERT: F 83 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7927 (p) REVERT: F 100 VAL cc_start: 0.8413 (p) cc_final: 0.8185 (t) REVERT: F 150 ASN cc_start: 0.5222 (OUTLIER) cc_final: 0.5002 (m-40) REVERT: F 180 GLU cc_start: 0.4862 (OUTLIER) cc_final: 0.4493 (pp20) REVERT: F 187 ASP cc_start: 0.7919 (t0) cc_final: 0.7703 (t0) REVERT: G 74 ASN cc_start: 0.7739 (t0) cc_final: 0.7441 (t0) REVERT: I 20 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.7960 (p) REVERT: I 26 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: I 32 MET cc_start: 0.7819 (tmm) cc_final: 0.7323 (tmm) REVERT: I 37 MET cc_start: 0.8447 (ptm) cc_final: 0.8165 (ptm) REVERT: I 38 SER cc_start: 0.8456 (m) cc_final: 0.8119 (p) REVERT: I 81 LEU cc_start: 0.8376 (tp) cc_final: 0.7985 (tp) REVERT: I 96 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7936 (m-70) REVERT: I 106 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6684 (mt-10) REVERT: I 112 THR cc_start: 0.8035 (m) cc_final: 0.7810 (p) REVERT: I 135 SER cc_start: 0.8996 (m) cc_final: 0.8410 (t) REVERT: I 180 GLU cc_start: 0.5014 (OUTLIER) cc_final: 0.4695 (pp20) REVERT: J 58 MET cc_start: 0.7143 (mmt) cc_final: 0.6853 (mmt) REVERT: J 74 ASN cc_start: 0.7786 (t0) cc_final: 0.7491 (t0) REVERT: K 4 CYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5497 (p) REVERT: K 38 SER cc_start: 0.8462 (m) cc_final: 0.8201 (p) REVERT: K 51 THR cc_start: 0.8113 (t) cc_final: 0.7842 (p) REVERT: K 115 ASP cc_start: 0.7507 (t0) cc_final: 0.7113 (t0) REVERT: K 129 ASP cc_start: 0.7167 (p0) cc_final: 0.6927 (p0) REVERT: K 180 GLU cc_start: 0.4851 (OUTLIER) cc_final: 0.4638 (pp20) REVERT: L 74 ASN cc_start: 0.7771 (t0) cc_final: 0.7482 (t0) REVERT: M 32 MET cc_start: 0.7723 (tmm) cc_final: 0.7348 (tmm) REVERT: M 38 SER cc_start: 0.8416 (m) cc_final: 0.8158 (p) REVERT: M 56 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: M 96 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8186 (m-70) REVERT: M 115 ASP cc_start: 0.7429 (t0) cc_final: 0.7184 (t0) REVERT: M 135 SER cc_start: 0.8911 (m) cc_final: 0.8482 (t) REVERT: M 180 GLU cc_start: 0.5290 (OUTLIER) cc_final: 0.4965 (pp20) REVERT: N 74 ASN cc_start: 0.7629 (t0) cc_final: 0.7273 (t0) outliers start: 88 outliers final: 53 residues processed: 467 average time/residue: 0.1077 time to fit residues: 79.4082 Evaluate side-chains 456 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 384 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 GLU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN F 79 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN N 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.177365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.153007 restraints weight = 25561.911| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.41 r_work: 0.3823 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17969 Z= 0.132 Angle : 0.677 9.840 24367 Z= 0.351 Chirality : 0.046 0.201 2737 Planarity : 0.004 0.049 3080 Dihedral : 6.884 59.680 2808 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 5.44 % Allowed : 19.01 % Favored : 75.55 % 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 are not related in a simple way. whole: -1.79 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.47 (0.17), residues: 868 loop : -2.61 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 44 TYR 0.017 0.001 TYR K 53 PHE 0.018 0.001 PHE A 185 TRP 0.011 0.001 TRP M 13 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00298 (17920) covalent geometry : angle 0.66210 (24255) SS BOND : bond 0.00476 ( 35) SS BOND : angle 2.15136 ( 70) hydrogen bonds : bond 0.03365 ( 552) hydrogen bonds : angle 4.55550 ( 2193) link_NAG-ASN : bond 0.00129 ( 14) link_NAG-ASN : angle 2.19963 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 404 time to evaluate : 0.604 Fit side-chains REVERT: A 11 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6511 (mpt180) REVERT: A 32 MET cc_start: 0.8064 (tmm) cc_final: 0.7807 (tmm) REVERT: A 38 SER cc_start: 0.8568 (m) cc_final: 0.8221 (p) REVERT: A 51 THR cc_start: 0.8383 (t) cc_final: 0.8158 (p) REVERT: A 55 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7083 (pp) REVERT: A 91 LEU cc_start: 0.8295 (mm) cc_final: 0.8063 (mt) REVERT: A 113 LYS cc_start: 0.5929 (mmtm) cc_final: 0.4603 (tttp) REVERT: A 135 SER cc_start: 0.8926 (m) cc_final: 0.8445 (t) REVERT: A 180 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.4422 (pp20) REVERT: A 196 CYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5893 (t) REVERT: B 32 MET cc_start: 0.7844 (tmm) cc_final: 0.7490 (tmm) REVERT: B 38 SER cc_start: 0.8520 (m) cc_final: 0.8243 (p) REVERT: B 51 THR cc_start: 0.8482 (t) cc_final: 0.8226 (p) REVERT: B 99 SER cc_start: 0.8529 (m) cc_final: 0.8046 (t) REVERT: B 127 SER cc_start: 0.8320 (m) cc_final: 0.8069 (p) REVERT: B 140 VAL cc_start: 0.8017 (t) cc_final: 0.7773 (p) REVERT: B 180 GLU cc_start: 0.5113 (OUTLIER) cc_final: 0.4825 (pp20) REVERT: B 196 CYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6646 (t) REVERT: C 8 ASN cc_start: 0.6890 (t0) cc_final: 0.6688 (m-40) REVERT: D 7 ARG cc_start: 0.5862 (tpt170) cc_final: 0.5606 (tpt170) REVERT: D 32 MET cc_start: 0.8006 (tmm) cc_final: 0.7546 (tmm) REVERT: D 115 ASP cc_start: 0.7611 (t0) cc_final: 0.7178 (t0) REVERT: E 0 MET cc_start: 0.5691 (mmm) cc_final: 0.5439 (mmm) REVERT: F 23 VAL cc_start: 0.7841 (p) cc_final: 0.7518 (m) REVERT: F 32 MET cc_start: 0.8352 (tmm) cc_final: 0.7801 (tmm) REVERT: F 38 SER cc_start: 0.8423 (m) cc_final: 0.8162 (p) REVERT: F 41 TYR cc_start: 0.8207 (t80) cc_final: 0.7960 (t80) REVERT: F 50 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7431 (pt) REVERT: F 83 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8061 (p) REVERT: F 96 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.8298 (m-70) REVERT: F 180 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.4752 (pp20) REVERT: G 74 ASN cc_start: 0.7816 (t0) cc_final: 0.7549 (t0) REVERT: I 11 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6571 (mpt180) REVERT: I 20 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8017 (p) REVERT: I 26 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: I 31 ILE cc_start: 0.8523 (mm) cc_final: 0.8261 (mm) REVERT: I 32 MET cc_start: 0.8261 (tmm) cc_final: 0.7732 (tmm) REVERT: I 37 MET cc_start: 0.8577 (ptm) cc_final: 0.8304 (ptm) REVERT: I 38 SER cc_start: 0.8635 (m) cc_final: 0.8280 (p) REVERT: I 51 THR cc_start: 0.8449 (t) cc_final: 0.8145 (p) REVERT: I 81 LEU cc_start: 0.8412 (tp) cc_final: 0.8026 (tp) REVERT: I 96 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.7917 (m-70) REVERT: I 105 MET cc_start: 0.8338 (mmt) cc_final: 0.8027 (mmp) REVERT: I 135 SER cc_start: 0.8961 (m) cc_final: 0.8415 (t) REVERT: I 180 GLU cc_start: 0.5085 (OUTLIER) cc_final: 0.4784 (pp20) REVERT: J 58 MET cc_start: 0.7246 (mmt) cc_final: 0.6997 (mmt) REVERT: J 74 ASN cc_start: 0.7788 (t0) cc_final: 0.7538 (t0) REVERT: K 14 TYR cc_start: 0.8242 (m-10) cc_final: 0.7990 (m-10) REVERT: K 26 ASP cc_start: 0.7844 (m-30) cc_final: 0.7637 (m-30) REVERT: K 38 SER cc_start: 0.8508 (m) cc_final: 0.8240 (p) REVERT: K 55 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7376 (pp) REVERT: K 115 ASP cc_start: 0.7769 (t0) cc_final: 0.7420 (t0) REVERT: K 180 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4779 (pp20) REVERT: L 57 TYR cc_start: 0.7315 (m-10) cc_final: 0.6961 (m-80) REVERT: L 74 ASN cc_start: 0.7821 (t0) cc_final: 0.7572 (t0) REVERT: M 32 MET cc_start: 0.8084 (tmm) cc_final: 0.7692 (tmm) REVERT: M 38 SER cc_start: 0.8444 (m) cc_final: 0.8229 (p) REVERT: M 115 ASP cc_start: 0.7651 (t0) cc_final: 0.7396 (t0) REVERT: M 135 SER cc_start: 0.8834 (m) cc_final: 0.8410 (t) REVERT: M 180 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.5150 (pp20) REVERT: N 8 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.5959 (m-40) REVERT: N 74 ASN cc_start: 0.7746 (t0) cc_final: 0.7391 (t0) outliers start: 107 outliers final: 63 residues processed: 477 average time/residue: 0.1077 time to fit residues: 80.9770 Evaluate side-chains 480 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 398 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 8 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 132 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 178 optimal weight: 0.2980 chunk 94 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 89 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.175123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.150751 restraints weight = 24991.244| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.33 r_work: 0.3785 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17969 Z= 0.143 Angle : 0.680 9.835 24367 Z= 0.353 Chirality : 0.046 0.158 2737 Planarity : 0.004 0.052 3080 Dihedral : 6.557 59.853 2799 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.54 % Allowed : 20.13 % Favored : 74.33 % 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 are not related in a simple way. whole: -1.76 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.47 (0.17), residues: 868 loop : -2.56 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 44 TYR 0.019 0.001 TYR K 53 PHE 0.017 0.001 PHE A 185 TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00322 (17920) covalent geometry : angle 0.66551 (24255) SS BOND : bond 0.00494 ( 35) SS BOND : angle 2.14103 ( 70) hydrogen bonds : bond 0.03441 ( 552) hydrogen bonds : angle 4.54639 ( 2193) link_NAG-ASN : bond 0.00117 ( 14) link_NAG-ASN : angle 2.15486 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 405 time to evaluate : 0.556 Fit side-chains REVERT: A 11 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6586 (mpt180) REVERT: A 32 MET cc_start: 0.8128 (tmm) cc_final: 0.7862 (tmm) REVERT: A 38 SER cc_start: 0.8445 (m) cc_final: 0.8149 (p) REVERT: A 51 THR cc_start: 0.8481 (t) cc_final: 0.8238 (p) REVERT: A 91 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 133 ASN cc_start: 0.8264 (m-40) cc_final: 0.7994 (m-40) REVERT: A 135 SER cc_start: 0.8911 (m) cc_final: 0.8469 (t) REVERT: A 180 GLU cc_start: 0.4684 (OUTLIER) cc_final: 0.4366 (pp20) REVERT: A 196 CYS cc_start: 0.6319 (OUTLIER) cc_final: 0.5915 (t) REVERT: B 32 MET cc_start: 0.7885 (tmm) cc_final: 0.7538 (tmm) REVERT: B 38 SER cc_start: 0.8527 (m) cc_final: 0.8248 (p) REVERT: B 51 THR cc_start: 0.8529 (t) cc_final: 0.8288 (p) REVERT: B 99 SER cc_start: 0.8517 (m) cc_final: 0.8077 (t) REVERT: B 127 SER cc_start: 0.8361 (m) cc_final: 0.8016 (p) REVERT: B 140 VAL cc_start: 0.7963 (t) cc_final: 0.7666 (p) REVERT: B 167 TYR cc_start: 0.8376 (t80) cc_final: 0.8166 (t80) REVERT: B 180 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.4686 (pp20) REVERT: B 196 CYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6664 (t) REVERT: D 7 ARG cc_start: 0.5795 (tpt170) cc_final: 0.5584 (tpt170) REVERT: D 32 MET cc_start: 0.8066 (tmm) cc_final: 0.7683 (tmm) REVERT: D 37 MET cc_start: 0.8408 (ttp) cc_final: 0.8166 (ptm) REVERT: D 115 ASP cc_start: 0.7618 (t0) cc_final: 0.7195 (t0) REVERT: E 0 MET cc_start: 0.5677 (mmm) cc_final: 0.5389 (mmm) REVERT: F 11 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6459 (mpt180) REVERT: F 32 MET cc_start: 0.8333 (tmm) cc_final: 0.7869 (tmm) REVERT: F 38 SER cc_start: 0.8494 (m) cc_final: 0.8179 (p) REVERT: F 41 TYR cc_start: 0.8229 (t80) cc_final: 0.8015 (t80) REVERT: F 50 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7559 (pt) REVERT: F 83 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.8002 (p) REVERT: F 95 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8209 (m170) REVERT: F 96 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8305 (m-70) REVERT: F 180 GLU cc_start: 0.5084 (OUTLIER) cc_final: 0.4713 (pp20) REVERT: G 74 ASN cc_start: 0.7779 (t0) cc_final: 0.7554 (t0) REVERT: I 11 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6711 (mpt180) REVERT: I 20 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8034 (p) REVERT: I 32 MET cc_start: 0.8250 (tmm) cc_final: 0.7773 (tmm) REVERT: I 37 MET cc_start: 0.8513 (ptm) cc_final: 0.8260 (ptm) REVERT: I 38 SER cc_start: 0.8568 (m) cc_final: 0.8224 (p) REVERT: I 51 THR cc_start: 0.8473 (t) cc_final: 0.8193 (p) REVERT: I 96 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7937 (m-70) REVERT: I 135 SER cc_start: 0.8971 (m) cc_final: 0.8446 (t) REVERT: J 58 MET cc_start: 0.7337 (mmt) cc_final: 0.7104 (mmt) REVERT: K 14 TYR cc_start: 0.8246 (m-10) cc_final: 0.8007 (m-10) REVERT: K 55 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7319 (pp) REVERT: K 91 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8076 (mp) REVERT: K 115 ASP cc_start: 0.7688 (t0) cc_final: 0.7352 (t0) REVERT: K 180 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.4780 (pp20) REVERT: L 57 TYR cc_start: 0.7353 (m-10) cc_final: 0.7009 (m-80) REVERT: M 32 MET cc_start: 0.8099 (tmm) cc_final: 0.7741 (tmm) REVERT: M 38 SER cc_start: 0.8484 (m) cc_final: 0.8231 (p) REVERT: M 115 ASP cc_start: 0.7629 (t0) cc_final: 0.7357 (t0) REVERT: M 135 SER cc_start: 0.8855 (m) cc_final: 0.8457 (t) REVERT: M 180 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.5210 (pp20) REVERT: N 8 ASN cc_start: 0.6850 (OUTLIER) cc_final: 0.6153 (m-40) REVERT: N 74 ASN cc_start: 0.7785 (t0) cc_final: 0.7496 (t0) outliers start: 109 outliers final: 70 residues processed: 477 average time/residue: 0.1060 time to fit residues: 79.4831 Evaluate side-chains 491 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 401 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 195 ILE Chi-restraints excluded: chain N residue 8 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 8 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 114 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 97 ASN D 89 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN F 96 HIS F 141 ASN ** F 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 97 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN M 141 ASN ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.170544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146261 restraints weight = 24856.503| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.29 r_work: 0.3727 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17969 Z= 0.227 Angle : 0.783 11.178 24367 Z= 0.410 Chirality : 0.050 0.199 2737 Planarity : 0.005 0.066 3080 Dihedral : 7.093 58.727 2797 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 6.10 % Allowed : 20.23 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.22 (0.17), residues: 882 loop : -2.62 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 11 TYR 0.026 0.002 TYR A 53 PHE 0.019 0.002 PHE A 185 TRP 0.008 0.002 TRP J 68 HIS 0.006 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00519 (17920) covalent geometry : angle 0.76725 (24255) SS BOND : bond 0.00726 ( 35) SS BOND : angle 2.50722 ( 70) hydrogen bonds : bond 0.04033 ( 552) hydrogen bonds : angle 4.83197 ( 2193) link_NAG-ASN : bond 0.00272 ( 14) link_NAG-ASN : angle 2.31179 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 397 time to evaluate : 0.692 Fit side-chains REVERT: A 11 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6835 (mpt180) REVERT: A 32 MET cc_start: 0.8158 (tmm) cc_final: 0.7891 (tmm) REVERT: A 38 SER cc_start: 0.8508 (m) cc_final: 0.8224 (p) REVERT: A 51 THR cc_start: 0.8550 (t) cc_final: 0.8318 (p) REVERT: A 91 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 133 ASN cc_start: 0.8295 (m-40) cc_final: 0.8064 (m-40) REVERT: A 135 SER cc_start: 0.8909 (m) cc_final: 0.8490 (t) REVERT: A 180 GLU cc_start: 0.4626 (OUTLIER) cc_final: 0.4314 (pp20) REVERT: A 196 CYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5882 (t) REVERT: B 11 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6822 (mpt180) REVERT: B 32 MET cc_start: 0.7967 (tmm) cc_final: 0.7646 (tmm) REVERT: B 38 SER cc_start: 0.8509 (m) cc_final: 0.8227 (p) REVERT: B 51 THR cc_start: 0.8609 (t) cc_final: 0.8374 (p) REVERT: B 99 SER cc_start: 0.8485 (m) cc_final: 0.8112 (t) REVERT: B 140 VAL cc_start: 0.8031 (t) cc_final: 0.7763 (p) REVERT: B 167 TYR cc_start: 0.8430 (t80) cc_final: 0.8165 (t80) REVERT: B 180 GLU cc_start: 0.5016 (OUTLIER) cc_final: 0.4708 (pp20) REVERT: B 196 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6646 (t) REVERT: D 11 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6961 (mpt180) REVERT: D 32 MET cc_start: 0.8070 (tmm) cc_final: 0.7677 (tmm) REVERT: D 37 MET cc_start: 0.8502 (ttp) cc_final: 0.8192 (ptm) REVERT: D 115 ASP cc_start: 0.7667 (t0) cc_final: 0.7071 (t0) REVERT: E 0 MET cc_start: 0.5637 (mmm) cc_final: 0.5301 (mmm) REVERT: F 11 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6955 (mpt180) REVERT: F 23 VAL cc_start: 0.8011 (p) cc_final: 0.7630 (m) REVERT: F 32 MET cc_start: 0.8456 (tmm) cc_final: 0.7929 (tmm) REVERT: F 38 SER cc_start: 0.8381 (m) cc_final: 0.8120 (p) REVERT: F 50 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7457 (mp) REVERT: F 83 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.8010 (p) REVERT: F 95 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8328 (m170) REVERT: F 100 VAL cc_start: 0.8469 (p) cc_final: 0.8265 (t) REVERT: G 74 ASN cc_start: 0.7860 (t0) cc_final: 0.7643 (t0) REVERT: I 20 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8075 (p) REVERT: I 32 MET cc_start: 0.8198 (tmm) cc_final: 0.7785 (tmm) REVERT: I 38 SER cc_start: 0.8546 (m) cc_final: 0.8198 (p) REVERT: I 96 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7862 (m-70) REVERT: I 135 SER cc_start: 0.8956 (m) cc_final: 0.8437 (t) REVERT: I 160 TYR cc_start: 0.7968 (m-10) cc_final: 0.7666 (m-80) REVERT: J 58 MET cc_start: 0.7421 (mmt) cc_final: 0.7204 (mmt) REVERT: K 14 TYR cc_start: 0.8318 (m-10) cc_final: 0.7951 (m-10) REVERT: K 55 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7314 (pp) REVERT: K 115 ASP cc_start: 0.7827 (t0) cc_final: 0.7484 (t0) REVERT: M 32 MET cc_start: 0.8176 (tmm) cc_final: 0.7813 (tmm) REVERT: M 38 SER cc_start: 0.8500 (m) cc_final: 0.8263 (p) REVERT: M 92 ASP cc_start: 0.7061 (t0) cc_final: 0.6858 (t0) REVERT: M 115 ASP cc_start: 0.7539 (t0) cc_final: 0.7250 (t0) REVERT: M 135 SER cc_start: 0.8917 (m) cc_final: 0.8490 (t) REVERT: N 74 ASN cc_start: 0.7866 (t0) cc_final: 0.7666 (t0) outliers start: 120 outliers final: 83 residues processed: 478 average time/residue: 0.1166 time to fit residues: 86.6736 Evaluate side-chains 494 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 396 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER 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 83 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN D 89 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN K 89 GLN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.172354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148396 restraints weight = 25158.512| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.30 r_work: 0.3754 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17969 Z= 0.174 Angle : 0.736 10.205 24367 Z= 0.383 Chirality : 0.047 0.167 2737 Planarity : 0.005 0.054 3080 Dihedral : 6.569 59.517 2788 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 5.74 % Allowed : 21.05 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.29 (0.17), residues: 868 loop : -2.59 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 11 TYR 0.021 0.001 TYR A 53 PHE 0.015 0.001 PHE A 185 TRP 0.007 0.001 TRP N 68 HIS 0.005 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00397 (17920) covalent geometry : angle 0.72223 (24255) SS BOND : bond 0.00601 ( 35) SS BOND : angle 2.28246 ( 70) hydrogen bonds : bond 0.03623 ( 552) hydrogen bonds : angle 4.63214 ( 2193) link_NAG-ASN : bond 0.00182 ( 14) link_NAG-ASN : angle 2.18349 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 391 time to evaluate : 0.630 Fit side-chains REVERT: A 11 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6685 (mpt180) REVERT: A 32 MET cc_start: 0.8125 (tmm) cc_final: 0.7876 (tmm) REVERT: A 38 SER cc_start: 0.8523 (m) cc_final: 0.8234 (p) REVERT: A 51 THR cc_start: 0.8539 (t) cc_final: 0.8332 (p) REVERT: A 55 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7134 (pp) REVERT: A 91 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 135 SER cc_start: 0.8886 (m) cc_final: 0.8510 (t) REVERT: A 180 GLU cc_start: 0.4690 (OUTLIER) cc_final: 0.4396 (pp20) REVERT: A 196 CYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5873 (t) REVERT: B 11 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6718 (mpt180) REVERT: B 32 MET cc_start: 0.8077 (tmm) cc_final: 0.7764 (tmm) REVERT: B 38 SER cc_start: 0.8489 (m) cc_final: 0.8251 (p) REVERT: B 51 THR cc_start: 0.8560 (t) cc_final: 0.8330 (p) REVERT: B 99 SER cc_start: 0.8466 (m) cc_final: 0.8116 (t) REVERT: B 127 SER cc_start: 0.8485 (m) cc_final: 0.7983 (p) REVERT: B 140 VAL cc_start: 0.7988 (t) cc_final: 0.7709 (p) REVERT: B 173 TYR cc_start: 0.8332 (m-80) cc_final: 0.7666 (m-80) REVERT: B 180 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.4758 (pp20) REVERT: B 196 CYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6463 (t) REVERT: D 32 MET cc_start: 0.8103 (tmm) cc_final: 0.7754 (tmm) REVERT: D 115 ASP cc_start: 0.7676 (t0) cc_final: 0.7108 (t0) REVERT: E 0 MET cc_start: 0.5842 (mmm) cc_final: 0.5480 (mmm) REVERT: F 11 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6666 (mpt180) REVERT: F 23 VAL cc_start: 0.7915 (p) cc_final: 0.7605 (m) REVERT: F 32 MET cc_start: 0.8498 (tmm) cc_final: 0.7962 (tmm) REVERT: F 38 SER cc_start: 0.8433 (m) cc_final: 0.8175 (p) REVERT: F 41 TYR cc_start: 0.8291 (t80) cc_final: 0.8059 (t80) REVERT: F 50 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7593 (pt) REVERT: F 95 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8335 (m170) REVERT: F 100 VAL cc_start: 0.8458 (p) cc_final: 0.8247 (t) REVERT: F 180 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.4645 (pp20) REVERT: G 74 ASN cc_start: 0.7815 (t0) cc_final: 0.7604 (t0) REVERT: I 20 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8054 (p) REVERT: I 32 MET cc_start: 0.8222 (tmm) cc_final: 0.7782 (tmm) REVERT: I 38 SER cc_start: 0.8543 (m) cc_final: 0.8216 (p) REVERT: I 41 TYR cc_start: 0.8139 (t80) cc_final: 0.7925 (t80) REVERT: I 66 GLN cc_start: 0.8565 (mt0) cc_final: 0.8358 (mt0) REVERT: I 96 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.7936 (m-70) REVERT: I 135 SER cc_start: 0.8977 (m) cc_final: 0.8463 (t) REVERT: J 58 MET cc_start: 0.7555 (mmt) cc_final: 0.7334 (mmt) REVERT: J 74 ASN cc_start: 0.7783 (t0) cc_final: 0.7499 (t0) REVERT: K 14 TYR cc_start: 0.8280 (m-10) cc_final: 0.7954 (m-10) REVERT: K 55 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7279 (pp) REVERT: K 115 ASP cc_start: 0.7835 (t0) cc_final: 0.7485 (t0) REVERT: M 32 MET cc_start: 0.8159 (tmm) cc_final: 0.7795 (tmm) REVERT: M 38 SER cc_start: 0.8535 (m) cc_final: 0.8279 (p) REVERT: M 115 ASP cc_start: 0.7505 (t0) cc_final: 0.7205 (t0) REVERT: M 135 SER cc_start: 0.8884 (m) cc_final: 0.8505 (t) REVERT: N 74 ASN cc_start: 0.7849 (t0) cc_final: 0.7615 (t0) outliers start: 113 outliers final: 87 residues processed: 468 average time/residue: 0.1128 time to fit residues: 82.3356 Evaluate side-chains 489 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 387 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 95 HIS Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 178 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 100 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** F 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN M 96 HIS ** M 150 ASN ** 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 = 0.4166 r_free = 0.4166 target = 0.175209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151427 restraints weight = 25158.731| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.36 r_work: 0.3779 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17969 Z= 0.133 Angle : 0.686 9.836 24367 Z= 0.356 Chirality : 0.045 0.152 2737 Planarity : 0.004 0.051 3080 Dihedral : 6.095 59.723 2788 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 4.83 % Allowed : 21.76 % Favored : 73.41 % 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 are not related in a simple way. whole: -1.83 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.31 (0.17), residues: 868 loop : -2.52 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.016 0.001 TYR K 53 PHE 0.015 0.001 PHE A 185 TRP 0.006 0.001 TRP F 13 HIS 0.005 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00298 (17920) covalent geometry : angle 0.67372 (24255) SS BOND : bond 0.00493 ( 35) SS BOND : angle 2.02487 ( 70) hydrogen bonds : bond 0.03280 ( 552) hydrogen bonds : angle 4.45866 ( 2193) link_NAG-ASN : bond 0.00131 ( 14) link_NAG-ASN : angle 2.08363 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 399 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6510 (mpt180) REVERT: A 32 MET cc_start: 0.8156 (tmm) cc_final: 0.7896 (tmm) REVERT: A 38 SER cc_start: 0.8516 (m) cc_final: 0.8202 (p) REVERT: A 51 THR cc_start: 0.8467 (t) cc_final: 0.8225 (p) REVERT: A 55 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7231 (pp) REVERT: A 135 SER cc_start: 0.8844 (m) cc_final: 0.8489 (t) REVERT: A 180 GLU cc_start: 0.4686 (OUTLIER) cc_final: 0.4404 (pp20) REVERT: A 196 CYS cc_start: 0.5893 (OUTLIER) cc_final: 0.5521 (t) REVERT: B 11 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6667 (mpt180) REVERT: B 32 MET cc_start: 0.8051 (tmm) cc_final: 0.7692 (tmm) REVERT: B 38 SER cc_start: 0.8468 (m) cc_final: 0.8214 (p) REVERT: B 44 ARG cc_start: 0.6219 (tpt-90) cc_final: 0.5985 (tpp80) REVERT: B 51 THR cc_start: 0.8518 (t) cc_final: 0.8243 (p) REVERT: B 99 SER cc_start: 0.8501 (m) cc_final: 0.8093 (t) REVERT: B 127 SER cc_start: 0.8417 (m) cc_final: 0.7992 (p) REVERT: B 140 VAL cc_start: 0.8012 (t) cc_final: 0.7708 (p) REVERT: B 180 GLU cc_start: 0.4967 (OUTLIER) cc_final: 0.4760 (pp20) REVERT: D 32 MET cc_start: 0.7989 (tmm) cc_final: 0.7655 (tmm) REVERT: D 115 ASP cc_start: 0.7634 (t0) cc_final: 0.7099 (t0) REVERT: E 0 MET cc_start: 0.5907 (mmm) cc_final: 0.5525 (mmm) REVERT: F 4 CYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6014 (p) REVERT: F 11 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6484 (mpt180) REVERT: F 23 VAL cc_start: 0.7806 (p) cc_final: 0.7481 (m) REVERT: F 32 MET cc_start: 0.8428 (tmm) cc_final: 0.7900 (tmm) REVERT: F 38 SER cc_start: 0.8403 (m) cc_final: 0.8145 (p) REVERT: F 41 TYR cc_start: 0.8254 (t80) cc_final: 0.8017 (t80) REVERT: F 50 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7425 (pt) REVERT: F 95 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8168 (m170) REVERT: F 135 SER cc_start: 0.8886 (m) cc_final: 0.8105 (t) REVERT: F 180 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.4679 (pp20) REVERT: G 6 TYR cc_start: 0.1510 (OUTLIER) cc_final: 0.0713 (t80) REVERT: G 74 ASN cc_start: 0.7797 (t0) cc_final: 0.7581 (t0) REVERT: H 0 MET cc_start: 0.6579 (mmp) cc_final: 0.5767 (tpp) REVERT: I 32 MET cc_start: 0.8259 (tmm) cc_final: 0.7784 (tmm) REVERT: I 38 SER cc_start: 0.8444 (m) cc_final: 0.8131 (p) REVERT: I 41 TYR cc_start: 0.8162 (t80) cc_final: 0.7884 (t80) REVERT: I 96 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7964 (m-70) REVERT: I 135 SER cc_start: 0.8981 (m) cc_final: 0.8448 (t) REVERT: J 58 MET cc_start: 0.7502 (mmt) cc_final: 0.7286 (mmt) REVERT: K 14 TYR cc_start: 0.8265 (m-10) cc_final: 0.7974 (m-10) REVERT: K 38 SER cc_start: 0.8574 (m) cc_final: 0.8184 (p) REVERT: K 55 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7306 (pp) REVERT: K 115 ASP cc_start: 0.7788 (t0) cc_final: 0.7415 (t0) REVERT: L 8 ASN cc_start: 0.6565 (t0) cc_final: 0.5792 (m110) REVERT: L 58 MET cc_start: 0.7532 (mmt) cc_final: 0.7218 (mmt) REVERT: M 32 MET cc_start: 0.8122 (tmm) cc_final: 0.7781 (tmm) REVERT: M 38 SER cc_start: 0.8574 (m) cc_final: 0.8292 (p) REVERT: M 115 ASP cc_start: 0.7511 (t0) cc_final: 0.7196 (t0) REVERT: M 135 SER cc_start: 0.8837 (m) cc_final: 0.8456 (t) REVERT: N 74 ASN cc_start: 0.7794 (t0) cc_final: 0.7535 (t0) outliers start: 95 outliers final: 69 residues processed: 464 average time/residue: 0.1131 time to fit residues: 82.0819 Evaluate side-chains 476 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 393 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 HIS ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN F 45 ASN ** F 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN I 141 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.170072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146012 restraints weight = 25095.370| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.26 r_work: 0.3716 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 17969 Z= 0.248 Angle : 0.810 10.518 24367 Z= 0.421 Chirality : 0.049 0.206 2737 Planarity : 0.005 0.064 3080 Dihedral : 6.776 58.537 2785 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.78 % Favored : 88.17 % Rotamer: Outliers : 5.19 % Allowed : 22.17 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.09 (0.17), residues: 889 loop : -2.62 (0.15), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 7 TYR 0.024 0.002 TYR K 53 PHE 0.017 0.002 PHE D 185 TRP 0.008 0.002 TRP L 68 HIS 0.007 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00565 (17920) covalent geometry : angle 0.79477 (24255) SS BOND : bond 0.00756 ( 35) SS BOND : angle 2.46599 ( 70) hydrogen bonds : bond 0.04075 ( 552) hydrogen bonds : angle 4.80705 ( 2193) link_NAG-ASN : bond 0.00298 ( 14) link_NAG-ASN : angle 2.29791 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 398 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6894 (mpt180) REVERT: A 32 MET cc_start: 0.8200 (tmm) cc_final: 0.7924 (tmm) REVERT: A 38 SER cc_start: 0.8506 (m) cc_final: 0.8227 (p) REVERT: A 51 THR cc_start: 0.8591 (t) cc_final: 0.8345 (p) REVERT: A 107 MET cc_start: 0.6203 (mtp) cc_final: 0.5996 (mtp) REVERT: A 135 SER cc_start: 0.8898 (m) cc_final: 0.8505 (t) REVERT: A 180 GLU cc_start: 0.4585 (OUTLIER) cc_final: 0.4371 (pp20) REVERT: A 196 CYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5837 (t) REVERT: B 11 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6890 (mpt180) REVERT: B 32 MET cc_start: 0.8054 (tmm) cc_final: 0.7713 (tmm) REVERT: B 38 SER cc_start: 0.8440 (m) cc_final: 0.8163 (p) REVERT: B 51 THR cc_start: 0.8512 (t) cc_final: 0.8277 (p) REVERT: B 95 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8194 (m170) REVERT: B 99 SER cc_start: 0.8486 (m) cc_final: 0.8096 (t) REVERT: B 140 VAL cc_start: 0.8001 (t) cc_final: 0.7724 (p) REVERT: B 167 TYR cc_start: 0.8414 (t80) cc_final: 0.8060 (t80) REVERT: B 180 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.4759 (pp20) REVERT: D 32 MET cc_start: 0.8089 (tmm) cc_final: 0.7763 (tmm) REVERT: D 115 ASP cc_start: 0.7676 (t0) cc_final: 0.7095 (t0) REVERT: F 11 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6936 (mpt180) REVERT: F 23 VAL cc_start: 0.8015 (p) cc_final: 0.7646 (m) REVERT: F 32 MET cc_start: 0.8523 (tmm) cc_final: 0.8019 (tmm) REVERT: F 38 SER cc_start: 0.8388 (m) cc_final: 0.8113 (p) REVERT: F 41 TYR cc_start: 0.8357 (t80) cc_final: 0.7941 (t80) REVERT: F 50 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7553 (mp) REVERT: F 73 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7850 (mt-10) REVERT: F 95 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8339 (m170) REVERT: F 180 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.4592 (pp20) REVERT: G 6 TYR cc_start: 0.1367 (OUTLIER) cc_final: 0.0628 (t80) REVERT: G 74 ASN cc_start: 0.7823 (t0) cc_final: 0.7613 (t0) REVERT: I 20 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8135 (p) REVERT: I 32 MET cc_start: 0.8231 (tmm) cc_final: 0.7829 (tmm) REVERT: I 81 LEU cc_start: 0.8525 (tp) cc_final: 0.8022 (tp) REVERT: I 96 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.7869 (m-70) REVERT: I 105 MET cc_start: 0.8104 (mmt) cc_final: 0.7806 (mtp) REVERT: I 135 SER cc_start: 0.8949 (m) cc_final: 0.8371 (t) REVERT: J 74 ASN cc_start: 0.7823 (t0) cc_final: 0.7543 (t0) REVERT: K 14 TYR cc_start: 0.8306 (m-10) cc_final: 0.7942 (m-10) REVERT: K 55 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7198 (pp) REVERT: K 115 ASP cc_start: 0.7811 (t0) cc_final: 0.7436 (t0) REVERT: M 32 MET cc_start: 0.8099 (tmm) cc_final: 0.7711 (tmm) REVERT: M 38 SER cc_start: 0.8562 (m) cc_final: 0.8308 (p) REVERT: M 115 ASP cc_start: 0.7533 (t0) cc_final: 0.7196 (t0) REVERT: M 135 SER cc_start: 0.8923 (m) cc_final: 0.8480 (t) outliers start: 102 outliers final: 79 residues processed: 470 average time/residue: 0.1103 time to fit residues: 81.8757 Evaluate side-chains 490 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 397 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER 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 95 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** F 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN I 45 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 ASN ** 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 = 0.4107 r_free = 0.4107 target = 0.170008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145670 restraints weight = 24884.599| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.33 r_work: 0.3717 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17969 Z= 0.253 Angle : 0.831 10.731 24367 Z= 0.434 Chirality : 0.050 0.208 2737 Planarity : 0.005 0.059 3080 Dihedral : 6.899 58.411 2785 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 4.93 % Allowed : 22.93 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.16 (0.17), residues: 875 loop : -2.73 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 11 TYR 0.025 0.002 TYR K 53 PHE 0.018 0.002 PHE A 185 TRP 0.009 0.002 TRP N 32 HIS 0.006 0.001 HIS N 73 Details of bonding type rmsd covalent geometry : bond 0.00581 (17920) covalent geometry : angle 0.81676 (24255) SS BOND : bond 0.00769 ( 35) SS BOND : angle 2.48337 ( 70) hydrogen bonds : bond 0.04077 ( 552) hydrogen bonds : angle 4.79299 ( 2193) link_NAG-ASN : bond 0.00340 ( 14) link_NAG-ASN : angle 2.31658 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4228 Ramachandran restraints generated. 2114 Oldfield, 0 Emsley, 2114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 380 time to evaluate : 0.591 Fit side-chains REVERT: A 11 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6788 (mpt180) REVERT: A 32 MET cc_start: 0.8193 (tmm) cc_final: 0.7905 (tmm) REVERT: A 38 SER cc_start: 0.8513 (m) cc_final: 0.8202 (p) REVERT: A 51 THR cc_start: 0.8555 (t) cc_final: 0.8324 (p) REVERT: A 135 SER cc_start: 0.8898 (m) cc_final: 0.8473 (t) REVERT: A 180 GLU cc_start: 0.4713 (OUTLIER) cc_final: 0.4506 (pp20) REVERT: B 11 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6869 (mpt180) REVERT: B 32 MET cc_start: 0.8085 (tmm) cc_final: 0.7700 (tmm) REVERT: B 38 SER cc_start: 0.8447 (m) cc_final: 0.8155 (p) REVERT: B 51 THR cc_start: 0.8481 (t) cc_final: 0.8259 (p) REVERT: B 95 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8264 (m170) REVERT: B 99 SER cc_start: 0.8487 (m) cc_final: 0.8073 (t) REVERT: B 140 VAL cc_start: 0.7982 (t) cc_final: 0.7702 (p) REVERT: B 180 GLU cc_start: 0.4969 (OUTLIER) cc_final: 0.4759 (pp20) REVERT: D 32 MET cc_start: 0.8101 (tmm) cc_final: 0.7718 (tmm) REVERT: D 107 MET cc_start: 0.6225 (mtp) cc_final: 0.6016 (mtp) REVERT: D 115 ASP cc_start: 0.7685 (t0) cc_final: 0.7113 (t0) REVERT: F 11 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7015 (mpt180) REVERT: F 23 VAL cc_start: 0.8002 (p) cc_final: 0.7629 (m) REVERT: F 32 MET cc_start: 0.8502 (tmm) cc_final: 0.7950 (tmm) REVERT: F 38 SER cc_start: 0.8401 (m) cc_final: 0.8104 (p) REVERT: F 41 TYR cc_start: 0.8358 (t80) cc_final: 0.7954 (t80) REVERT: F 50 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7508 (mp) REVERT: F 73 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7872 (mt-10) REVERT: F 95 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8326 (m170) REVERT: F 180 GLU cc_start: 0.4907 (OUTLIER) cc_final: 0.4569 (pp20) REVERT: G 6 TYR cc_start: 0.1275 (OUTLIER) cc_final: 0.0565 (t80) REVERT: I 32 MET cc_start: 0.8233 (tmm) cc_final: 0.7803 (tmm) REVERT: I 96 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7896 (m-70) REVERT: I 105 MET cc_start: 0.8201 (mmt) cc_final: 0.7913 (mtp) REVERT: I 135 SER cc_start: 0.8854 (m) cc_final: 0.8317 (t) REVERT: J 0 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.5300 (tpp) REVERT: J 74 ASN cc_start: 0.7807 (t0) cc_final: 0.7531 (t0) REVERT: K 14 TYR cc_start: 0.8304 (m-10) cc_final: 0.7925 (m-10) REVERT: K 23 VAL cc_start: 0.8192 (p) cc_final: 0.7848 (m) REVERT: K 55 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7265 (pp) REVERT: K 115 ASP cc_start: 0.7839 (t0) cc_final: 0.7439 (t0) REVERT: L 58 MET cc_start: 0.7534 (mmt) cc_final: 0.7308 (mmt) REVERT: M 32 MET cc_start: 0.8141 (tmm) cc_final: 0.7779 (tmm) REVERT: M 38 SER cc_start: 0.8564 (m) cc_final: 0.8327 (p) REVERT: M 115 ASP cc_start: 0.7506 (t0) cc_final: 0.7168 (t0) REVERT: M 135 SER cc_start: 0.8889 (m) cc_final: 0.8447 (t) outliers start: 97 outliers final: 81 residues processed: 451 average time/residue: 0.1100 time to fit residues: 78.0678 Evaluate side-chains 470 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 376 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER 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 95 HIS Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain J residue 0 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 95 HIS Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 194 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 178 optimal weight: 1.9990 chunk 195 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN D 97 ASN D 155 HIS F 45 ASN F 97 ASN ** F 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 97 ASN M 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.176288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152284 restraints weight = 25268.911| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.38 r_work: 0.3794 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17969 Z= 0.128 Angle : 0.713 10.727 24367 Z= 0.368 Chirality : 0.045 0.142 2737 Planarity : 0.004 0.053 3080 Dihedral : 6.046 59.817 2785 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 3.97 % Allowed : 24.20 % Favored : 71.84 % 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 are not related in a simple way. whole: -1.88 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.26 (0.17), residues: 875 loop : -2.56 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 44 TYR 0.016 0.001 TYR K 53 PHE 0.012 0.001 PHE D 185 TRP 0.008 0.001 TRP K 13 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00285 (17920) covalent geometry : angle 0.70170 (24255) SS BOND : bond 0.00559 ( 35) SS BOND : angle 1.98860 ( 70) hydrogen bonds : bond 0.03237 ( 552) hydrogen bonds : angle 4.40666 ( 2193) link_NAG-ASN : bond 0.00148 ( 14) link_NAG-ASN : angle 2.04789 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4606.38 seconds wall clock time: 79 minutes 24.44 seconds (4764.44 seconds total)