Starting phenix.real_space_refine on Sun May 18 20:25:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxx_29547/05_2025/8fxx_29547_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxx_29547/05_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_29547/05_2025/8fxx_29547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxx_29547/05_2025/8fxx_29547.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxx_29547/05_2025/8fxx_29547_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxx_29547/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.94, per 1000 atoms: 0.57 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: 4.42 Conformation dependent library (CDL) restraints added in 2.3 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: 3.44 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: 6.23 Time building geometry restraints manager: 5.17 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.950 Find NCS groups from input model: 0.730 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- 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 : 2.035 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: 0.2465 time to fit residues: 207.5905 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 : 1.793 ------------------------------------------------------------------------------- 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 = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149883 restraints weight = 25521.790| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.48 r_work: 0.3753 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 3.10290 ( 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 : 1.879 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.7863 (tmm) cc_final: 0.7547 (tmm) REVERT: A 38 SER cc_start: 0.8448 (m) cc_final: 0.8082 (p) REVERT: A 51 THR cc_start: 0.8427 (t) cc_final: 0.8171 (p) REVERT: A 78 ASP cc_start: 0.7467 (t0) cc_final: 0.6936 (t0) REVERT: A 135 SER cc_start: 0.8961 (m) cc_final: 0.8364 (t) REVERT: A 159 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7833 (mmtp) REVERT: A 180 GLU cc_start: 0.4664 (OUTLIER) cc_final: 0.4286 (pp20) REVERT: A 196 CYS cc_start: 0.5807 (OUTLIER) cc_final: 0.5514 (t) REVERT: B 32 MET cc_start: 0.7659 (tmm) cc_final: 0.7038 (tmm) REVERT: B 38 SER cc_start: 0.8510 (m) cc_final: 0.8171 (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: 0.7938 (p) REVERT: B 140 VAL cc_start: 0.7916 (t) cc_final: 0.7526 (p) REVERT: B 165 SER cc_start: 0.8368 (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: 0.6098 (t) REVERT: D 38 SER cc_start: 0.8424 (m) cc_final: 0.8223 (p) REVERT: D 115 ASP cc_start: 0.7462 (t0) cc_final: 0.6884 (t0) REVERT: D 180 GLU cc_start: 0.4938 (OUTLIER) cc_final: 0.4592 (pp20) REVERT: E 0 MET cc_start: 0.5787 (mmm) cc_final: 0.5446 (mmm) REVERT: F 23 VAL cc_start: 0.7652 (p) cc_final: 0.7403 (m) REVERT: F 32 MET cc_start: 0.7884 (tmm) cc_final: 0.7341 (tmm) REVERT: F 38 SER cc_start: 0.8393 (m) cc_final: 0.8067 (p) REVERT: F 41 TYR cc_start: 0.8249 (t80) cc_final: 0.8026 (t80) REVERT: F 100 VAL cc_start: 0.8399 (p) cc_final: 0.8177 (t) REVERT: F 107 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5838 (ttm) REVERT: F 170 ARG cc_start: 0.7516 (ptm-80) cc_final: 0.7111 (ptm160) REVERT: F 180 GLU cc_start: 0.4790 (OUTLIER) cc_final: 0.4429 (pp20) REVERT: G 74 ASN cc_start: 0.7871 (t0) cc_final: 0.7540 (t0) REVERT: I 32 MET cc_start: 0.7696 (tmm) cc_final: 0.7154 (tmm) REVERT: I 37 MET cc_start: 0.8451 (ptm) cc_final: 0.8135 (ptm) REVERT: I 38 SER cc_start: 0.8440 (m) cc_final: 0.8060 (p) REVERT: I 41 TYR cc_start: 0.8209 (t80) cc_final: 0.7996 (t80) REVERT: I 131 THR cc_start: 0.7960 (p) cc_final: 0.7691 (m) REVERT: I 135 SER cc_start: 0.8923 (m) cc_final: 0.8380 (t) REVERT: J 58 MET cc_start: 0.7153 (mmt) cc_final: 0.6884 (mmt) REVERT: J 74 ASN cc_start: 0.7845 (t0) cc_final: 0.7549 (t0) REVERT: K 38 SER cc_start: 0.8546 (m) cc_final: 0.8181 (p) REVERT: K 51 THR cc_start: 0.8073 (t) cc_final: 0.7801 (p) REVERT: K 99 SER cc_start: 0.8010 (m) cc_final: 0.7710 (m) REVERT: K 115 ASP cc_start: 0.7579 (t0) cc_final: 0.7175 (t0) REVERT: K 129 ASP cc_start: 0.6809 (p0) cc_final: 0.6572 (p0) REVERT: K 180 GLU cc_start: 0.4694 (OUTLIER) cc_final: 0.4370 (pp20) REVERT: L 74 ASN cc_start: 0.7873 (t0) cc_final: 0.7562 (t0) REVERT: M 32 MET cc_start: 0.7734 (tmm) cc_final: 0.7327 (tmm) REVERT: M 38 SER cc_start: 0.8426 (m) cc_final: 0.8188 (p) REVERT: M 44 ARG cc_start: 0.6413 (tpt-90) cc_final: 0.6114 (tpp80) REVERT: M 99 SER cc_start: 0.8145 (m) cc_final: 0.7935 (m) REVERT: M 115 ASP cc_start: 0.7450 (t0) cc_final: 0.7180 (t0) REVERT: M 127 SER cc_start: 0.8504 (p) cc_final: 0.8304 (p) REVERT: M 135 SER cc_start: 0.8925 (m) cc_final: 0.8495 (t) REVERT: M 180 GLU cc_start: 0.5133 (OUTLIER) cc_final: 0.4815 (pp20) outliers start: 99 outliers final: 45 residues processed: 483 average time/residue: 0.2455 time to fit residues: 187.1078 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 : 1.803 ------------------------------------------------------------------------------- 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: 0.4980 chunk 126 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 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: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.170152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146043 restraints weight = 24819.842| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.26 r_work: 0.3730 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17969 Z= 0.218 Angle : 0.792 11.536 24367 Z= 0.412 Chirality : 0.049 0.205 2737 Planarity : 0.005 0.065 3080 Dihedral : 7.975 59.815 2816 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 5.69 % Allowed : 17.49 % Favored : 76.82 % 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: -2.07 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.24 (0.17), residues: 868 loop : -2.77 (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 0.004 0.001 ARG F 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 14) link_NAG-ASN : angle 2.29758 ( 42) hydrogen bonds : bond 0.04057 ( 552) hydrogen bonds : angle 4.93637 ( 2193) SS BOND : bond 0.00647 ( 35) SS BOND : angle 2.84482 ( 70) covalent geometry : bond 0.00504 (17920) covalent geometry : angle 0.77319 (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: 112 poor density : 405 time to evaluate : 1.915 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6840 (mpt180) REVERT: A 32 MET cc_start: 0.8138 (tmm) cc_final: 0.7831 (tmm) REVERT: A 38 SER cc_start: 0.8563 (m) cc_final: 0.8219 (p) REVERT: A 51 THR cc_start: 0.8514 (t) cc_final: 0.8298 (p) REVERT: A 78 ASP cc_start: 0.7614 (t0) cc_final: 0.7114 (t0) REVERT: A 113 LYS cc_start: 0.6262 (mptt) cc_final: 0.4326 (tttp) REVERT: A 133 ASN cc_start: 0.8330 (m-40) cc_final: 0.8048 (m-40) REVERT: A 135 SER cc_start: 0.8927 (m) cc_final: 0.8468 (t) REVERT: A 159 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7984 (mmtp) REVERT: A 180 GLU cc_start: 0.4715 (OUTLIER) cc_final: 0.4424 (pp20) REVERT: A 196 CYS cc_start: 0.6359 (OUTLIER) cc_final: 0.6029 (t) REVERT: B 11 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6849 (mpt180) REVERT: B 32 MET cc_start: 0.7994 (tmm) cc_final: 0.7602 (tmm) REVERT: B 38 SER cc_start: 0.8548 (m) cc_final: 0.8273 (p) REVERT: B 51 THR cc_start: 0.8541 (t) cc_final: 0.8323 (p) REVERT: B 140 VAL cc_start: 0.7980 (t) cc_final: 0.7768 (p) REVERT: B 165 SER cc_start: 0.8414 (m) cc_final: 0.8160 (t) REVERT: B 180 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4763 (pp20) REVERT: C 8 ASN cc_start: 0.6924 (t0) cc_final: 0.6675 (m-40) REVERT: D 7 ARG cc_start: 0.6256 (tpt170) cc_final: 0.6024 (tpt170) REVERT: D 115 ASP cc_start: 0.7650 (t0) cc_final: 0.7078 (t0) REVERT: D 180 GLU cc_start: 0.5114 (OUTLIER) cc_final: 0.4801 (pp20) REVERT: E 0 MET cc_start: 0.5797 (mmm) cc_final: 0.5547 (mmm) REVERT: F 11 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6553 (mpt180) REVERT: F 23 VAL cc_start: 0.7968 (p) cc_final: 0.7560 (m) REVERT: F 32 MET cc_start: 0.8409 (tmm) cc_final: 0.7838 (tmm) REVERT: F 38 SER cc_start: 0.8542 (m) cc_final: 0.8197 (p) REVERT: F 41 TYR cc_start: 0.8322 (t80) cc_final: 0.8094 (t80) REVERT: F 95 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8295 (m170) REVERT: F 96 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.8221 (m-70) REVERT: F 100 VAL cc_start: 0.8504 (p) cc_final: 0.8270 (t) REVERT: G 74 ASN cc_start: 0.7964 (t0) cc_final: 0.7704 (t0) REVERT: I 11 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6864 (mpt180) REVERT: I 20 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8067 (p) REVERT: I 32 MET cc_start: 0.8116 (tmm) cc_final: 0.7614 (tmm) REVERT: I 37 MET cc_start: 0.8612 (ptm) cc_final: 0.8376 (ptm) REVERT: I 38 SER cc_start: 0.8507 (m) cc_final: 0.8141 (p) REVERT: I 96 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.7972 (m-70) REVERT: I 108 ASN cc_start: 0.7464 (m-40) cc_final: 0.7228 (m-40) REVERT: I 131 THR cc_start: 0.8141 (p) cc_final: 0.7815 (m) REVERT: I 135 SER cc_start: 0.8969 (m) cc_final: 0.8457 (t) REVERT: I 180 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.4930 (pp20) REVERT: J 58 MET cc_start: 0.7437 (mmt) cc_final: 0.7162 (mmt) REVERT: J 74 ASN cc_start: 0.7864 (t0) cc_final: 0.7611 (t0) REVERT: K 51 THR cc_start: 0.8322 (t) cc_final: 0.8026 (p) REVERT: K 99 SER cc_start: 0.8220 (m) cc_final: 0.7980 (m) REVERT: K 115 ASP cc_start: 0.7809 (t0) cc_final: 0.7407 (t0) REVERT: K 129 ASP cc_start: 0.7219 (p0) cc_final: 0.6961 (p0) REVERT: K 159 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8135 (mmtp) REVERT: K 160 TYR cc_start: 0.7692 (m-10) cc_final: 0.7463 (m-10) REVERT: L 40 LEU cc_start: 0.8624 (mt) cc_final: 0.8350 (mm) REVERT: L 74 ASN cc_start: 0.7918 (t0) cc_final: 0.7671 (t0) REVERT: M 20 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8192 (p) REVERT: M 32 MET cc_start: 0.8081 (tmm) cc_final: 0.7695 (tmm) REVERT: M 38 SER cc_start: 0.8547 (m) cc_final: 0.8297 (p) REVERT: M 44 ARG cc_start: 0.6804 (tpt-90) cc_final: 0.6497 (tpp80) REVERT: M 99 SER cc_start: 0.8309 (m) cc_final: 0.8015 (m) REVERT: M 115 ASP cc_start: 0.7609 (t0) cc_final: 0.7352 (t0) REVERT: M 135 SER cc_start: 0.8936 (m) cc_final: 0.8523 (t) REVERT: N 74 ASN cc_start: 0.7840 (t0) cc_final: 0.7531 (t0) outliers start: 112 outliers final: 73 residues processed: 481 average time/residue: 0.2601 time to fit residues: 194.0383 Evaluate side-chains 476 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 389 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 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 35 CYS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 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 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 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 138 THR 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: 4.9990 chunk 153 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.171268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.147303 restraints weight = 24883.977| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.26 r_work: 0.3754 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17969 Z= 0.174 Angle : 0.745 10.848 24367 Z= 0.387 Chirality : 0.047 0.189 2737 Planarity : 0.004 0.059 3080 Dihedral : 7.415 59.405 2801 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 5.80 % Allowed : 18.71 % Favored : 75.50 % 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: -1.98 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.29 (0.17), residues: 868 loop : -2.69 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 13 HIS 0.004 0.001 HIS I 96 PHE 0.019 0.001 PHE A 185 TYR 0.024 0.001 TYR K 53 ARG 0.004 0.001 ARG M 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 14) link_NAG-ASN : angle 2.31890 ( 42) hydrogen bonds : bond 0.03695 ( 552) hydrogen bonds : angle 4.76105 ( 2193) SS BOND : bond 0.00599 ( 35) SS BOND : angle 2.55216 ( 70) covalent geometry : bond 0.00400 (17920) covalent geometry : angle 0.72763 (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 486 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 372 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6636 (mpt180) REVERT: A 32 MET cc_start: 0.7998 (tmm) cc_final: 0.7720 (tmm) REVERT: A 38 SER cc_start: 0.8525 (m) cc_final: 0.8199 (p) REVERT: A 51 THR cc_start: 0.8487 (t) cc_final: 0.8285 (p) REVERT: A 113 LYS cc_start: 0.6197 (mptt) cc_final: 0.4242 (tttm) REVERT: A 133 ASN cc_start: 0.8290 (m-40) cc_final: 0.8021 (m-40) REVERT: A 135 SER cc_start: 0.8922 (m) cc_final: 0.8507 (t) REVERT: A 180 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.4253 (pp20) REVERT: A 196 CYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5930 (t) REVERT: B 32 MET cc_start: 0.7939 (tmm) cc_final: 0.7551 (tmm) REVERT: B 38 SER cc_start: 0.8558 (m) cc_final: 0.8272 (p) REVERT: B 96 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8279 (m-70) REVERT: B 127 SER cc_start: 0.8444 (m) cc_final: 0.7988 (p) REVERT: B 140 VAL cc_start: 0.8017 (t) cc_final: 0.7701 (p) REVERT: B 165 SER cc_start: 0.8379 (m) cc_final: 0.8116 (t) REVERT: B 180 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.4649 (pp20) REVERT: C 8 ASN cc_start: 0.6931 (t0) cc_final: 0.6720 (m-40) REVERT: D 11 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6841 (mpt180) REVERT: D 32 MET cc_start: 0.8037 (tmm) cc_final: 0.7541 (tmm) REVERT: D 107 MET cc_start: 0.6139 (mtp) cc_final: 0.5930 (mtp) REVERT: D 180 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4839 (pp20) REVERT: E 0 MET cc_start: 0.5767 (mmm) cc_final: 0.5472 (mmm) REVERT: F 20 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8257 (p) REVERT: F 23 VAL cc_start: 0.7985 (p) cc_final: 0.7566 (m) REVERT: F 32 MET cc_start: 0.8318 (tmm) cc_final: 0.7775 (tmm) REVERT: F 38 SER cc_start: 0.8475 (m) cc_final: 0.8170 (p) REVERT: F 41 TYR cc_start: 0.8311 (t80) cc_final: 0.8053 (t80) REVERT: F 50 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7410 (mp) REVERT: F 95 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8250 (m170) REVERT: F 100 VAL cc_start: 0.8475 (p) cc_final: 0.8259 (t) REVERT: F 169 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6805 (mmm) REVERT: G 74 ASN cc_start: 0.7843 (t0) cc_final: 0.7611 (t0) REVERT: I 20 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8062 (p) REVERT: I 32 MET cc_start: 0.8145 (tmm) cc_final: 0.7641 (tmm) REVERT: I 37 MET cc_start: 0.8605 (ptm) cc_final: 0.8383 (ptm) REVERT: I 38 SER cc_start: 0.8517 (m) cc_final: 0.8139 (p) REVERT: I 96 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.7951 (m-70) REVERT: I 131 THR cc_start: 0.8046 (p) cc_final: 0.7766 (m) REVERT: I 135 SER cc_start: 0.8913 (m) cc_final: 0.8360 (t) REVERT: I 180 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4623 (pp20) REVERT: J 58 MET cc_start: 0.7455 (mmt) cc_final: 0.7239 (mmt) REVERT: J 74 ASN cc_start: 0.7770 (t0) cc_final: 0.7569 (t0) REVERT: K 51 THR cc_start: 0.8269 (t) cc_final: 0.7976 (p) REVERT: K 55 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7289 (pp) REVERT: K 99 SER cc_start: 0.8216 (m) cc_final: 0.7951 (m) REVERT: K 115 ASP cc_start: 0.7794 (t0) cc_final: 0.7389 (t0) REVERT: K 129 ASP cc_start: 0.7193 (p0) cc_final: 0.6932 (p0) REVERT: M 20 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8204 (p) REVERT: M 26 ASP cc_start: 0.7919 (m-30) cc_final: 0.7665 (m-30) REVERT: M 32 MET cc_start: 0.8089 (tmm) cc_final: 0.7711 (tmm) REVERT: M 44 ARG cc_start: 0.6610 (tpt-90) cc_final: 0.6352 (tpp80) REVERT: M 55 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7515 (pp) REVERT: M 96 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.8050 (m-70) REVERT: M 99 SER cc_start: 0.8371 (m) cc_final: 0.8140 (m) REVERT: M 115 ASP cc_start: 0.7614 (t0) cc_final: 0.7343 (t0) REVERT: M 129 ASP cc_start: 0.6453 (p0) cc_final: 0.6101 (p0) REVERT: M 135 SER cc_start: 0.8903 (m) cc_final: 0.8541 (t) REVERT: N 74 ASN cc_start: 0.7820 (t0) cc_final: 0.7545 (t0) REVERT: N 101 MET cc_start: 0.7687 (tpp) cc_final: 0.7456 (tpp) outliers start: 114 outliers final: 69 residues processed: 455 average time/residue: 0.2650 time to fit residues: 186.6396 Evaluate side-chains 455 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 368 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 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 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 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 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 165 SER Chi-restraints excluded: chain F residue 169 MET 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 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 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 55 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 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: 2.9990 chunk 177 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 97 ASN I 141 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN M 133 ASN N 8 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144510 restraints weight = 25096.057| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.26 r_work: 0.3722 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17969 Z= 0.228 Angle : 0.787 11.195 24367 Z= 0.411 Chirality : 0.049 0.194 2737 Planarity : 0.005 0.068 3080 Dihedral : 7.564 59.075 2800 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 6.76 % Allowed : 19.22 % Favored : 74.02 % 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: -2.12 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.09 (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 F 13 HIS 0.005 0.001 HIS M 96 PHE 0.021 0.001 PHE A 185 TYR 0.027 0.002 TYR K 53 ARG 0.007 0.001 ARG M 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 14) link_NAG-ASN : angle 2.36659 ( 42) hydrogen bonds : bond 0.04052 ( 552) hydrogen bonds : angle 4.89881 ( 2193) SS BOND : bond 0.00747 ( 35) SS BOND : angle 2.70345 ( 70) covalent geometry : bond 0.00522 (17920) covalent geometry : angle 0.76869 (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 535 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 402 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6819 (mpt180) REVERT: A 32 MET cc_start: 0.8088 (tmm) cc_final: 0.7816 (tmm) REVERT: A 38 SER cc_start: 0.8492 (m) cc_final: 0.8221 (p) REVERT: A 113 LYS cc_start: 0.6531 (mptt) cc_final: 0.4442 (tttm) REVERT: A 133 ASN cc_start: 0.8289 (m-40) cc_final: 0.8027 (m-40) REVERT: A 135 SER cc_start: 0.8923 (m) cc_final: 0.8521 (t) REVERT: A 180 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.4323 (pp20) REVERT: A 196 CYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5916 (t) REVERT: B 11 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6786 (mpt180) REVERT: B 32 MET cc_start: 0.8000 (tmm) cc_final: 0.7643 (tmm) REVERT: B 38 SER cc_start: 0.8558 (m) cc_final: 0.8272 (p) REVERT: B 95 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8184 (m170) REVERT: B 99 SER cc_start: 0.8397 (m) cc_final: 0.8054 (t) REVERT: B 140 VAL cc_start: 0.8050 (t) cc_final: 0.7758 (p) REVERT: B 165 SER cc_start: 0.8348 (m) cc_final: 0.8101 (t) REVERT: B 180 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4706 (pp20) REVERT: D 11 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6941 (mpt180) REVERT: D 32 MET cc_start: 0.8082 (tmm) cc_final: 0.7680 (tmm) REVERT: D 115 ASP cc_start: 0.7692 (t0) cc_final: 0.7101 (t0) REVERT: D 180 GLU cc_start: 0.5195 (OUTLIER) cc_final: 0.4884 (pp20) REVERT: E 0 MET cc_start: 0.5652 (mmm) cc_final: 0.5296 (mmm) REVERT: F 11 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6989 (mpt180) REVERT: F 23 VAL cc_start: 0.8020 (p) cc_final: 0.7673 (m) REVERT: F 32 MET cc_start: 0.8392 (tmm) cc_final: 0.7877 (tmm) REVERT: F 38 SER cc_start: 0.8427 (m) cc_final: 0.8136 (p) REVERT: F 41 TYR cc_start: 0.8353 (t80) cc_final: 0.8144 (t80) REVERT: F 95 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8206 (m170) REVERT: F 100 VAL cc_start: 0.8470 (p) cc_final: 0.8247 (t) REVERT: F 169 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6730 (mmp) REVERT: F 180 GLU cc_start: 0.5090 (OUTLIER) cc_final: 0.4718 (pp20) REVERT: G 6 TYR cc_start: 0.1547 (OUTLIER) cc_final: 0.0768 (t80) REVERT: G 74 ASN cc_start: 0.7884 (t0) cc_final: 0.7644 (t0) REVERT: I 20 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8115 (p) REVERT: I 32 MET cc_start: 0.8226 (tmm) cc_final: 0.7732 (tmm) REVERT: I 37 MET cc_start: 0.8601 (ptm) cc_final: 0.8390 (ptm) REVERT: I 38 SER cc_start: 0.8536 (m) cc_final: 0.8153 (p) REVERT: I 81 LEU cc_start: 0.8507 (tp) cc_final: 0.8184 (tp) REVERT: I 92 ASP cc_start: 0.7309 (t0) cc_final: 0.7103 (t0) REVERT: I 96 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.7806 (m-70) REVERT: I 131 THR cc_start: 0.8109 (p) cc_final: 0.7784 (m) REVERT: I 135 SER cc_start: 0.8858 (m) cc_final: 0.8379 (t) REVERT: I 141 ASN cc_start: 0.7985 (t0) cc_final: 0.7784 (t0) REVERT: I 150 ASN cc_start: 0.6018 (OUTLIER) cc_final: 0.5746 (m-40) REVERT: J 58 MET cc_start: 0.7600 (mmt) cc_final: 0.7389 (mmt) REVERT: K 55 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7199 (pp) REVERT: K 115 ASP cc_start: 0.7844 (t0) cc_final: 0.7425 (t0) REVERT: K 129 ASP cc_start: 0.7370 (p0) cc_final: 0.6996 (p0) REVERT: M 20 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8253 (p) REVERT: M 32 MET cc_start: 0.8120 (tmm) cc_final: 0.7743 (tmm) REVERT: M 44 ARG cc_start: 0.6864 (tpt-90) cc_final: 0.6530 (tpp80) REVERT: M 96 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7986 (m-70) REVERT: M 99 SER cc_start: 0.8327 (m) cc_final: 0.7990 (m) REVERT: M 113 LYS cc_start: 0.6682 (mmtm) cc_final: 0.5177 (tttp) REVERT: M 115 ASP cc_start: 0.7582 (t0) cc_final: 0.7325 (t0) REVERT: M 135 SER cc_start: 0.8938 (m) cc_final: 0.8555 (t) REVERT: N 74 ASN cc_start: 0.7869 (t0) cc_final: 0.7651 (t0) REVERT: N 101 MET cc_start: 0.7805 (tpp) cc_final: 0.7580 (tpp) outliers start: 133 outliers final: 92 residues processed: 495 average time/residue: 0.2610 time to fit residues: 199.4531 Evaluate side-chains 508 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 397 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 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 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 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 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 38 SER 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 158 ASP 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 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 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 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 111 THR Chi-restraints excluded: chain I residue 150 ASN 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 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 138 THR 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 38 SER 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: 0.3980 chunk 79 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 96 HIS F 96 HIS F 108 ASN F 150 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.147491 restraints weight = 25093.729| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.30 r_work: 0.3756 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2927 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= 0.153 Angle : 0.722 9.811 24367 Z= 0.375 Chirality : 0.046 0.158 2737 Planarity : 0.004 0.052 3080 Dihedral : 7.081 59.715 2798 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 5.44 % Allowed : 20.79 % Favored : 73.77 % 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: -1.96 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.24 (0.17), residues: 875 loop : -2.64 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 13 HIS 0.005 0.001 HIS D 96 PHE 0.016 0.001 PHE A 185 TYR 0.019 0.001 TYR K 53 ARG 0.003 0.000 ARG M 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 14) link_NAG-ASN : angle 2.27791 ( 42) hydrogen bonds : bond 0.03516 ( 552) hydrogen bonds : angle 4.64996 ( 2193) SS BOND : bond 0.00576 ( 35) SS BOND : angle 2.27610 ( 70) covalent geometry : bond 0.00347 (17920) covalent geometry : angle 0.70684 (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 491 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 384 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6619 (mpt180) REVERT: A 32 MET cc_start: 0.8107 (tmm) cc_final: 0.7840 (tmm) REVERT: A 38 SER cc_start: 0.8575 (m) cc_final: 0.8240 (p) REVERT: A 78 ASP cc_start: 0.7682 (t0) cc_final: 0.7251 (t0) REVERT: A 105 MET cc_start: 0.8253 (mmt) cc_final: 0.8017 (mtp) REVERT: A 113 LYS cc_start: 0.6137 (mptt) cc_final: 0.4239 (tttm) REVERT: A 135 SER cc_start: 0.8876 (m) cc_final: 0.8511 (t) REVERT: A 180 GLU cc_start: 0.4743 (OUTLIER) cc_final: 0.4442 (pp20) REVERT: A 196 CYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5657 (t) REVERT: B 32 MET cc_start: 0.8013 (tmm) cc_final: 0.7700 (tmm) REVERT: B 38 SER cc_start: 0.8502 (m) cc_final: 0.8269 (p) REVERT: B 99 SER cc_start: 0.8473 (m) cc_final: 0.8075 (t) REVERT: B 127 SER cc_start: 0.8455 (m) cc_final: 0.8023 (p) REVERT: B 140 VAL cc_start: 0.7992 (t) cc_final: 0.7679 (p) REVERT: B 165 SER cc_start: 0.8392 (m) cc_final: 0.8113 (t) REVERT: B 180 GLU cc_start: 0.5084 (OUTLIER) cc_final: 0.4765 (pp20) REVERT: D 11 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6862 (mpt180) REVERT: D 32 MET cc_start: 0.7999 (tmm) cc_final: 0.7618 (tmm) REVERT: D 115 ASP cc_start: 0.7705 (t0) cc_final: 0.7133 (t0) REVERT: D 180 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4875 (pp20) REVERT: F 11 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6679 (mpt180) REVERT: F 20 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8304 (p) REVERT: F 23 VAL cc_start: 0.7963 (p) cc_final: 0.7570 (m) REVERT: F 32 MET cc_start: 0.8442 (tmm) cc_final: 0.7885 (tmm) REVERT: F 38 SER cc_start: 0.8537 (m) cc_final: 0.8246 (p) REVERT: F 41 TYR cc_start: 0.8268 (t80) cc_final: 0.8023 (t80) REVERT: F 95 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.8222 (m170) REVERT: F 100 VAL cc_start: 0.8442 (p) cc_final: 0.8208 (t) REVERT: F 160 TYR cc_start: 0.7928 (m-10) cc_final: 0.7701 (m-80) REVERT: F 169 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6713 (mmp) REVERT: F 180 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.4631 (pp20) REVERT: G 74 ASN cc_start: 0.7862 (t0) cc_final: 0.7625 (t0) REVERT: I 20 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8001 (p) REVERT: I 32 MET cc_start: 0.8122 (tmm) cc_final: 0.7616 (tmm) REVERT: I 37 MET cc_start: 0.8563 (ptm) cc_final: 0.8362 (ptm) REVERT: I 38 SER cc_start: 0.8542 (m) cc_final: 0.8175 (p) REVERT: I 51 THR cc_start: 0.8497 (t) cc_final: 0.8195 (p) REVERT: I 96 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7886 (m-70) REVERT: I 131 THR cc_start: 0.8007 (p) cc_final: 0.7747 (m) REVERT: I 135 SER cc_start: 0.8802 (m) cc_final: 0.8304 (t) REVERT: I 160 TYR cc_start: 0.8001 (m-10) cc_final: 0.7619 (m-80) REVERT: J 58 MET cc_start: 0.7588 (mmt) cc_final: 0.7371 (mmt) REVERT: K 55 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7305 (pp) REVERT: K 115 ASP cc_start: 0.7835 (t0) cc_final: 0.7408 (t0) REVERT: K 129 ASP cc_start: 0.7322 (p0) cc_final: 0.7027 (p0) REVERT: M 20 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8220 (p) REVERT: M 32 MET cc_start: 0.8136 (tmm) cc_final: 0.7747 (tmm) REVERT: M 37 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8062 (ttp) REVERT: M 44 ARG cc_start: 0.6474 (tpt-90) cc_final: 0.6205 (tpp80) REVERT: M 96 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8047 (m-70) REVERT: M 99 SER cc_start: 0.8342 (m) cc_final: 0.8105 (m) REVERT: M 115 ASP cc_start: 0.7542 (t0) cc_final: 0.7251 (t0) REVERT: M 127 SER cc_start: 0.8629 (p) cc_final: 0.8414 (p) REVERT: M 135 SER cc_start: 0.8887 (m) cc_final: 0.8544 (t) REVERT: N 74 ASN cc_start: 0.7798 (t0) cc_final: 0.7589 (t0) outliers start: 107 outliers final: 75 residues processed: 461 average time/residue: 0.2580 time to fit residues: 183.9075 Evaluate side-chains 468 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 376 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 85 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 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 96 HIS 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 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 27 ILE Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER 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 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 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 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 111 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain K residue 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 138 THR 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 37 MET 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: 0.7980 chunk 126 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.166270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141990 restraints weight = 24645.209| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.23 r_work: 0.3687 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17969 Z= 0.307 Angle : 0.851 11.226 24367 Z= 0.446 Chirality : 0.052 0.223 2737 Planarity : 0.006 0.073 3080 Dihedral : 7.871 59.753 2798 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.54 % Favored : 87.42 % Rotamer: Outliers : 6.86 % Allowed : 20.03 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 5.36 % Twisted General : 0.05 % 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: -2.22 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: -0.02 (0.17), residues: 882 loop : -2.76 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 13 HIS 0.006 0.001 HIS M 96 PHE 0.018 0.002 PHE A 185 TYR 0.029 0.002 TYR K 53 ARG 0.005 0.001 ARG A 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 14) link_NAG-ASN : angle 2.49868 ( 42) hydrogen bonds : bond 0.04413 ( 552) hydrogen bonds : angle 5.02829 ( 2193) SS BOND : bond 0.00840 ( 35) SS BOND : angle 2.73245 ( 70) covalent geometry : bond 0.00704 (17920) covalent geometry : angle 0.83407 (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 527 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 392 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6982 (mpt180) REVERT: A 32 MET cc_start: 0.8222 (tmm) cc_final: 0.7934 (tmm) REVERT: A 38 SER cc_start: 0.8497 (m) cc_final: 0.8219 (p) REVERT: A 135 SER cc_start: 0.8922 (m) cc_final: 0.8496 (t) REVERT: A 180 GLU cc_start: 0.4540 (OUTLIER) cc_final: 0.4328 (pp20) REVERT: A 196 CYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5838 (t) REVERT: B 11 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6982 (mpt180) REVERT: B 32 MET cc_start: 0.8149 (tmm) cc_final: 0.7794 (tmm) REVERT: B 38 SER cc_start: 0.8471 (m) cc_final: 0.8221 (p) REVERT: B 95 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.8164 (m170) REVERT: B 99 SER cc_start: 0.8502 (m) cc_final: 0.8106 (t) REVERT: B 140 VAL cc_start: 0.8033 (t) cc_final: 0.7715 (p) REVERT: B 165 SER cc_start: 0.8308 (m) cc_final: 0.8020 (t) REVERT: B 180 GLU cc_start: 0.5137 (OUTLIER) cc_final: 0.4811 (pp20) REVERT: D 32 MET cc_start: 0.8122 (tmm) cc_final: 0.7756 (tmm) REVERT: D 115 ASP cc_start: 0.7661 (t0) cc_final: 0.7092 (t0) REVERT: F 11 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7161 (mpt180) REVERT: F 20 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8293 (p) REVERT: F 23 VAL cc_start: 0.8016 (p) cc_final: 0.7664 (m) REVERT: F 32 MET cc_start: 0.8500 (tmm) cc_final: 0.7993 (tmm) REVERT: F 38 SER cc_start: 0.8559 (m) cc_final: 0.8265 (p) REVERT: F 92 ASP cc_start: 0.7386 (t0) cc_final: 0.7175 (t0) REVERT: F 95 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8255 (m170) REVERT: F 107 MET cc_start: 0.7301 (mtp) cc_final: 0.6977 (mmm) REVERT: F 169 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6859 (mmp) REVERT: F 180 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4660 (pp20) REVERT: G 6 TYR cc_start: 0.1379 (OUTLIER) cc_final: 0.0613 (t80) REVERT: I 32 MET cc_start: 0.8146 (tmm) cc_final: 0.7691 (tmm) REVERT: I 38 SER cc_start: 0.8601 (m) cc_final: 0.8245 (p) REVERT: I 81 LEU cc_start: 0.8563 (tp) cc_final: 0.8231 (tp) REVERT: I 89 GLN cc_start: 0.7694 (tt0) cc_final: 0.7251 (tt0) REVERT: I 107 MET cc_start: 0.7075 (mtp) cc_final: 0.6425 (mmm) REVERT: I 135 SER cc_start: 0.8851 (m) cc_final: 0.8361 (t) REVERT: I 141 ASN cc_start: 0.8019 (t0) cc_final: 0.7805 (t0) REVERT: I 160 TYR cc_start: 0.8035 (m-10) cc_final: 0.7644 (m-80) REVERT: J 74 ASN cc_start: 0.7873 (t0) cc_final: 0.7654 (t0) REVERT: K 51 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8029 (p) REVERT: K 55 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7216 (pp) REVERT: K 89 GLN cc_start: 0.7609 (tt0) cc_final: 0.7154 (tt0) REVERT: K 115 ASP cc_start: 0.7834 (t0) cc_final: 0.7350 (t0) REVERT: K 129 ASP cc_start: 0.7292 (p0) cc_final: 0.7088 (p0) REVERT: K 197 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7261 (t80) REVERT: M 20 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8288 (p) REVERT: M 32 MET cc_start: 0.8166 (tmm) cc_final: 0.7786 (tmm) REVERT: M 44 ARG cc_start: 0.7056 (tpt-90) cc_final: 0.6775 (tpp80) REVERT: M 96 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.8026 (m-70) REVERT: M 99 SER cc_start: 0.8270 (m) cc_final: 0.7979 (m) REVERT: M 113 LYS cc_start: 0.6760 (mmtm) cc_final: 0.5229 (tttp) REVERT: M 115 ASP cc_start: 0.7574 (t0) cc_final: 0.7262 (t0) REVERT: M 135 SER cc_start: 0.8962 (m) cc_final: 0.8549 (t) REVERT: M 180 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.5214 (pp20) outliers start: 135 outliers final: 93 residues processed: 487 average time/residue: 0.2628 time to fit residues: 197.4620 Evaluate side-chains 500 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 389 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 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 138 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 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 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 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 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 165 SER Chi-restraints excluded: chain D residue 178 MET 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 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 29 VAL Chi-restraints excluded: chain G residue 73 HIS Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 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 101 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain 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 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 138 THR Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 161 LEU 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 38 SER 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: 1.9990 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 146 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN D 89 GLN I 89 GLN ** 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 = 0.4127 r_free = 0.4127 target = 0.171431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.147331 restraints weight = 24980.276| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.29 r_work: 0.3746 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3224 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= 0.160 Angle : 0.745 10.050 24367 Z= 0.387 Chirality : 0.047 0.158 2737 Planarity : 0.005 0.054 3080 Dihedral : 7.047 59.435 2793 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 4.98 % Allowed : 22.57 % Favored : 72.45 % 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: 0.18 (0.17), residues: 875 loop : -2.67 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 13 HIS 0.004 0.001 HIS I 96 PHE 0.016 0.001 PHE A 185 TYR 0.019 0.001 TYR K 53 ARG 0.009 0.001 ARG D 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 14) link_NAG-ASN : angle 2.23303 ( 42) hydrogen bonds : bond 0.03570 ( 552) hydrogen bonds : angle 4.67406 ( 2193) SS BOND : bond 0.00646 ( 35) SS BOND : angle 2.28056 ( 70) covalent geometry : bond 0.00362 (17920) covalent geometry : angle 0.73086 (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 485 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 387 time to evaluate : 1.915 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6633 (mpt180) REVERT: A 32 MET cc_start: 0.8129 (tmm) cc_final: 0.7872 (tmm) REVERT: A 38 SER cc_start: 0.8592 (m) cc_final: 0.8241 (p) REVERT: A 113 LYS cc_start: 0.6126 (mptt) cc_final: 0.4199 (tttm) REVERT: A 135 SER cc_start: 0.8889 (m) cc_final: 0.8519 (t) REVERT: A 180 GLU cc_start: 0.4729 (OUTLIER) cc_final: 0.4427 (pp20) REVERT: B 3 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6389 (mp) REVERT: B 11 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6770 (mpt180) REVERT: B 32 MET cc_start: 0.8027 (tmm) cc_final: 0.7697 (tmm) REVERT: B 38 SER cc_start: 0.8463 (m) cc_final: 0.8200 (p) REVERT: B 95 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8289 (m170) REVERT: B 99 SER cc_start: 0.8462 (m) cc_final: 0.8078 (t) REVERT: B 127 SER cc_start: 0.8475 (m) cc_final: 0.8000 (p) REVERT: B 140 VAL cc_start: 0.8017 (t) cc_final: 0.7707 (p) REVERT: B 165 SER cc_start: 0.8347 (m) cc_final: 0.8094 (t) REVERT: B 173 TYR cc_start: 0.8344 (m-80) cc_final: 0.7748 (m-80) REVERT: B 180 GLU cc_start: 0.5081 (OUTLIER) cc_final: 0.4856 (pp20) REVERT: D 32 MET cc_start: 0.7959 (tmm) cc_final: 0.7595 (tmm) REVERT: D 115 ASP cc_start: 0.7689 (t0) cc_final: 0.7107 (t0) REVERT: F 11 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6706 (mpt180) REVERT: F 20 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8283 (p) REVERT: F 23 VAL cc_start: 0.7943 (p) cc_final: 0.7542 (m) REVERT: F 32 MET cc_start: 0.8424 (tmm) cc_final: 0.7872 (tmm) REVERT: F 38 SER cc_start: 0.8538 (m) cc_final: 0.8226 (p) REVERT: F 41 TYR cc_start: 0.8303 (t80) cc_final: 0.8066 (t80) REVERT: F 73 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7829 (mt-10) REVERT: F 169 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6738 (mmp) REVERT: F 170 ARG cc_start: 0.7410 (ptm-80) cc_final: 0.7111 (ttp80) REVERT: F 180 GLU cc_start: 0.5000 (OUTLIER) cc_final: 0.4682 (pp20) REVERT: F 187 ASP cc_start: 0.8012 (t0) cc_final: 0.7728 (t0) REVERT: G 6 TYR cc_start: 0.1269 (OUTLIER) cc_final: 0.0563 (t80) REVERT: I 20 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8115 (p) REVERT: I 32 MET cc_start: 0.8140 (tmm) cc_final: 0.7645 (tmm) REVERT: I 105 MET cc_start: 0.8257 (mmt) cc_final: 0.8002 (mtp) REVERT: I 107 MET cc_start: 0.6978 (mtp) cc_final: 0.6761 (mtp) REVERT: I 112 THR cc_start: 0.8227 (m) cc_final: 0.8022 (p) REVERT: I 131 THR cc_start: 0.7999 (p) cc_final: 0.7729 (m) REVERT: I 135 SER cc_start: 0.8858 (m) cc_final: 0.8349 (t) REVERT: I 160 TYR cc_start: 0.8003 (m-10) cc_final: 0.7697 (m-80) REVERT: K 51 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (p) REVERT: K 55 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7322 (pp) REVERT: K 115 ASP cc_start: 0.7832 (t0) cc_final: 0.7367 (t0) REVERT: L 58 MET cc_start: 0.7521 (mmt) cc_final: 0.7285 (mmt) REVERT: M 20 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8245 (p) REVERT: M 32 MET cc_start: 0.8102 (tmm) cc_final: 0.7733 (tmm) REVERT: M 96 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8052 (m-70) REVERT: M 115 ASP cc_start: 0.7517 (t0) cc_final: 0.7201 (t0) REVERT: M 127 SER cc_start: 0.8671 (p) cc_final: 0.8446 (p) REVERT: M 135 SER cc_start: 0.8896 (m) cc_final: 0.8535 (t) outliers start: 98 outliers final: 70 residues processed: 459 average time/residue: 0.2626 time to fit residues: 185.7766 Evaluate side-chains 466 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 380 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 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 B residue 3 ILE 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 96 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 C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 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 75 VAL 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 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 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 186 LEU 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 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 138 THR 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 38 SER 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 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 175 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 ASN I 89 GLN I 141 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.170749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146366 restraints weight = 25121.015| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.33 r_work: 0.3728 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3274 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= 0.183 Angle : 0.762 10.453 24367 Z= 0.396 Chirality : 0.047 0.179 2737 Planarity : 0.005 0.062 3080 Dihedral : 6.854 59.207 2790 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 5.19 % Allowed : 22.47 % Favored : 72.34 % 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: -2.04 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.07 (0.17), residues: 889 loop : -2.62 (0.15), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 13 HIS 0.005 0.001 HIS I 96 PHE 0.016 0.001 PHE A 185 TYR 0.021 0.001 TYR K 53 ARG 0.005 0.001 ARG D 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 14) link_NAG-ASN : angle 2.22522 ( 42) hydrogen bonds : bond 0.03731 ( 552) hydrogen bonds : angle 4.69335 ( 2193) SS BOND : bond 0.00632 ( 35) SS BOND : angle 2.33232 ( 70) covalent geometry : bond 0.00419 (17920) covalent geometry : angle 0.74766 (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 493 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 391 time to evaluate : 2.168 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6735 (mpt180) REVERT: A 32 MET cc_start: 0.8132 (tmm) cc_final: 0.7858 (tmm) REVERT: A 38 SER cc_start: 0.8609 (m) cc_final: 0.8226 (p) REVERT: A 113 LYS cc_start: 0.6123 (mptt) cc_final: 0.4156 (tttm) REVERT: A 135 SER cc_start: 0.8896 (m) cc_final: 0.8531 (t) REVERT: A 180 GLU cc_start: 0.4579 (OUTLIER) cc_final: 0.4257 (pp20) REVERT: B 11 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6894 (mpt180) REVERT: B 32 MET cc_start: 0.8060 (tmm) cc_final: 0.7733 (tmm) REVERT: B 38 SER cc_start: 0.8498 (m) cc_final: 0.8189 (p) REVERT: B 95 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8343 (m170) REVERT: B 99 SER cc_start: 0.8446 (m) cc_final: 0.8056 (t) REVERT: B 127 SER cc_start: 0.8432 (m) cc_final: 0.7948 (p) REVERT: B 140 VAL cc_start: 0.7966 (t) cc_final: 0.7654 (p) REVERT: B 165 SER cc_start: 0.8381 (m) cc_final: 0.8132 (t) REVERT: B 180 GLU cc_start: 0.5064 (OUTLIER) cc_final: 0.4845 (pp20) REVERT: D 32 MET cc_start: 0.8009 (tmm) cc_final: 0.7664 (tmm) REVERT: D 115 ASP cc_start: 0.7682 (t0) cc_final: 0.7085 (t0) REVERT: F 11 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6773 (mpt180) REVERT: F 20 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8292 (p) REVERT: F 23 VAL cc_start: 0.7954 (p) cc_final: 0.7570 (m) REVERT: F 32 MET cc_start: 0.8416 (tmm) cc_final: 0.7901 (tmm) REVERT: F 38 SER cc_start: 0.8553 (m) cc_final: 0.8215 (p) REVERT: F 41 TYR cc_start: 0.8336 (t80) cc_final: 0.8120 (t80) REVERT: F 73 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7882 (mt-10) REVERT: F 95 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8218 (m170) REVERT: F 107 MET cc_start: 0.7132 (mtp) cc_final: 0.6879 (mmm) REVERT: F 169 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6795 (mmp) REVERT: F 180 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.4658 (pp20) REVERT: G 6 TYR cc_start: 0.1304 (OUTLIER) cc_final: 0.0583 (t80) REVERT: I 20 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8126 (p) REVERT: I 32 MET cc_start: 0.8163 (tmm) cc_final: 0.7692 (tmm) REVERT: I 38 SER cc_start: 0.8470 (m) cc_final: 0.8180 (p) REVERT: I 89 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6642 (mt0) REVERT: I 107 MET cc_start: 0.7109 (mtp) cc_final: 0.6875 (mtp) REVERT: I 113 LYS cc_start: 0.6250 (mmtm) cc_final: 0.4873 (tttp) REVERT: I 131 THR cc_start: 0.8001 (p) cc_final: 0.7741 (m) REVERT: I 135 SER cc_start: 0.8820 (m) cc_final: 0.8317 (t) REVERT: I 160 TYR cc_start: 0.8035 (m-10) cc_final: 0.7724 (m-80) REVERT: J 74 ASN cc_start: 0.7807 (t0) cc_final: 0.7498 (t0) REVERT: K 51 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7953 (p) REVERT: K 55 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7289 (pp) REVERT: K 89 GLN cc_start: 0.7569 (tt0) cc_final: 0.7323 (tt0) REVERT: K 115 ASP cc_start: 0.7855 (t0) cc_final: 0.7391 (t0) REVERT: L 58 MET cc_start: 0.7564 (mmt) cc_final: 0.7341 (mmt) REVERT: M 20 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8162 (p) REVERT: M 32 MET cc_start: 0.8138 (tmm) cc_final: 0.7748 (tmm) REVERT: M 96 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8048 (m-70) REVERT: M 115 ASP cc_start: 0.7561 (t0) cc_final: 0.7229 (t0) REVERT: M 129 ASP cc_start: 0.6445 (p0) cc_final: 0.6221 (p0) REVERT: M 135 SER cc_start: 0.8896 (m) cc_final: 0.8507 (t) REVERT: M 180 GLU cc_start: 0.5475 (OUTLIER) cc_final: 0.5183 (pp20) REVERT: M 187 ASP cc_start: 0.7700 (t0) cc_final: 0.7440 (t0) outliers start: 102 outliers final: 78 residues processed: 461 average time/residue: 0.2805 time to fit residues: 199.2616 Evaluate side-chains 485 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 389 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 91 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 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 95 HIS Chi-restraints excluded: chain B residue 96 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 C residue 0 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS 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 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 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 73 HIS 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 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 89 GLN Chi-restraints excluded: chain I residue 95 HIS 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 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 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 138 THR 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 37 MET Chi-restraints excluded: chain M residue 38 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 154 optimal weight: 0.0060 chunk 38 optimal weight: 0.0270 chunk 70 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN D 97 ASN F 97 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 ASN K 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152382 restraints weight = 25493.770| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.28 r_work: 0.3790 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17969 Z= 0.127 Angle : 0.706 10.961 24367 Z= 0.366 Chirality : 0.045 0.163 2737 Planarity : 0.004 0.049 3080 Dihedral : 6.267 58.929 2789 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 4.02 % Allowed : 23.84 % Favored : 72.14 % 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: -1.85 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.29 (0.17), residues: 875 loop : -2.54 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 13 HIS 0.007 0.001 HIS I 155 PHE 0.013 0.001 PHE A 185 TYR 0.016 0.001 TYR F 25 ARG 0.004 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 14) link_NAG-ASN : angle 2.08796 ( 42) hydrogen bonds : bond 0.03224 ( 552) hydrogen bonds : angle 4.47897 ( 2193) SS BOND : bond 0.00466 ( 35) SS BOND : angle 2.00201 ( 70) covalent geometry : bond 0.00283 (17920) covalent geometry : angle 0.69407 (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 462 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 383 time to evaluate : 2.048 Fit side-chains REVERT: A 11 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6429 (mpt180) REVERT: A 32 MET cc_start: 0.8043 (tmm) cc_final: 0.7811 (tmm) REVERT: A 38 SER cc_start: 0.8426 (m) cc_final: 0.8179 (p) REVERT: A 113 LYS cc_start: 0.6256 (mptt) cc_final: 0.4400 (tttp) REVERT: A 135 SER cc_start: 0.8831 (m) cc_final: 0.8566 (t) REVERT: A 180 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.4442 (pp20) REVERT: B 32 MET cc_start: 0.7930 (tmm) cc_final: 0.7586 (tmm) REVERT: B 38 SER cc_start: 0.8560 (m) cc_final: 0.8294 (p) REVERT: B 95 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8428 (m170) REVERT: B 99 SER cc_start: 0.8406 (m) cc_final: 0.8063 (t) REVERT: B 127 SER cc_start: 0.8429 (m) cc_final: 0.8084 (p) REVERT: B 140 VAL cc_start: 0.8014 (t) cc_final: 0.7705 (p) REVERT: B 165 SER cc_start: 0.8404 (m) cc_final: 0.8128 (t) REVERT: D 32 MET cc_start: 0.7869 (tmm) cc_final: 0.7587 (tmm) REVERT: D 115 ASP cc_start: 0.7652 (t0) cc_final: 0.7109 (t0) REVERT: F 23 VAL cc_start: 0.7837 (p) cc_final: 0.7427 (m) REVERT: F 32 MET cc_start: 0.8382 (tmm) cc_final: 0.7801 (tmm) REVERT: F 38 SER cc_start: 0.8543 (m) cc_final: 0.8253 (p) REVERT: F 41 TYR cc_start: 0.8265 (t80) cc_final: 0.7988 (t80) REVERT: F 73 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7786 (mt-10) REVERT: F 107 MET cc_start: 0.7025 (mtp) cc_final: 0.6750 (mmm) REVERT: F 150 ASN cc_start: 0.4377 (OUTLIER) cc_final: 0.3628 (m-40) REVERT: F 170 ARG cc_start: 0.7407 (ptm-80) cc_final: 0.7107 (ttp80) REVERT: F 180 GLU cc_start: 0.4998 (OUTLIER) cc_final: 0.4677 (pp20) REVERT: F 187 ASP cc_start: 0.7830 (t0) cc_final: 0.7597 (t0) REVERT: G 6 TYR cc_start: 0.1349 (OUTLIER) cc_final: 0.0494 (t80) REVERT: I 32 MET cc_start: 0.8100 (tmm) cc_final: 0.7629 (tmm) REVERT: I 131 THR cc_start: 0.7867 (p) cc_final: 0.7605 (m) REVERT: I 135 SER cc_start: 0.8801 (m) cc_final: 0.8362 (t) REVERT: J 58 MET cc_start: 0.7185 (mmm) cc_final: 0.6755 (mmm) REVERT: J 74 ASN cc_start: 0.7717 (t0) cc_final: 0.7455 (t0) REVERT: K 51 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7882 (p) REVERT: K 55 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7383 (pp) REVERT: K 91 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8065 (mp) REVERT: K 115 ASP cc_start: 0.7789 (t0) cc_final: 0.7347 (t0) REVERT: M 20 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8199 (p) REVERT: M 32 MET cc_start: 0.8101 (tmm) cc_final: 0.7748 (tmm) REVERT: M 96 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8060 (m-70) REVERT: M 115 ASP cc_start: 0.7507 (t0) cc_final: 0.7196 (t0) REVERT: M 127 SER cc_start: 0.8673 (p) cc_final: 0.8454 (p) REVERT: M 135 SER cc_start: 0.8872 (m) cc_final: 0.8568 (t) REVERT: M 187 ASP cc_start: 0.7718 (t0) cc_final: 0.7445 (t0) outliers start: 79 outliers final: 57 residues processed: 438 average time/residue: 0.2667 time to fit residues: 182.2633 Evaluate side-chains 443 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 375 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 91 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 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 96 HIS Chi-restraints excluded: chain B residue 107 MET 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 56 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET 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 27 ILE Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain G residue 73 HIS Chi-restraints excluded: chain I residue 4 CYS Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 181 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 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 138 THR 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 38 SER 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 165 SER 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: 0.3980 chunk 164 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 193 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 GLN I 141 ASN ** I 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146572 restraints weight = 25036.775| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.34 r_work: 0.3737 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17969 Z= 0.196 Angle : 0.765 10.529 24367 Z= 0.400 Chirality : 0.048 0.185 2737 Planarity : 0.005 0.066 3080 Dihedral : 6.489 59.628 2782 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 3.81 % Allowed : 24.76 % Favored : 71.43 % 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: -1.91 (0.17), residues: 2114 helix: None (None), residues: 0 sheet: 0.16 (0.17), residues: 889 loop : -2.54 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 13 HIS 0.005 0.001 HIS B 96 PHE 0.017 0.001 PHE A 185 TYR 0.020 0.002 TYR B 53 ARG 0.005 0.001 ARG D 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 14) link_NAG-ASN : angle 2.17934 ( 42) hydrogen bonds : bond 0.03752 ( 552) hydrogen bonds : angle 4.65473 ( 2193) SS BOND : bond 0.00643 ( 35) SS BOND : angle 2.27906 ( 70) covalent geometry : bond 0.00448 (17920) covalent geometry : angle 0.75105 (24255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9747.76 seconds wall clock time: 169 minutes 11.97 seconds (10151.97 seconds total)