Starting phenix.real_space_refine on Sun Jun 15 14:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxx_29547/06_2025/8fxx_29547_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxx_29547/06_2025/8fxx_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_29547/06_2025/8fxx_29547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxx_29547/06_2025/8fxx_29547.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxx_29547/06_2025/8fxx_29547_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxx_29547/06_2025/8fxx_29547_neut.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.52, per 1000 atoms: 0.66 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: 4.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 3.49 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: 5.92 Time building geometry restraints manager: 4.90 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.710 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.002 TRP K 13 HIS 0.005 0.001 HIS E 99 PHE 0.017 0.002 PHE M 185 TYR 0.020 0.002 TYR K 53 ARG 0.004 0.000 ARG D 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 14) link_NAG-ASN : angle 2.39828 ( 42) hydrogen bonds : bond 0.13682 ( 552) hydrogen bonds : angle 6.33174 ( 2193) SS BOND : bond 0.02078 ( 35) SS BOND : angle 1.64460 ( 70) covalent geometry : bond 0.00516 (17920) covalent geometry : angle 0.70224 (24255) *********************** 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 : 1.800 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: 0.6913 (pp) REVERT: A 82 SER cc_start: 0.8609 (p) cc_final: 0.8259 (t) REVERT: A 115 ASP cc_start: 0.7177 (t0) cc_final: 0.6675 (t0) REVERT: A 130 ILE cc_start: 0.8077 (mt) cc_final: 0.7735 (tt) REVERT: A 135 SER cc_start: 0.8956 (m) cc_final: 0.8258 (t) REVERT: A 159 LYS cc_start: 0.8240 (mmtm) cc_final: 0.8033 (mmtp) REVERT: A 180 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.4039 (pp20) REVERT: B 23 VAL cc_start: 0.7632 (p) cc_final: 0.7365 (m) REVERT: B 32 MET cc_start: 0.7589 (tmm) cc_final: 0.6964 (tmm) REVERT: B 38 SER cc_start: 0.8598 (m) cc_final: 0.8188 (p) REVERT: B 51 THR cc_start: 0.8531 (t) cc_final: 0.8233 (p) REVERT: B 140 VAL cc_start: 0.7916 (t) cc_final: 0.7690 (p) REVERT: B 165 SER cc_start: 0.8294 (m) cc_final: 0.8069 (t) REVERT: B 180 GLU cc_start: 0.4737 (OUTLIER) cc_final: 0.4373 (pp20) REVERT: D 38 SER cc_start: 0.8478 (m) cc_final: 0.8190 (p) REVERT: D 55 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7166 (pt) REVERT: D 99 SER cc_start: 0.8548 (m) cc_final: 0.8338 (m) 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: 0.4343 (pp20) REVERT: F 19 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6835 (pt) REVERT: F 23 VAL cc_start: 0.7886 (p) cc_final: 0.7432 (m) REVERT: F 32 MET cc_start: 0.7698 (tmm) cc_final: 0.7165 (tmm) REVERT: F 38 SER cc_start: 0.8570 (m) cc_final: 0.8083 (p) REVERT: F 55 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7332 (pp) REVERT: F 100 VAL cc_start: 0.8469 (p) cc_final: 0.8244 (t) REVERT: F 101 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7936 (m) REVERT: F 180 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.4235 (pp20) REVERT: G 57 TYR cc_start: 0.7233 (m-10) cc_final: 0.6974 (m-10) REVERT: G 74 ASN cc_start: 0.7931 (t0) cc_final: 0.7695 (t0) REVERT: H 0 MET cc_start: 0.5723 (mmt) cc_final: 0.5326 (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: 0.5907 (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: 0.7441 (mt) REVERT: I 97 ASN cc_start: 0.8608 (m110) cc_final: 0.8296 (m-40) REVERT: I 133 ASN cc_start: 0.8415 (m-40) cc_final: 0.8196 (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: 0.7707 (t0) REVERT: K 23 VAL cc_start: 0.8236 (p) cc_final: 0.7974 (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: 0.6998 (pp) REVERT: K 60 THR cc_start: 0.8380 (m) cc_final: 0.8177 (t) REVERT: K 99 SER cc_start: 0.8146 (m) cc_final: 0.7789 (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: 0.7937 (t0) cc_final: 0.7705 (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: 0.8129 (p) REVERT: M 51 THR cc_start: 0.8550 (t) cc_final: 0.8331 (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: 0.7700 (m) REVERT: M 115 ASP cc_start: 0.7342 (t0) cc_final: 0.7057 (t0) REVERT: M 135 SER cc_start: 0.8877 (m) cc_final: 0.8359 (t) REVERT: M 180 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.4237 (pp20) outliers start: 79 outliers final: 37 residues processed: 536 average time/residue: 0.2670 time to fit residues: 225.2885 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 : 2.152 ------------------------------------------------------------------------------- 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 177 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 0.0970 chunk 190 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN B 150 ASN C 8 ASN C 102 ASN D 89 GLN I 45 ASN J 8 ASN J 102 ASN K 89 GLN L 8 ASN N 102 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.174975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149843 restraints weight = 25521.788| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.48 r_work: 0.3752 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17969 Z= 0.160 Angle : 0.787 13.873 24367 Z= 0.407 Chirality : 0.048 0.184 2737 Planarity : 0.004 0.060 3080 Dihedral : 8.820 59.847 2860 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.03 % Allowed : 14.59 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.17 (0.17), residues: 868 loop : -2.82 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 68 HIS 0.004 0.001 HIS I 96 PHE 0.022 0.001 PHE A 185 TYR 0.022 0.001 TYR F 25 ARG 0.004 0.001 ARG I 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 14) link_NAG-ASN : angle 2.36278 ( 42) hydrogen bonds : bond 0.03851 ( 552) hydrogen bonds : angle 4.88791 ( 2193) SS BOND : bond 0.00748 ( 35) SS BOND : angle 3.10291 ( 70) covalent geometry : bond 0.00366 (17920) covalent geometry : angle 0.76520 (24255) *********************** 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 517 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 418 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.7861 (tmm) cc_final: 0.7544 (tmm) REVERT: A 38 SER cc_start: 0.8449 (m) cc_final: 0.8084 (p) REVERT: A 51 THR cc_start: 0.8426 (t) cc_final: 0.8171 (p) REVERT: A 78 ASP cc_start: 0.7468 (t0) cc_final: 0.6935 (t0) REVERT: A 135 SER cc_start: 0.8961 (m) cc_final: 0.8364 (t) REVERT: A 159 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7833 (mmtp) REVERT: A 180 GLU cc_start: 0.4666 (OUTLIER) cc_final: 0.4288 (pp20) REVERT: A 196 CYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5518 (t) REVERT: B 32 MET cc_start: 0.7657 (tmm) cc_final: 0.7034 (tmm) REVERT: B 38 SER cc_start: 0.8511 (m) cc_final: 0.8173 (p) REVERT: B 51 THR cc_start: 0.8428 (t) cc_final: 0.8171 (p) REVERT: B 127 SER cc_start: 0.8295 (m) cc_final: 0.7939 (p) REVERT: B 140 VAL cc_start: 0.7916 (t) cc_final: 0.7525 (p) REVERT: B 165 SER cc_start: 0.8369 (m) cc_final: 0.8152 (t) REVERT: B 180 GLU cc_start: 0.5003 (OUTLIER) cc_final: 0.4611 (pp20) REVERT: B 196 CYS cc_start: 0.6406 (OUTLIER) cc_final: 0.6099 (t) REVERT: D 38 SER cc_start: 0.8425 (m) cc_final: 0.8224 (p) REVERT: D 115 ASP cc_start: 0.7465 (t0) cc_final: 0.6887 (t0) REVERT: D 180 GLU cc_start: 0.4939 (OUTLIER) cc_final: 0.4593 (pp20) REVERT: E 0 MET cc_start: 0.5787 (mmm) cc_final: 0.5445 (mmm) REVERT: F 23 VAL cc_start: 0.7653 (p) cc_final: 0.7404 (m) REVERT: F 32 MET cc_start: 0.7883 (tmm) cc_final: 0.7339 (tmm) REVERT: F 38 SER cc_start: 0.8392 (m) cc_final: 0.8067 (p) REVERT: F 41 TYR cc_start: 0.8248 (t80) cc_final: 0.8025 (t80) REVERT: F 100 VAL cc_start: 0.8400 (p) cc_final: 0.8177 (t) REVERT: F 107 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5839 (ttm) REVERT: F 170 ARG cc_start: 0.7516 (ptm-80) cc_final: 0.7111 (ptm160) REVERT: F 180 GLU cc_start: 0.4789 (OUTLIER) cc_final: 0.4428 (pp20) REVERT: G 74 ASN cc_start: 0.7870 (t0) cc_final: 0.7538 (t0) REVERT: I 32 MET cc_start: 0.7687 (tmm) cc_final: 0.7147 (tmm) REVERT: I 37 MET cc_start: 0.8450 (ptm) cc_final: 0.8136 (ptm) REVERT: I 38 SER cc_start: 0.8441 (m) cc_final: 0.8060 (p) REVERT: I 41 TYR cc_start: 0.8208 (t80) cc_final: 0.7997 (t80) REVERT: I 131 THR cc_start: 0.7958 (p) cc_final: 0.7689 (m) REVERT: I 135 SER cc_start: 0.8923 (m) cc_final: 0.8380 (t) REVERT: J 58 MET cc_start: 0.7154 (mmt) cc_final: 0.6886 (mmt) REVERT: J 74 ASN cc_start: 0.7842 (t0) cc_final: 0.7543 (t0) REVERT: K 38 SER cc_start: 0.8548 (m) cc_final: 0.8183 (p) REVERT: K 51 THR cc_start: 0.8073 (t) cc_final: 0.7802 (p) REVERT: K 99 SER cc_start: 0.8011 (m) cc_final: 0.7711 (m) REVERT: K 115 ASP cc_start: 0.7578 (t0) cc_final: 0.7175 (t0) REVERT: K 129 ASP cc_start: 0.6810 (p0) cc_final: 0.6573 (p0) REVERT: K 180 GLU cc_start: 0.4697 (OUTLIER) cc_final: 0.4371 (pp20) REVERT: L 74 ASN cc_start: 0.7874 (t0) cc_final: 0.7561 (t0) REVERT: M 32 MET cc_start: 0.7735 (tmm) cc_final: 0.7330 (tmm) REVERT: M 38 SER cc_start: 0.8429 (m) cc_final: 0.8191 (p) REVERT: M 44 ARG cc_start: 0.6412 (tpt-90) cc_final: 0.6112 (tpp80) REVERT: M 99 SER cc_start: 0.8145 (m) cc_final: 0.7936 (m) REVERT: M 115 ASP cc_start: 0.7449 (t0) cc_final: 0.7180 (t0) REVERT: M 127 SER cc_start: 0.8504 (p) cc_final: 0.8303 (p) REVERT: M 135 SER cc_start: 0.8925 (m) cc_final: 0.8496 (t) REVERT: M 180 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4811 (pp20) outliers start: 99 outliers final: 45 residues processed: 483 average time/residue: 0.2994 time to fit residues: 229.6611 Evaluate side-chains 451 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 397 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 150 ASN 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 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 B residue 196 CYS 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 40 SER Chi-restraints excluded: chain F residue 50 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 59 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 101 THR 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 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 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 150 ASN 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 56 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN F 79 ASN F 150 ASN I 150 ASN M 133 ASN M 141 ASN N 8 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145680 restraints weight = 24820.415| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.26 r_work: 0.3728 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17969 Z= 0.226 Angle : 0.799 11.724 24367 Z= 0.416 Chirality : 0.049 0.212 2737 Planarity : 0.005 0.067 3080 Dihedral : 8.021 59.786 2816 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 5.74 % Allowed : 17.49 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.23 (0.17), residues: 868 loop : -2.78 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 68 HIS 0.005 0.001 HIS M 96 PHE 0.024 0.001 PHE A 185 TYR 0.027 0.002 TYR K 53 ARG 0.003 0.001 ARG A 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 14) link_NAG-ASN : angle 2.31912 ( 42) hydrogen bonds : bond 0.04097 ( 552) hydrogen bonds : angle 4.94559 ( 2193) SS BOND : bond 0.00666 ( 35) SS BOND : angle 2.91172 ( 70) covalent geometry : bond 0.00522 (17920) covalent geometry : angle 0.77978 (24255) *********************** 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 517 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 404 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6862 (mpt180) REVERT: A 32 MET cc_start: 0.8153 (tmm) cc_final: 0.7842 (tmm) REVERT: A 38 SER cc_start: 0.8564 (m) cc_final: 0.8219 (p) REVERT: A 51 THR cc_start: 0.8515 (t) cc_final: 0.8294 (p) REVERT: A 78 ASP cc_start: 0.7626 (t0) cc_final: 0.7130 (t0) REVERT: A 113 LYS cc_start: 0.6261 (mptt) cc_final: 0.4310 (tttp) REVERT: A 133 ASN cc_start: 0.8330 (m-40) cc_final: 0.8044 (m-40) REVERT: A 135 SER cc_start: 0.8925 (m) cc_final: 0.8459 (t) REVERT: A 159 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7976 (mmtp) REVERT: A 180 GLU cc_start: 0.4718 (OUTLIER) cc_final: 0.4427 (pp20) REVERT: A 196 CYS cc_start: 0.6378 (OUTLIER) cc_final: 0.6052 (t) REVERT: B 11 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6847 (mpt180) REVERT: B 32 MET cc_start: 0.7999 (tmm) cc_final: 0.7606 (tmm) REVERT: B 38 SER cc_start: 0.8553 (m) cc_final: 0.8273 (p) REVERT: B 51 THR cc_start: 0.8541 (t) cc_final: 0.8320 (p) REVERT: B 140 VAL cc_start: 0.7979 (t) cc_final: 0.7759 (p) REVERT: B 165 SER cc_start: 0.8413 (m) cc_final: 0.8157 (t) REVERT: B 180 GLU cc_start: 0.5208 (OUTLIER) cc_final: 0.4773 (pp20) REVERT: C 8 ASN cc_start: 0.6922 (t0) cc_final: 0.6672 (m-40) REVERT: D 7 ARG cc_start: 0.6274 (tpt170) cc_final: 0.6043 (tpt170) REVERT: D 115 ASP cc_start: 0.7652 (t0) cc_final: 0.7071 (t0) REVERT: D 180 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4801 (pp20) REVERT: E 0 MET cc_start: 0.5793 (mmm) cc_final: 0.5544 (mmm) REVERT: F 11 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6577 (mpt180) REVERT: F 23 VAL cc_start: 0.7969 (p) cc_final: 0.7560 (m) REVERT: F 32 MET cc_start: 0.8410 (tmm) cc_final: 0.7843 (tmm) REVERT: F 38 SER cc_start: 0.8536 (m) cc_final: 0.8186 (p) REVERT: F 41 TYR cc_start: 0.8324 (t80) cc_final: 0.8094 (t80) REVERT: F 95 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8297 (m170) REVERT: F 96 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8229 (m-70) REVERT: F 100 VAL cc_start: 0.8505 (p) cc_final: 0.8272 (t) REVERT: G 74 ASN cc_start: 0.7970 (t0) cc_final: 0.7709 (t0) REVERT: I 11 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6883 (mpt180) REVERT: I 20 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8069 (p) REVERT: I 32 MET cc_start: 0.8112 (tmm) cc_final: 0.7608 (tmm) REVERT: I 37 MET cc_start: 0.8609 (ptm) cc_final: 0.8377 (ptm) REVERT: I 38 SER cc_start: 0.8510 (m) cc_final: 0.8148 (p) REVERT: I 96 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7985 (m-70) REVERT: I 108 ASN cc_start: 0.7464 (m-40) cc_final: 0.7219 (m-40) REVERT: I 135 SER cc_start: 0.8970 (m) cc_final: 0.8450 (t) REVERT: I 180 GLU cc_start: 0.5297 (OUTLIER) cc_final: 0.4928 (pp20) REVERT: J 58 MET cc_start: 0.7445 (mmt) cc_final: 0.7173 (mmt) REVERT: J 74 ASN cc_start: 0.7863 (t0) cc_final: 0.7609 (t0) REVERT: K 51 THR cc_start: 0.8311 (t) cc_final: 0.8014 (p) REVERT: K 99 SER cc_start: 0.8224 (m) cc_final: 0.7978 (m) REVERT: K 115 ASP cc_start: 0.7784 (t0) cc_final: 0.7377 (t0) REVERT: K 129 ASP cc_start: 0.7223 (p0) cc_final: 0.6939 (p0) REVERT: K 159 LYS cc_start: 0.8350 (mmtm) cc_final: 0.8142 (mmtp) REVERT: K 160 TYR cc_start: 0.7702 (m-10) cc_final: 0.7471 (m-10) REVERT: L 40 LEU cc_start: 0.8623 (mt) cc_final: 0.8348 (mm) REVERT: L 74 ASN cc_start: 0.7923 (t0) cc_final: 0.7675 (t0) REVERT: M 20 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8188 (p) REVERT: M 32 MET cc_start: 0.8081 (tmm) cc_final: 0.7712 (tmm) REVERT: M 38 SER cc_start: 0.8549 (m) cc_final: 0.8299 (p) REVERT: M 44 ARG cc_start: 0.6810 (tpt-90) cc_final: 0.6506 (tpp80) REVERT: M 56 GLU cc_start: 0.8164 (pt0) cc_final: 0.7960 (tt0) REVERT: M 99 SER cc_start: 0.8311 (m) cc_final: 0.8016 (m) REVERT: M 115 ASP cc_start: 0.7619 (t0) cc_final: 0.7363 (t0) REVERT: M 135 SER cc_start: 0.8937 (m) cc_final: 0.8512 (t) REVERT: N 74 ASN cc_start: 0.7851 (t0) cc_final: 0.7550 (t0) outliers start: 113 outliers final: 69 residues processed: 482 average time/residue: 0.2704 time to fit residues: 205.3081 Evaluate side-chains 469 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 386 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 20 THR Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 98 ILE 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 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 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 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 180 GLU 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 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 95 HIS 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 150 ASN Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 195 ILE 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 50 LEU 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 101 THR 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 20 THR Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 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 M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 91 LEU 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 96 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 141 ASN ** F 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN N 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.170801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146761 restraints weight = 24838.475| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.26 r_work: 0.3743 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17969 Z= 0.195 Angle : 0.764 11.020 24367 Z= 0.397 Chirality : 0.048 0.175 2737 Planarity : 0.005 0.061 3080 Dihedral : 7.537 59.949 2801 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 6.20 % Allowed : 18.00 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.25 (0.17), residues: 868 loop : -2.71 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 13 HIS 0.004 0.001 HIS I 96 PHE 0.020 0.001 PHE A 185 TYR 0.025 0.002 TYR K 53 ARG 0.003 0.001 ARG M 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 14) link_NAG-ASN : angle 2.34155 ( 42) hydrogen bonds : bond 0.03826 ( 552) hydrogen bonds : angle 4.82081 ( 2193) SS BOND : bond 0.00635 ( 35) SS BOND : angle 2.63603 ( 70) covalent geometry : bond 0.00447 (17920) covalent geometry : angle 0.74641 (24255) *********************** 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 495 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 373 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6702 (mpt180) REVERT: A 32 MET cc_start: 0.8060 (tmm) cc_final: 0.7782 (tmm) REVERT: A 38 SER cc_start: 0.8542 (m) cc_final: 0.8220 (p) REVERT: A 51 THR cc_start: 0.8560 (t) cc_final: 0.8357 (p) REVERT: A 113 LYS cc_start: 0.6185 (mptt) cc_final: 0.4256 (tttm) REVERT: A 135 SER cc_start: 0.8943 (m) cc_final: 0.8524 (t) REVERT: A 180 GLU cc_start: 0.4599 (OUTLIER) cc_final: 0.4270 (pp20) REVERT: A 196 CYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5947 (t) REVERT: B 32 MET cc_start: 0.7974 (tmm) cc_final: 0.7617 (tmm) REVERT: B 38 SER cc_start: 0.8539 (m) cc_final: 0.8286 (p) REVERT: B 85 LEU cc_start: 0.7653 (mt) cc_final: 0.7448 (mt) REVERT: B 96 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8263 (m-70) REVERT: B 140 VAL cc_start: 0.8020 (t) cc_final: 0.7695 (p) REVERT: B 165 SER cc_start: 0.8376 (m) cc_final: 0.8131 (t) REVERT: B 180 GLU cc_start: 0.5067 (OUTLIER) cc_final: 0.4667 (pp20) REVERT: D 11 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6871 (mpt180) REVERT: D 32 MET cc_start: 0.8030 (tmm) cc_final: 0.7558 (tmm) REVERT: D 180 GLU cc_start: 0.5174 (OUTLIER) cc_final: 0.4866 (pp20) REVERT: E 0 MET cc_start: 0.5726 (mmm) cc_final: 0.5429 (mmm) REVERT: F 20 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8268 (p) REVERT: F 23 VAL cc_start: 0.8005 (p) cc_final: 0.7608 (m) REVERT: F 32 MET cc_start: 0.8350 (tmm) cc_final: 0.7806 (tmm) REVERT: F 38 SER cc_start: 0.8477 (m) cc_final: 0.8178 (p) REVERT: F 41 TYR cc_start: 0.8336 (t80) cc_final: 0.8072 (t80) REVERT: F 73 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7978 (mt-10) REVERT: F 95 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8226 (m170) REVERT: F 100 VAL cc_start: 0.8485 (p) cc_final: 0.8254 (t) REVERT: F 169 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6848 (mmp) REVERT: F 180 GLU cc_start: 0.5102 (OUTLIER) cc_final: 0.4715 (pp20) REVERT: G 74 ASN cc_start: 0.7893 (t0) cc_final: 0.7635 (t0) REVERT: I 11 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6981 (mpt180) REVERT: I 20 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8075 (p) REVERT: I 32 MET cc_start: 0.8181 (tmm) cc_final: 0.7665 (tmm) REVERT: I 37 MET cc_start: 0.8609 (ptm) cc_final: 0.8394 (ptm) REVERT: I 38 SER cc_start: 0.8528 (m) cc_final: 0.8156 (p) REVERT: I 96 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7938 (m-70) REVERT: I 131 THR cc_start: 0.8063 (p) cc_final: 0.7767 (m) REVERT: I 135 SER cc_start: 0.8914 (m) cc_final: 0.8371 (t) REVERT: I 180 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.4638 (pp20) REVERT: J 58 MET cc_start: 0.7551 (mmt) cc_final: 0.7336 (mmt) REVERT: J 74 ASN cc_start: 0.7808 (t0) cc_final: 0.7600 (t0) REVERT: K 55 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7276 (pp) REVERT: K 115 ASP cc_start: 0.7829 (t0) cc_final: 0.7430 (t0) REVERT: K 129 ASP cc_start: 0.7267 (p0) cc_final: 0.6940 (p0) REVERT: M 20 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8236 (p) REVERT: M 32 MET cc_start: 0.8118 (tmm) cc_final: 0.7738 (tmm) REVERT: M 38 SER cc_start: 0.8413 (m) cc_final: 0.8204 (p) REVERT: M 44 ARG cc_start: 0.6701 (tpt-90) cc_final: 0.6433 (tpp80) REVERT: M 96 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8051 (m-70) REVERT: M 99 SER cc_start: 0.8374 (m) cc_final: 0.8160 (m) REVERT: M 115 ASP cc_start: 0.7644 (t0) cc_final: 0.7372 (t0) REVERT: M 135 SER cc_start: 0.8905 (m) cc_final: 0.8540 (t) REVERT: N 74 ASN cc_start: 0.7858 (t0) cc_final: 0.7588 (t0) REVERT: N 101 MET cc_start: 0.7743 (tpp) cc_final: 0.7488 (tpp) outliers start: 122 outliers final: 76 residues processed: 459 average time/residue: 0.2696 time to fit residues: 192.2789 Evaluate side-chains 465 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 371 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 56 GLU Chi-restraints excluded: chain A residue 75 VAL 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 56 GLU 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 158 ASP 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 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 55 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 180 GLU 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 20 THR 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 95 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 169 MET 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 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 27 ILE 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 96 HIS Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 180 GLU 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 50 LEU 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 161 LEU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 96 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 F 89 GLN F 96 HIS ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN I 141 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145578 restraints weight = 25124.981| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.29 r_work: 0.3729 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17969 Z= 0.204 Angle : 0.761 10.930 24367 Z= 0.396 Chirality : 0.048 0.182 2737 Planarity : 0.005 0.062 3080 Dihedral : 7.400 58.962 2800 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 6.46 % Allowed : 19.42 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.11 (0.17), residues: 889 loop : -2.68 (0.15), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 13 HIS 0.005 0.001 HIS F 96 PHE 0.020 0.001 PHE A 185 TYR 0.024 0.002 TYR K 53 ARG 0.006 0.001 ARG M 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 14) link_NAG-ASN : angle 2.35146 ( 42) hydrogen bonds : bond 0.03872 ( 552) hydrogen bonds : angle 4.79854 ( 2193) SS BOND : bond 0.00668 ( 35) SS BOND : angle 2.60091 ( 70) covalent geometry : bond 0.00465 (17920) covalent geometry : angle 0.74387 (24255) *********************** 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 512 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 385 time to evaluate : 2.275 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6750 (mpt180) REVERT: A 32 MET cc_start: 0.8118 (tmm) cc_final: 0.7823 (tmm) REVERT: A 38 SER cc_start: 0.8497 (m) cc_final: 0.8217 (p) REVERT: A 113 LYS cc_start: 0.6549 (mptt) cc_final: 0.4494 (tttm) REVERT: A 135 SER cc_start: 0.8922 (m) cc_final: 0.8530 (t) REVERT: A 180 GLU cc_start: 0.4566 (OUTLIER) cc_final: 0.4236 (pp20) REVERT: A 196 CYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5888 (t) REVERT: B 11 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6761 (mpt180) REVERT: B 32 MET cc_start: 0.7988 (tmm) cc_final: 0.7648 (tmm) REVERT: B 38 SER cc_start: 0.8522 (m) cc_final: 0.8269 (p) REVERT: B 95 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8220 (m170) REVERT: B 140 VAL cc_start: 0.8035 (t) cc_final: 0.7744 (p) REVERT: B 165 SER cc_start: 0.8365 (m) cc_final: 0.8091 (t) REVERT: B 180 GLU cc_start: 0.5044 (OUTLIER) cc_final: 0.4708 (pp20) REVERT: D 11 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6918 (mpt180) REVERT: D 32 MET cc_start: 0.8090 (tmm) cc_final: 0.7669 (tmm) REVERT: D 115 ASP cc_start: 0.7692 (t0) cc_final: 0.7104 (t0) REVERT: D 180 GLU cc_start: 0.5184 (OUTLIER) cc_final: 0.4878 (pp20) REVERT: E 0 MET cc_start: 0.5653 (mmm) cc_final: 0.5308 (mmm) REVERT: F 11 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6799 (mpt180) REVERT: F 23 VAL cc_start: 0.8034 (p) cc_final: 0.7655 (m) REVERT: F 32 MET cc_start: 0.8363 (tmm) cc_final: 0.7851 (tmm) REVERT: F 38 SER cc_start: 0.8425 (m) cc_final: 0.8142 (p) REVERT: F 41 TYR cc_start: 0.8331 (t80) cc_final: 0.8098 (t80) REVERT: F 73 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7991 (mt-10) REVERT: F 95 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8188 (m170) REVERT: F 100 VAL cc_start: 0.8469 (p) cc_final: 0.8234 (t) REVERT: F 107 MET cc_start: 0.6383 (mtp) cc_final: 0.5483 (mtp) REVERT: F 169 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6745 (mmp) REVERT: F 180 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4749 (pp20) REVERT: G 6 TYR cc_start: 0.1544 (OUTLIER) cc_final: 0.0811 (t80) REVERT: G 74 ASN cc_start: 0.7881 (t0) cc_final: 0.7652 (t0) REVERT: I 20 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8107 (p) REVERT: I 32 MET cc_start: 0.8216 (tmm) cc_final: 0.7720 (tmm) REVERT: I 37 MET cc_start: 0.8591 (ptm) cc_final: 0.8379 (ptm) REVERT: I 38 SER cc_start: 0.8538 (m) cc_final: 0.8172 (p) REVERT: I 89 GLN cc_start: 0.7711 (tt0) cc_final: 0.7253 (mt0) REVERT: I 96 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7884 (m-70) REVERT: I 131 THR cc_start: 0.8088 (p) cc_final: 0.7786 (m) REVERT: I 135 SER cc_start: 0.8845 (m) cc_final: 0.8358 (t) REVERT: J 58 MET cc_start: 0.7629 (mmt) cc_final: 0.7407 (mmt) REVERT: K 55 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7234 (pp) REVERT: K 115 ASP cc_start: 0.7839 (t0) cc_final: 0.7430 (t0) REVERT: K 129 ASP cc_start: 0.7330 (p0) cc_final: 0.7045 (p0) REVERT: M 20 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8242 (p) REVERT: M 32 MET cc_start: 0.8114 (tmm) cc_final: 0.7750 (tmm) REVERT: M 38 SER cc_start: 0.8514 (m) cc_final: 0.8302 (p) REVERT: M 44 ARG cc_start: 0.6775 (tpt-90) cc_final: 0.6464 (tpp80) REVERT: M 96 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.8036 (m-70) REVERT: M 99 SER cc_start: 0.8309 (m) cc_final: 0.8014 (m) REVERT: M 113 LYS cc_start: 0.6653 (mmtm) cc_final: 0.5168 (tttp) REVERT: M 115 ASP cc_start: 0.7635 (t0) cc_final: 0.7387 (t0) REVERT: M 135 SER cc_start: 0.8909 (m) cc_final: 0.8554 (t) REVERT: N 74 ASN cc_start: 0.7848 (t0) cc_final: 0.7627 (t0) REVERT: N 101 MET cc_start: 0.7794 (tpp) cc_final: 0.7583 (tpp) outliers start: 127 outliers final: 90 residues processed: 473 average time/residue: 0.2880 time to fit residues: 211.6212 Evaluate side-chains 490 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 382 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 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 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 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 195 ILE Chi-restraints excluded: chain C residue 0 MET Chi-restraints excluded: chain D residue 7 ARG 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 50 LEU Chi-restraints excluded: chain D residue 55 LEU 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 180 GLU 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 27 ILE Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER 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 161 LEU Chi-restraints excluded: chain F residue 169 MET 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 G residue 29 VAL 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 96 HIS Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 165 SER 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 50 LEU 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 186 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 95 HIS Chi-restraints excluded: chain M residue 96 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 34 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN D 96 HIS ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN M 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.171750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147553 restraints weight = 25107.435| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.33 r_work: 0.3751 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17969 Z= 0.163 Angle : 0.722 10.038 24367 Z= 0.376 Chirality : 0.047 0.175 2737 Planarity : 0.004 0.055 3080 Dihedral : 7.112 59.976 2798 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 5.85 % Allowed : 20.39 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.23 (0.17), residues: 875 loop : -2.64 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.005 0.001 HIS D 96 PHE 0.017 0.001 PHE A 185 TYR 0.021 0.001 TYR K 53 ARG 0.003 0.000 ARG M 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 14) link_NAG-ASN : angle 2.27208 ( 42) hydrogen bonds : bond 0.03593 ( 552) hydrogen bonds : angle 4.68235 ( 2193) SS BOND : bond 0.00573 ( 35) SS BOND : angle 2.34510 ( 70) covalent geometry : bond 0.00370 (17920) covalent geometry : angle 0.70666 (24255) *********************** 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 499 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 384 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6610 (mpt180) REVERT: A 32 MET cc_start: 0.8093 (tmm) cc_final: 0.7828 (tmm) REVERT: A 38 SER cc_start: 0.8572 (m) cc_final: 0.8234 (p) REVERT: A 78 ASP cc_start: 0.7645 (t0) cc_final: 0.7211 (t0) REVERT: A 113 LYS cc_start: 0.6141 (mptt) cc_final: 0.4179 (tttm) REVERT: A 135 SER cc_start: 0.8885 (m) cc_final: 0.8532 (t) REVERT: A 180 GLU cc_start: 0.4729 (OUTLIER) cc_final: 0.4425 (pp20) REVERT: A 196 CYS cc_start: 0.6026 (OUTLIER) cc_final: 0.5763 (t) REVERT: B 11 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6721 (mpt180) REVERT: B 32 MET cc_start: 0.8006 (tmm) cc_final: 0.7702 (tmm) REVERT: B 38 SER cc_start: 0.8494 (m) cc_final: 0.8257 (p) REVERT: B 95 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8200 (m170) REVERT: B 99 SER cc_start: 0.8492 (m) cc_final: 0.8201 (t) REVERT: B 127 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.7986 (p) REVERT: B 140 VAL cc_start: 0.7968 (t) cc_final: 0.7655 (p) REVERT: B 165 SER cc_start: 0.8370 (m) cc_final: 0.8108 (t) REVERT: B 180 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4743 (pp20) REVERT: D 11 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6859 (mpt180) REVERT: D 32 MET cc_start: 0.8011 (tmm) cc_final: 0.7636 (tmm) REVERT: D 44 ARG cc_start: 0.6762 (tpt-90) cc_final: 0.6473 (tpp80) REVERT: D 115 ASP cc_start: 0.7709 (t0) cc_final: 0.7129 (t0) REVERT: D 180 GLU cc_start: 0.5150 (OUTLIER) cc_final: 0.4867 (pp20) REVERT: F 11 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6699 (mpt180) REVERT: F 20 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8305 (p) REVERT: F 23 VAL cc_start: 0.7996 (p) cc_final: 0.7579 (m) REVERT: F 32 MET cc_start: 0.8404 (tmm) cc_final: 0.7875 (tmm) REVERT: F 38 SER cc_start: 0.8519 (m) cc_final: 0.8216 (p) REVERT: F 41 TYR cc_start: 0.8297 (t80) cc_final: 0.8079 (t80) REVERT: F 95 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8171 (m170) REVERT: F 100 VAL cc_start: 0.8429 (p) cc_final: 0.8205 (t) REVERT: F 107 MET cc_start: 0.6185 (mtp) cc_final: 0.5797 (mtp) REVERT: F 169 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6723 (mmp) REVERT: F 180 GLU cc_start: 0.4888 (OUTLIER) cc_final: 0.4542 (pp20) REVERT: G 6 TYR cc_start: 0.1433 (OUTLIER) cc_final: 0.0614 (t80) REVERT: G 74 ASN cc_start: 0.7844 (t0) cc_final: 0.7616 (t0) REVERT: I 20 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8041 (p) REVERT: I 32 MET cc_start: 0.8142 (tmm) cc_final: 0.7652 (tmm) REVERT: I 37 MET cc_start: 0.8577 (ptm) cc_final: 0.8364 (ptm) REVERT: I 38 SER cc_start: 0.8559 (m) cc_final: 0.8170 (p) REVERT: I 51 THR cc_start: 0.8502 (t) cc_final: 0.8199 (p) REVERT: I 96 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7912 (m-70) REVERT: I 131 THR cc_start: 0.8005 (p) cc_final: 0.7737 (m) REVERT: I 135 SER cc_start: 0.8869 (m) cc_final: 0.8381 (t) REVERT: J 58 MET cc_start: 0.7560 (mmt) cc_final: 0.7352 (mmt) REVERT: K 55 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7284 (pp) REVERT: K 115 ASP cc_start: 0.7836 (t0) cc_final: 0.7410 (t0) REVERT: L 74 ASN cc_start: 0.7860 (t0) cc_final: 0.7627 (t0) REVERT: M 20 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8227 (p) REVERT: M 32 MET cc_start: 0.8121 (tmm) cc_final: 0.7733 (tmm) REVERT: M 38 SER cc_start: 0.8522 (m) cc_final: 0.8294 (p) REVERT: M 44 ARG cc_start: 0.6546 (tpt-90) cc_final: 0.6287 (tpp80) REVERT: M 96 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8054 (m-70) REVERT: M 99 SER cc_start: 0.8373 (m) cc_final: 0.8129 (m) REVERT: M 115 ASP cc_start: 0.7605 (t0) cc_final: 0.7321 (t0) REVERT: M 135 SER cc_start: 0.8881 (m) cc_final: 0.8557 (t) REVERT: N 74 ASN cc_start: 0.7811 (t0) cc_final: 0.7602 (t0) outliers start: 115 outliers final: 76 residues processed: 467 average time/residue: 0.2719 time to fit residues: 197.0905 Evaluate side-chains 473 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 377 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 75 VAL 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 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 56 GLU 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 96 HIS Chi-restraints excluded: chain B residue 127 SER 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 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 50 LEU 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 180 GLU 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 20 THR Chi-restraints excluded: chain F residue 35 CYS 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 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 169 MET 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 G residue 8 ASN 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 96 HIS Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 165 SER 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 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 165 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR 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 81 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 95 HIS Chi-restraints excluded: chain M residue 96 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN D 155 HIS ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142882 restraints weight = 24666.698| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.25 r_work: 0.3701 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17969 Z= 0.283 Angle : 0.837 11.249 24367 Z= 0.438 Chirality : 0.051 0.218 2737 Planarity : 0.006 0.071 3080 Dihedral : 7.745 59.676 2798 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 6.91 % Allowed : 20.44 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.00 (0.17), residues: 882 loop : -2.72 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 32 HIS 0.006 0.001 HIS M 96 PHE 0.018 0.002 PHE A 185 TYR 0.028 0.002 TYR K 53 ARG 0.005 0.001 ARG A 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 14) link_NAG-ASN : angle 2.43102 ( 42) hydrogen bonds : bond 0.04284 ( 552) hydrogen bonds : angle 4.98563 ( 2193) SS BOND : bond 0.00810 ( 35) SS BOND : angle 2.70542 ( 70) covalent geometry : bond 0.00646 (17920) covalent geometry : angle 0.81963 (24255) *********************** 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 530 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 394 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6925 (mpt180) REVERT: A 32 MET cc_start: 0.8209 (tmm) cc_final: 0.7929 (tmm) REVERT: A 38 SER cc_start: 0.8513 (m) cc_final: 0.8242 (p) REVERT: A 133 ASN cc_start: 0.8288 (m-40) cc_final: 0.8084 (m-40) REVERT: A 135 SER cc_start: 0.8907 (m) cc_final: 0.8503 (t) REVERT: A 180 GLU cc_start: 0.4573 (OUTLIER) cc_final: 0.4335 (pp20) REVERT: A 196 CYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5810 (t) REVERT: B 11 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7010 (mpt180) REVERT: B 32 MET cc_start: 0.8167 (tmm) cc_final: 0.7814 (tmm) REVERT: B 38 SER cc_start: 0.8465 (m) cc_final: 0.8246 (p) REVERT: B 95 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8219 (m170) REVERT: B 99 SER cc_start: 0.8460 (m) cc_final: 0.8169 (t) REVERT: B 140 VAL cc_start: 0.8044 (t) cc_final: 0.7726 (p) REVERT: B 165 SER cc_start: 0.8323 (m) cc_final: 0.8058 (t) REVERT: B 180 GLU cc_start: 0.5153 (OUTLIER) cc_final: 0.4833 (pp20) REVERT: D 32 MET cc_start: 0.8114 (tmm) cc_final: 0.7736 (tmm) REVERT: D 115 ASP cc_start: 0.7699 (t0) cc_final: 0.7128 (t0) REVERT: F 11 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7032 (mpt180) REVERT: F 20 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8329 (p) REVERT: F 23 VAL cc_start: 0.8035 (p) cc_final: 0.7715 (m) REVERT: F 32 MET cc_start: 0.8474 (tmm) cc_final: 0.7969 (tmm) REVERT: F 38 SER cc_start: 0.8559 (m) cc_final: 0.8268 (p) REVERT: F 92 ASP cc_start: 0.7347 (t0) cc_final: 0.7099 (t0) REVERT: F 95 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.8232 (m170) REVERT: F 107 MET cc_start: 0.6330 (mtp) cc_final: 0.6118 (ttm) REVERT: F 169 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6802 (mmp) REVERT: F 180 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4521 (pp20) REVERT: G 6 TYR cc_start: 0.1318 (OUTLIER) cc_final: 0.0546 (t80) REVERT: I 20 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8152 (p) REVERT: I 32 MET cc_start: 0.8159 (tmm) cc_final: 0.7701 (tmm) REVERT: I 38 SER cc_start: 0.8516 (m) cc_final: 0.8172 (p) REVERT: I 105 MET cc_start: 0.8190 (mmt) cc_final: 0.7965 (mtp) REVERT: I 131 THR cc_start: 0.8111 (p) cc_final: 0.7789 (m) REVERT: I 135 SER cc_start: 0.8822 (m) cc_final: 0.8367 (t) REVERT: J 74 ASN cc_start: 0.7858 (t0) cc_final: 0.7627 (t0) REVERT: K 51 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8016 (p) REVERT: K 55 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7210 (pp) REVERT: K 115 ASP cc_start: 0.7825 (t0) cc_final: 0.7366 (t0) REVERT: K 197 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7151 (t80) REVERT: L 74 ASN cc_start: 0.7939 (t0) cc_final: 0.7739 (t0) REVERT: M 20 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8294 (p) REVERT: M 32 MET cc_start: 0.8172 (tmm) cc_final: 0.7799 (tmm) REVERT: M 44 ARG cc_start: 0.7013 (tpt-90) cc_final: 0.6753 (tpp80) REVERT: M 96 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8041 (m-70) REVERT: M 99 SER cc_start: 0.8299 (m) cc_final: 0.7979 (m) REVERT: M 113 LYS cc_start: 0.6764 (mmtm) cc_final: 0.5202 (tttp) REVERT: M 115 ASP cc_start: 0.7580 (t0) cc_final: 0.7292 (t0) REVERT: M 135 SER cc_start: 0.8937 (m) cc_final: 0.8573 (t) REVERT: M 180 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.5220 (pp20) outliers start: 136 outliers final: 92 residues processed: 489 average time/residue: 0.3278 time to fit residues: 247.1831 Evaluate side-chains 501 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 390 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 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 56 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 95 HIS 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 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 158 ASP 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 20 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 35 CYS 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 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 169 MET 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 0 MET Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 73 HIS 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 75 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 165 SER 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 50 LEU Chi-restraints excluded: chain K residue 51 THR 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 158 ASP 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 197 TYR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR 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 81 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 95 HIS Chi-restraints excluded: chain M residue 96 HIS 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 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 170 optimal weight: 5.9990 chunk 114 optimal weight: 0.2980 chunk 111 optimal weight: 0.0770 chunk 146 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 148 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 F 97 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 HIS J 88 HIS K 89 GLN K 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.150842 restraints weight = 25142.647| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.33 r_work: 0.3781 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17969 Z= 0.130 Angle : 0.713 9.804 24367 Z= 0.369 Chirality : 0.045 0.161 2737 Planarity : 0.004 0.049 3080 Dihedral : 6.719 59.823 2792 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.47 % Allowed : 22.98 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.25 (0.17), residues: 875 loop : -2.59 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 13 HIS 0.003 0.001 HIS I 155 PHE 0.013 0.001 PHE A 185 TYR 0.017 0.001 TYR F 25 ARG 0.005 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 14) link_NAG-ASN : angle 2.17629 ( 42) hydrogen bonds : bond 0.03270 ( 552) hydrogen bonds : angle 4.55048 ( 2193) SS BOND : bond 0.00495 ( 35) SS BOND : angle 2.09694 ( 70) covalent geometry : bond 0.00291 (17920) covalent geometry : angle 0.69989 (24255) *********************** 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 478 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 390 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6412 (mpt180) REVERT: A 32 MET cc_start: 0.8099 (tmm) cc_final: 0.7866 (tmm) REVERT: A 38 SER cc_start: 0.8595 (m) cc_final: 0.8232 (p) REVERT: A 105 MET cc_start: 0.8242 (mmt) cc_final: 0.8022 (mtp) REVERT: A 113 LYS cc_start: 0.6072 (mptt) cc_final: 0.4169 (tttm) REVERT: A 135 SER cc_start: 0.8866 (m) cc_final: 0.8519 (t) REVERT: A 180 GLU cc_start: 0.4639 (OUTLIER) cc_final: 0.4338 (pp20) REVERT: B 25 TYR cc_start: 0.8140 (p90) cc_final: 0.7768 (p90) REVERT: B 32 MET cc_start: 0.7998 (tmm) cc_final: 0.7627 (tmm) REVERT: B 38 SER cc_start: 0.8475 (m) cc_final: 0.8245 (p) REVERT: B 99 SER cc_start: 0.8477 (m) cc_final: 0.8150 (t) REVERT: B 127 SER cc_start: 0.8432 (m) cc_final: 0.8048 (p) REVERT: B 140 VAL cc_start: 0.8002 (t) cc_final: 0.7656 (p) REVERT: B 165 SER cc_start: 0.8365 (m) cc_final: 0.8134 (t) REVERT: D 32 MET cc_start: 0.7953 (tmm) cc_final: 0.7633 (tmm) REVERT: D 91 LEU cc_start: 0.8311 (mm) cc_final: 0.8085 (mp) REVERT: D 115 ASP cc_start: 0.7651 (t0) cc_final: 0.7099 (t0) REVERT: F 20 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8274 (p) REVERT: F 23 VAL cc_start: 0.7849 (p) cc_final: 0.7510 (m) REVERT: F 32 MET cc_start: 0.8420 (tmm) cc_final: 0.7818 (tmm) REVERT: F 38 SER cc_start: 0.8558 (m) cc_final: 0.8215 (p) REVERT: F 41 TYR cc_start: 0.8244 (t80) cc_final: 0.8033 (t80) REVERT: F 51 THR cc_start: 0.8150 (m) cc_final: 0.7646 (p) REVERT: F 169 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6771 (mmp) REVERT: F 177 PHE cc_start: 0.7538 (m-80) cc_final: 0.7315 (m-80) REVERT: F 180 GLU cc_start: 0.5006 (OUTLIER) cc_final: 0.4691 (pp20) REVERT: G 6 TYR cc_start: 0.1369 (OUTLIER) cc_final: 0.0557 (t80) REVERT: I 20 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8113 (p) REVERT: I 32 MET cc_start: 0.8113 (tmm) cc_final: 0.7612 (tmm) REVERT: I 38 SER cc_start: 0.8408 (m) cc_final: 0.8062 (p) REVERT: I 82 SER cc_start: 0.8505 (t) cc_final: 0.8246 (p) REVERT: I 131 THR cc_start: 0.7935 (p) cc_final: 0.7668 (m) REVERT: I 135 SER cc_start: 0.8756 (m) cc_final: 0.8302 (t) REVERT: K 51 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7869 (p) REVERT: K 55 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7357 (pp) REVERT: K 91 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8084 (mp) REVERT: K 106 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7329 (mt-10) REVERT: K 115 ASP cc_start: 0.7809 (t0) cc_final: 0.7344 (t0) REVERT: L 58 MET cc_start: 0.7519 (mmt) cc_final: 0.7243 (mmt) REVERT: L 74 ASN cc_start: 0.7818 (t0) cc_final: 0.7595 (t0) REVERT: M 20 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8231 (p) REVERT: M 32 MET cc_start: 0.8106 (tmm) cc_final: 0.7764 (tmm) REVERT: M 44 ARG cc_start: 0.6286 (tpt-90) cc_final: 0.6048 (tpp80) REVERT: M 96 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8054 (m-70) REVERT: M 115 ASP cc_start: 0.7510 (t0) cc_final: 0.7215 (t0) REVERT: M 127 SER cc_start: 0.8643 (p) cc_final: 0.8414 (p) REVERT: M 135 SER cc_start: 0.8874 (m) cc_final: 0.8538 (t) REVERT: M 187 ASP cc_start: 0.7791 (t0) cc_final: 0.7492 (t0) outliers start: 88 outliers final: 60 residues processed: 455 average time/residue: 0.3142 time to fit residues: 219.4407 Evaluate side-chains 450 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 378 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU 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 56 GLU Chi-restraints excluded: chain D residue 64 THR 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 20 THR Chi-restraints excluded: chain F residue 27 ILE 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 169 MET 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 H residue 40 LEU 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 56 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 165 SER 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 51 THR Chi-restraints excluded: chain K residue 55 LEU 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 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR 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 96 HIS Chi-restraints excluded: chain M residue 139 CYS 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 177 optimal weight: 3.9990 chunk 176 optimal weight: 0.0070 chunk 163 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN E 8 ASN F 45 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.170968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146688 restraints weight = 24901.328| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.26 r_work: 0.3711 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17969 Z= 0.256 Angle : 0.826 10.918 24367 Z= 0.431 Chirality : 0.050 0.211 2737 Planarity : 0.005 0.070 3080 Dihedral : 7.076 58.415 2787 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.97 % Favored : 87.98 % Rotamer: Outliers : 4.68 % Allowed : 22.83 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.07 (0.17), residues: 882 loop : -2.62 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 13 HIS 0.006 0.001 HIS B 96 PHE 0.020 0.002 PHE A 185 TYR 0.024 0.002 TYR K 53 ARG 0.004 0.001 ARG M 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 14) link_NAG-ASN : angle 2.33893 ( 42) hydrogen bonds : bond 0.04103 ( 552) hydrogen bonds : angle 4.85091 ( 2193) SS BOND : bond 0.00823 ( 35) SS BOND : angle 2.57684 ( 70) covalent geometry : bond 0.00589 (17920) covalent geometry : angle 0.81088 (24255) *********************** 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 490 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 398 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6867 (mpt180) REVERT: A 32 MET cc_start: 0.8201 (tmm) cc_final: 0.7930 (tmm) REVERT: A 38 SER cc_start: 0.8588 (m) cc_final: 0.8254 (p) REVERT: A 135 SER cc_start: 0.8893 (m) cc_final: 0.8525 (t) REVERT: A 180 GLU cc_start: 0.4577 (OUTLIER) cc_final: 0.4356 (pp20) REVERT: B 32 MET cc_start: 0.8024 (tmm) cc_final: 0.7698 (tmm) REVERT: B 38 SER cc_start: 0.8437 (m) cc_final: 0.8186 (p) REVERT: B 95 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8233 (m170) REVERT: B 99 SER cc_start: 0.8461 (m) cc_final: 0.8151 (t) REVERT: B 140 VAL cc_start: 0.8001 (t) cc_final: 0.7709 (p) REVERT: B 165 SER cc_start: 0.8343 (m) cc_final: 0.8104 (t) REVERT: D 32 MET cc_start: 0.8051 (tmm) cc_final: 0.7722 (tmm) REVERT: D 37 MET cc_start: 0.8454 (ttp) cc_final: 0.8240 (ttp) REVERT: D 107 MET cc_start: 0.6133 (mtp) cc_final: 0.5874 (mtp) REVERT: D 115 ASP cc_start: 0.7662 (t0) cc_final: 0.7095 (t0) REVERT: F 11 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6995 (mpt180) REVERT: F 20 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8284 (p) REVERT: F 23 VAL cc_start: 0.8033 (p) cc_final: 0.7633 (m) REVERT: F 32 MET cc_start: 0.8498 (tmm) cc_final: 0.8010 (tmm) REVERT: F 38 SER cc_start: 0.8547 (m) cc_final: 0.8233 (p) REVERT: F 73 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7736 (mt-10) REVERT: F 107 MET cc_start: 0.6575 (mtp) cc_final: 0.6079 (mtp) REVERT: F 169 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6863 (mmp) REVERT: F 180 GLU cc_start: 0.4787 (OUTLIER) cc_final: 0.4460 (pp20) REVERT: G 6 TYR cc_start: 0.1516 (OUTLIER) cc_final: 0.0714 (t80) REVERT: G 29 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7591 (p) REVERT: I 20 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8204 (p) REVERT: I 32 MET cc_start: 0.8139 (tmm) cc_final: 0.7681 (tmm) REVERT: I 81 LEU cc_start: 0.8521 (tp) cc_final: 0.8132 (tp) REVERT: I 113 LYS cc_start: 0.6383 (mmtm) cc_final: 0.4998 (tttp) REVERT: I 131 THR cc_start: 0.8052 (p) cc_final: 0.7749 (m) REVERT: I 135 SER cc_start: 0.8770 (m) cc_final: 0.8314 (t) REVERT: J 74 ASN cc_start: 0.7824 (t0) cc_final: 0.7588 (t0) REVERT: K 14 TYR cc_start: 0.8297 (m-10) cc_final: 0.7965 (m-10) REVERT: K 51 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8002 (p) REVERT: K 55 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7198 (pp) REVERT: K 115 ASP cc_start: 0.7837 (t0) cc_final: 0.7376 (t0) REVERT: L 0 MET cc_start: 0.4022 (OUTLIER) cc_final: 0.3686 (mmm) REVERT: M 20 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8192 (p) REVERT: M 32 MET cc_start: 0.8113 (tmm) cc_final: 0.7747 (tmm) REVERT: M 44 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6556 (tpp80) REVERT: M 96 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8057 (m-70) REVERT: M 113 LYS cc_start: 0.6768 (mmtm) cc_final: 0.5220 (tttp) REVERT: M 115 ASP cc_start: 0.7577 (t0) cc_final: 0.7280 (t0) REVERT: M 135 SER cc_start: 0.8875 (m) cc_final: 0.8480 (t) REVERT: M 180 GLU cc_start: 0.5491 (OUTLIER) cc_final: 0.5179 (pp20) outliers start: 92 outliers final: 66 residues processed: 467 average time/residue: 0.2808 time to fit residues: 203.9979 Evaluate side-chains 478 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 396 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP 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 85 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 4 CYS 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 56 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU 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 56 GLU 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 20 THR Chi-restraints excluded: chain F residue 27 ILE 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 129 ASP Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 169 MET 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 0 MET Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 73 HIS 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 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 101 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 50 LEU Chi-restraints excluded: chain K residue 51 THR 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 158 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 0 MET Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR 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 96 HIS Chi-restraints excluded: chain M residue 139 CYS Chi-restraints excluded: chain M residue 180 GLU 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 93 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 45 ASN D 89 GLN D 97 ASN F 45 ASN I 89 GLN M 133 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147052 restraints weight = 24964.091| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.32 r_work: 0.3729 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17969 Z= 0.187 Angle : 0.781 11.088 24367 Z= 0.406 Chirality : 0.048 0.173 2737 Planarity : 0.005 0.056 3080 Dihedral : 6.717 59.587 2786 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 4.12 % Allowed : 23.79 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.22 (0.17), residues: 875 loop : -2.64 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 13 HIS 0.005 0.001 HIS B 96 PHE 0.016 0.001 PHE A 185 TYR 0.022 0.002 TYR K 53 ARG 0.004 0.001 ARG D 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 14) link_NAG-ASN : angle 2.24546 ( 42) hydrogen bonds : bond 0.03729 ( 552) hydrogen bonds : angle 4.71941 ( 2193) SS BOND : bond 0.00654 ( 35) SS BOND : angle 2.35363 ( 70) covalent geometry : bond 0.00428 (17920) covalent geometry : angle 0.76673 (24255) ********************** 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: 81 poor density : 396 time to evaluate : 4.181 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6728 (mpt180) REVERT: A 32 MET cc_start: 0.8117 (tmm) cc_final: 0.7846 (tmm) REVERT: A 38 SER cc_start: 0.8518 (m) cc_final: 0.8199 (p) REVERT: A 135 SER cc_start: 0.8890 (m) cc_final: 0.8528 (t) REVERT: A 180 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.4441 (pp20) REVERT: B 32 MET cc_start: 0.7993 (tmm) cc_final: 0.7639 (tmm) REVERT: B 38 SER cc_start: 0.8511 (m) cc_final: 0.8231 (p) REVERT: B 95 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.8336 (m170) REVERT: B 99 SER cc_start: 0.8442 (m) cc_final: 0.8105 (t) REVERT: B 140 VAL cc_start: 0.7947 (t) cc_final: 0.7653 (p) REVERT: B 165 SER cc_start: 0.8371 (m) cc_final: 0.8135 (t) REVERT: D 32 MET cc_start: 0.7990 (tmm) cc_final: 0.7616 (tmm) REVERT: D 107 MET cc_start: 0.6034 (mtp) cc_final: 0.5781 (mtp) REVERT: D 115 ASP cc_start: 0.7735 (t0) cc_final: 0.7142 (t0) REVERT: F 11 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6779 (mpt180) REVERT: F 20 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8262 (p) REVERT: F 23 VAL cc_start: 0.7983 (p) cc_final: 0.7565 (m) REVERT: F 32 MET cc_start: 0.8450 (tmm) cc_final: 0.7904 (tmm) REVERT: F 38 SER cc_start: 0.8560 (m) cc_final: 0.8211 (p) REVERT: F 41 TYR cc_start: 0.8311 (t80) cc_final: 0.8069 (t80) REVERT: F 107 MET cc_start: 0.6479 (mtp) cc_final: 0.5869 (mtp) REVERT: F 169 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6780 (mmp) REVERT: F 180 GLU cc_start: 0.4865 (OUTLIER) cc_final: 0.4540 (pp20) REVERT: G 6 TYR cc_start: 0.1437 (OUTLIER) cc_final: 0.0650 (t80) REVERT: G 29 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7540 (p) REVERT: I 20 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8170 (p) REVERT: I 32 MET cc_start: 0.8114 (tmm) cc_final: 0.7607 (tmm) REVERT: I 36 HIS cc_start: 0.8078 (m90) cc_final: 0.7757 (m170) REVERT: I 81 LEU cc_start: 0.8445 (tp) cc_final: 0.8059 (tp) REVERT: I 89 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7178 (mt0) REVERT: I 131 THR cc_start: 0.8013 (p) cc_final: 0.7730 (m) REVERT: I 135 SER cc_start: 0.8753 (m) cc_final: 0.8288 (t) REVERT: J 58 MET cc_start: 0.7198 (mmm) cc_final: 0.6727 (mmm) REVERT: J 74 ASN cc_start: 0.7796 (t0) cc_final: 0.7504 (t0) REVERT: K 14 TYR cc_start: 0.8287 (m-10) cc_final: 0.8020 (m-10) REVERT: K 51 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7952 (p) REVERT: K 55 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7268 (pp) REVERT: K 115 ASP cc_start: 0.7878 (t0) cc_final: 0.7440 (t0) REVERT: L 101 MET cc_start: 0.7348 (tpp) cc_final: 0.7128 (tpp) REVERT: M 20 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8245 (p) REVERT: M 32 MET cc_start: 0.8133 (tmm) cc_final: 0.7758 (tmm) REVERT: M 44 ARG cc_start: 0.6629 (tpt-90) cc_final: 0.6386 (tpp80) REVERT: M 96 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8071 (m-70) REVERT: M 113 LYS cc_start: 0.6561 (mmtm) cc_final: 0.5085 (tttp) REVERT: M 115 ASP cc_start: 0.7589 (t0) cc_final: 0.7291 (t0) REVERT: M 135 SER cc_start: 0.8818 (m) cc_final: 0.8477 (t) REVERT: M 187 ASP cc_start: 0.7769 (t0) cc_final: 0.7502 (t0) outliers start: 81 outliers final: 65 residues processed: 453 average time/residue: 0.3021 time to fit residues: 214.1931 Evaluate side-chains 474 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 394 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 26 ASP 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 85 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 4 CYS 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 56 GLU 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 176 THR Chi-restraints excluded: chain B residue 186 LEU 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 56 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 158 ASP 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 20 THR Chi-restraints excluded: chain F residue 27 ILE 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 139 CYS Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain G residue 0 MET Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 73 HIS 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 64 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 101 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 50 LEU Chi-restraints excluded: chain K residue 51 THR 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 186 LEU Chi-restraints excluded: chain M residue 4 CYS Chi-restraints excluded: chain M residue 20 THR 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 81 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 95 HIS Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 139 CYS 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 97 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 0.0000 chunk 193 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 overall best weight: 1.0108 ------------------------------------------------------------------------------- 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 I 89 GLN K 45 ASN M 97 ASN M 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147023 restraints weight = 25043.794| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.33 r_work: 0.3736 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3407 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= 0.190 Angle : 0.775 11.183 24367 Z= 0.403 Chirality : 0.048 0.181 2737 Planarity : 0.005 0.061 3080 Dihedral : 6.657 59.174 2784 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 4.83 % Allowed : 23.18 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.09 (0.17), residues: 889 loop : -2.58 (0.15), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.005 0.001 HIS B 96 PHE 0.016 0.001 PHE A 185 TYR 0.021 0.001 TYR K 53 ARG 0.004 0.001 ARG D 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 14) link_NAG-ASN : angle 2.22346 ( 42) hydrogen bonds : bond 0.03754 ( 552) hydrogen bonds : angle 4.71146 ( 2193) SS BOND : bond 0.00654 ( 35) SS BOND : angle 2.30680 ( 70) covalent geometry : bond 0.00435 (17920) covalent geometry : angle 0.76117 (24255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11353.22 seconds wall clock time: 202 minutes 15.01 seconds (12135.01 seconds total)