Starting phenix.real_space_refine on Tue Aug 26 07:03:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxz_29549/08_2025/8fxz_29549_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxz_29549/08_2025/8fxz_29549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fxz_29549/08_2025/8fxz_29549_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxz_29549/08_2025/8fxz_29549_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fxz_29549/08_2025/8fxz_29549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxz_29549/08_2025/8fxz_29549.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 161 5.16 5 C 11109 2.51 5 N 2912 2.21 5 O 3493 1.98 5 H 16961 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34636 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3177 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "H" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1729 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3177 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1729 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "D" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3177 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1729 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "F" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3177 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "G" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1729 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "I" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3177 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "J" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1729 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "K" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3177 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "L" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1729 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "M" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3177 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "N" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1729 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 103} 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: 5.98, per 1000 atoms: 0.17 Number of scatterers: 34636 At special positions: 0 Unit cell: (185.9, 185.9, 67.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 161 16.00 O 3493 8.00 N 2912 7.00 C 11109 6.00 H 16961 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 82 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 82 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 82 " distance=2.03 Simple disulfide: pdb=" SG CYS I 56 " - pdb=" SG CYS I 217 " distance=2.03 Simple disulfide: pdb=" SG CYS I 125 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 160 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 82 " distance=2.03 Simple disulfide: pdb=" SG CYS K 56 " - pdb=" SG CYS K 217 " distance=2.03 Simple disulfide: pdb=" SG CYS K 125 " - pdb=" SG CYS K 157 " distance=2.02 Simple disulfide: pdb=" SG CYS K 160 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 16 " - pdb=" SG CYS L 82 " distance=2.03 Simple disulfide: pdb=" SG CYS M 56 " - pdb=" SG CYS M 217 " distance=2.03 Simple disulfide: pdb=" SG CYS M 125 " - pdb=" SG CYS M 157 " distance=2.02 Simple disulfide: pdb=" SG CYS M 160 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 82 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4130 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 28 sheets defined 8.6% alpha, 54.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.536A pdb=" N GLU A 211 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 26 removed outlier: 3.541A pdb=" N LEU H 25 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA H 26 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 55 removed outlier: 4.747A pdb=" N ASN H 55 " --> pdb=" O PRO H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.729A pdb=" N GLU H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.575A pdb=" N MET B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.512A pdb=" N GLU B 211 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 4.109A pdb=" N ALA C 26 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 removed outlier: 4.779A pdb=" N ASN C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.731A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.730A pdb=" N MET D 190 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 191 " --> pdb=" O TYR D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 191' Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'E' and resid 21 through 26 removed outlier: 4.236A pdb=" N ALA E 26 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 removed outlier: 4.757A pdb=" N ASN E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.716A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.555A pdb=" N MET F 190 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 removed outlier: 3.560A pdb=" N GLU F 211 " --> pdb=" O ASP F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 26 removed outlier: 4.033A pdb=" N ALA G 26 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 54 Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.622A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 191 Processing helix chain 'I' and resid 208 through 212 Processing helix chain 'J' and resid 21 through 26 removed outlier: 4.177A pdb=" N ALA J 26 " --> pdb=" O GLU J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 55 removed outlier: 4.707A pdb=" N ASN J 55 " --> pdb=" O PRO J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 77 removed outlier: 3.749A pdb=" N GLU J 77 " --> pdb=" O PRO J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 191 removed outlier: 3.630A pdb=" N MET K 190 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 212 Processing helix chain 'L' and resid 21 through 26 removed outlier: 3.530A pdb=" N LEU L 25 " --> pdb=" O VAL L 22 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA L 26 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 55 removed outlier: 4.731A pdb=" N ASN L 55 " --> pdb=" O PRO L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.718A pdb=" N GLU L 77 " --> pdb=" O PRO L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 191 Processing helix chain 'M' and resid 208 through 212 removed outlier: 3.518A pdb=" N GLU M 211 " --> pdb=" O ASP M 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 26 removed outlier: 3.516A pdb=" N LEU N 25 " --> pdb=" O VAL N 22 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA N 26 " --> pdb=" O GLU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 55 removed outlier: 4.709A pdb=" N ASN N 55 " --> pdb=" O PRO N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 77 removed outlier: 3.653A pdb=" N GLU N 77 " --> pdb=" O PRO N 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.617A pdb=" N CYS A 160 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N SER A 193 " --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS H 96 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY A 195 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG H 94 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL H 4 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS H 105 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS H 6 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.583A pdb=" N SER A 213 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 96 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 107 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 105 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 94 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER A 103 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL A 96 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS A 101 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 38 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 108 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N PHE A 36 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 160 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N SER A 193 " --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS H 96 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY A 195 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG H 94 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU H 88 " --> pdb=" O PHE H 92 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ARG H 94 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS H 86 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE H 30 " --> pdb=" O MET H 42 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LYS H 34 " --> pdb=" O MET H 38 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N MET H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 140 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 15 Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 removed outlier: 7.997A pdb=" N ALA B 37 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 165 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU B 39 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 163 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 41 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B 161 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY B 43 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N SER B 193 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS C 96 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLY B 195 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 216 removed outlier: 6.791A pdb=" N PHE B 107 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 105 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU B 94 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 103 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 96 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 101 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 38 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR B 108 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 36 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA B 37 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 165 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU B 39 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 163 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 41 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B 161 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY B 43 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N SER B 193 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS C 96 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLY B 195 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU C 88 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ARG C 94 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS C 86 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 96 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE C 30 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LYS C 34 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N MET C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 140 Processing sheet with id=AA8, first strand: chain 'C' and resid 12 through 15 Processing sheet with id=AA9, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.635A pdb=" N CYS D 160 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N SER D 193 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS E 96 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY D 195 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL E 4 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS E 105 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS E 6 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.641A pdb=" N SER D 213 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL D 96 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE D 107 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 105 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU D 94 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER D 103 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL D 96 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS D 101 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 38 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 108 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE D 36 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D 160 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N SER D 193 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS E 96 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY D 195 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU E 88 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG E 94 " --> pdb=" O LYS E 86 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS E 86 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS E 96 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE E 30 " --> pdb=" O MET E 42 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS E 34 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 133 through 140 Processing sheet with id=AB3, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AB4, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.679A pdb=" N CYS F 160 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER F 193 " --> pdb=" O HIS G 96 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS G 96 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY F 195 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 215 through 216 removed outlier: 6.776A pdb=" N PHE F 107 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA F 92 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU F 105 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU F 94 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER F 103 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL F 96 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS F 101 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 38 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR F 108 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE F 36 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS F 160 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER F 193 " --> pdb=" O HIS G 96 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS G 96 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY F 195 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU G 88 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG G 94 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS G 86 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS G 96 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE G 30 " --> pdb=" O MET G 42 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS G 34 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N MET G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 133 through 140 Processing sheet with id=AB7, first strand: chain 'G' and resid 12 through 15 Processing sheet with id=AB8, first strand: chain 'I' and resid 181 through 183 removed outlier: 7.898A pdb=" N ALA I 37 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR I 165 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU I 39 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU I 163 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR I 41 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL I 161 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY I 43 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER I 193 " --> pdb=" O HIS J 96 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N HIS J 96 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY I 195 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 213 through 216 removed outlier: 4.511A pdb=" N SER I 213 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL I 96 " --> pdb=" O SER I 213 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE I 107 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA I 92 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU I 105 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU I 94 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER I 103 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL I 96 " --> pdb=" O LYS I 101 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS I 101 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR I 108 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE I 36 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA I 37 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR I 165 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU I 39 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU I 163 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR I 41 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL I 161 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY I 43 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER I 193 " --> pdb=" O HIS J 96 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N HIS J 96 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY I 195 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU J 88 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG J 94 " --> pdb=" O LYS J 86 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS J 86 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE J 30 " --> pdb=" O MET J 42 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS J 34 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N MET J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 133 through 140 Processing sheet with id=AC2, first strand: chain 'J' and resid 12 through 15 Processing sheet with id=AC3, first strand: chain 'K' and resid 181 through 183 removed outlier: 7.917A pdb=" N ALA K 37 " --> pdb=" O THR K 165 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR K 165 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU K 39 " --> pdb=" O LEU K 163 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU K 163 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR K 41 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL K 161 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY K 43 " --> pdb=" O THR K 159 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N SER K 193 " --> pdb=" O HIS L 96 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS L 96 " --> pdb=" O SER K 193 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY K 195 " --> pdb=" O ARG L 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 213 through 216 removed outlier: 4.697A pdb=" N SER K 213 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL K 96 " --> pdb=" O SER K 213 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE K 107 " --> pdb=" O VAL K 90 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA K 92 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU K 105 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU K 94 " --> pdb=" O SER K 103 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER K 103 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL K 96 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS K 101 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA K 38 " --> pdb=" O LEU K 106 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR K 108 " --> pdb=" O PHE K 36 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N PHE K 36 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA K 37 " --> pdb=" O THR K 165 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR K 165 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU K 39 " --> pdb=" O LEU K 163 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU K 163 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR K 41 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL K 161 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY K 43 " --> pdb=" O THR K 159 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N SER K 193 " --> pdb=" O HIS L 96 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS L 96 " --> pdb=" O SER K 193 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY K 195 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU L 88 " --> pdb=" O PHE L 92 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG L 94 " --> pdb=" O LYS L 86 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS L 86 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS L 96 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE L 30 " --> pdb=" O MET L 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 133 through 140 removed outlier: 6.448A pdb=" N ILE K 153 " --> pdb=" O LYS K 134 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP K 136 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE K 151 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP K 138 " --> pdb=" O CYS K 149 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N CYS K 149 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 12 through 14 Processing sheet with id=AC7, first strand: chain 'M' and resid 181 through 183 removed outlier: 8.020A pdb=" N ALA M 37 " --> pdb=" O THR M 165 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR M 165 " --> pdb=" O ALA M 37 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU M 39 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU M 163 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR M 41 " --> pdb=" O VAL M 161 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL M 161 " --> pdb=" O THR M 41 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY M 43 " --> pdb=" O THR M 159 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N SER M 193 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N HIS N 96 " --> pdb=" O SER M 193 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLY M 195 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL N 4 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS N 105 " --> pdb=" O VAL N 4 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS N 6 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 214 through 216 removed outlier: 6.505A pdb=" N THR M 108 " --> pdb=" O PHE M 36 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE M 36 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA M 37 " --> pdb=" O THR M 165 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR M 165 " --> pdb=" O ALA M 37 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU M 39 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU M 163 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR M 41 " --> pdb=" O VAL M 161 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL M 161 " --> pdb=" O THR M 41 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY M 43 " --> pdb=" O THR M 159 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N SER M 193 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N HIS N 96 " --> pdb=" O SER M 193 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLY M 195 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE N 92 " --> pdb=" O GLU N 88 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU N 88 " --> pdb=" O PHE N 92 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG N 94 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS N 86 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS N 96 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE N 30 " --> pdb=" O MET N 42 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS N 34 " --> pdb=" O MET N 38 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N MET N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 133 through 140 removed outlier: 6.472A pdb=" N ILE M 153 " --> pdb=" O LYS M 134 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP M 136 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE M 151 " --> pdb=" O ASP M 136 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP M 138 " --> pdb=" O CYS M 149 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N CYS M 149 " --> pdb=" O ASP M 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 11 through 14 746 hydrogen bonds defined for protein. 1914 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: 9.62 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16940 1.03 - 1.23: 110 1.23 - 1.42: 7404 1.42 - 1.62: 10273 1.62 - 1.81: 245 Bond restraints: 34972 Sorted by residual: bond pdb=" C1 NAG K 303 " pdb=" O5 NAG K 303 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG M 303 " pdb=" O5 NAG M 303 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG B 301 " pdb=" C2 NAG B 301 " ideal model delta sigma weight residual 1.532 1.506 0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CB CYS D 125 " pdb=" SG CYS D 125 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.43e+00 ... (remaining 34967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 61098 1.33 - 2.66: 1717 2.66 - 4.00: 119 4.00 - 5.33: 10 5.33 - 6.66: 7 Bond angle restraints: 62951 Sorted by residual: angle pdb=" CA CYS B 157 " pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " ideal model delta sigma weight residual 114.40 107.74 6.66 2.30e+00 1.89e-01 8.38e+00 angle pdb=" CA CYS D 157 " pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " ideal model delta sigma weight residual 114.40 107.86 6.54 2.30e+00 1.89e-01 8.07e+00 angle pdb=" CA CYS A 157 " pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " ideal model delta sigma weight residual 114.40 108.26 6.14 2.30e+00 1.89e-01 7.12e+00 angle pdb=" CA CYS F 157 " pdb=" CB CYS F 157 " pdb=" SG CYS F 157 " ideal model delta sigma weight residual 114.40 108.27 6.13 2.30e+00 1.89e-01 7.11e+00 angle pdb=" CA CYS I 157 " pdb=" CB CYS I 157 " pdb=" SG CYS I 157 " ideal model delta sigma weight residual 114.40 108.62 5.78 2.30e+00 1.89e-01 6.31e+00 ... (remaining 62946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 15332 14.26 - 28.52: 1054 28.52 - 42.78: 289 42.78 - 57.04: 155 57.04 - 71.30: 33 Dihedral angle restraints: 16863 sinusoidal: 9338 harmonic: 7525 Sorted by residual: dihedral pdb=" CB CYS B 125 " pdb=" SG CYS B 125 " pdb=" SG CYS B 157 " pdb=" CB CYS B 157 " ideal model delta sinusoidal sigma weight residual 93.00 137.17 -44.17 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS K 125 " pdb=" SG CYS K 125 " pdb=" SG CYS K 157 " pdb=" CB CYS K 157 " ideal model delta sinusoidal sigma weight residual 93.00 134.33 -41.33 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual 93.00 132.37 -39.37 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 16860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1502 0.030 - 0.059: 803 0.059 - 0.089: 277 0.089 - 0.118: 184 0.118 - 0.148: 34 Chirality restraints: 2800 Sorted by residual: chirality pdb=" CA ILE M 42 " pdb=" N ILE M 42 " pdb=" C ILE M 42 " pdb=" CB ILE M 42 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE B 42 " pdb=" N ILE B 42 " pdb=" C ILE B 42 " pdb=" CB ILE B 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE D 42 " pdb=" N ILE D 42 " pdb=" C ILE D 42 " pdb=" CB ILE D 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2797 not shown) Planarity restraints: 5159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS M 176 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRO M 177 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO M 177 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO M 177 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 26 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO D 27 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 27 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 27 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 176 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO I 177 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO I 177 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 177 " -0.016 5.00e-02 4.00e+02 ... (remaining 5156 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 709 2.12 - 2.74: 62863 2.74 - 3.36: 89914 3.36 - 3.98: 123607 3.98 - 4.60: 192112 Nonbonded interactions: 469205 Sorted by model distance: nonbonded pdb="HH11 ARG G 56 " pdb=" O LEU G 70 " model vdw 1.500 2.450 nonbonded pdb="HH11 ARG J 56 " pdb=" O LEU J 70 " model vdw 1.536 2.450 nonbonded pdb="HH11 ARG L 56 " pdb=" O LEU L 70 " model vdw 1.548 2.450 nonbonded pdb="HH11 ARG C 56 " pdb=" O LEU C 70 " model vdw 1.556 2.450 nonbonded pdb="HH11 ARG N 56 " pdb=" O LEU N 70 " model vdw 1.566 2.450 ... (remaining 469200 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: 0.00 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: 2.130 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: 0.190 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.920 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:10.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.006 0.040 18039 Z= 0.259 Angle : 0.562 6.660 24444 Z= 0.297 Chirality : 0.045 0.148 2800 Planarity : 0.003 0.037 3066 Dihedral : 11.838 71.301 7014 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.22 % Favored : 95.46 % Rotamer: Outliers : 3.60 % Allowed : 5.62 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.19), residues: 2135 helix: -2.16 (0.90), residues: 42 sheet: 0.72 (0.16), residues: 1071 loop : -1.13 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 111 TYR 0.015 0.002 TYR I 46 PHE 0.007 0.001 PHE I 89 TRP 0.005 0.001 TRP C 32 HIS 0.007 0.001 HIS K 176 Details of bonding type rmsd covalent geometry : bond 0.00601 (18011) covalent geometry : angle 0.55700 (24388) SS BOND : bond 0.00579 ( 28) SS BOND : angle 1.64415 ( 56) hydrogen bonds : bond 0.14439 ( 665) hydrogen bonds : angle 6.52780 ( 1914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 484 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 THR cc_start: 0.8789 (m) cc_final: 0.8521 (t) REVERT: A 166 ASP cc_start: 0.7890 (m-30) cc_final: 0.7676 (m-30) REVERT: H 42 MET cc_start: 0.6034 (ttp) cc_final: 0.5482 (tmt) REVERT: B 98 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7945 (mmtm) REVERT: B 119 ILE cc_start: 0.8487 (mm) cc_final: 0.8219 (mp) REVERT: B 146 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7574 (mtmm) REVERT: B 152 THR cc_start: 0.8646 (m) cc_final: 0.8379 (t) REVERT: B 174 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6802 (p90) REVERT: B 182 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8587 (tt) REVERT: C 33 GLN cc_start: 0.7773 (pt0) cc_final: 0.7504 (pt0) REVERT: C 43 MET cc_start: 0.5805 (mtp) cc_final: 0.5466 (mtp) REVERT: C 57 THR cc_start: 0.7970 (m) cc_final: 0.7702 (p) REVERT: C 66 SER cc_start: 0.8093 (p) cc_final: 0.7884 (m) REVERT: D 32 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.8213 (mtm180) REVERT: D 53 MET cc_start: 0.7447 (mtp) cc_final: 0.7237 (mtp) REVERT: D 113 ASP cc_start: 0.7954 (p0) cc_final: 0.7662 (p0) REVERT: D 156 SER cc_start: 0.8326 (p) cc_final: 0.7979 (t) REVERT: D 190 MET cc_start: 0.8294 (mmp) cc_final: 0.7957 (mmp) REVERT: E 42 MET cc_start: 0.6744 (ttp) cc_final: 0.5828 (tmt) REVERT: F 32 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8098 (mtm180) REVERT: F 156 SER cc_start: 0.8560 (p) cc_final: 0.8308 (t) REVERT: F 164 GLU cc_start: 0.7240 (tp30) cc_final: 0.7007 (tp30) REVERT: F 182 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8708 (tt) REVERT: F 202 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6206 (pp) REVERT: F 215 ASP cc_start: 0.7641 (t70) cc_final: 0.7432 (t0) REVERT: I 118 ASN cc_start: 0.8439 (m-40) cc_final: 0.8215 (m-40) REVERT: I 190 MET cc_start: 0.8490 (mmp) cc_final: 0.8262 (mmp) REVERT: I 204 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6619 (pp30) REVERT: K 114 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8237 (mtmm) REVERT: M 53 MET cc_start: 0.7615 (mtp) cc_final: 0.7410 (mtp) REVERT: M 84 ASP cc_start: 0.8052 (t70) cc_final: 0.7847 (t0) REVERT: M 113 ASP cc_start: 0.7499 (p0) cc_final: 0.7189 (p0) REVERT: M 182 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8513 (tt) REVERT: M 204 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6686 (pp30) outliers start: 71 outliers final: 47 residues processed: 543 average time/residue: 0.9680 time to fit residues: 596.2473 Evaluate side-chains 490 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 203 ASN B 68 ASN B 203 ASN I 68 ASN I 203 ASN K 68 ASN M 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132499 restraints weight = 68045.192| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.14 r_work: 0.3472 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18039 Z= 0.151 Angle : 0.540 5.322 24444 Z= 0.290 Chirality : 0.045 0.137 2800 Planarity : 0.004 0.044 3066 Dihedral : 10.047 59.686 2924 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.12 % Favored : 95.55 % Rotamer: Outliers : 3.85 % Allowed : 11.80 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.19), residues: 2135 helix: -3.04 (0.79), residues: 42 sheet: 0.69 (0.16), residues: 1071 loop : -1.07 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 29 TYR 0.017 0.001 TYR D 174 PHE 0.010 0.001 PHE E 59 TRP 0.005 0.001 TRP J 32 HIS 0.005 0.001 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00341 (18011) covalent geometry : angle 0.53738 (24388) SS BOND : bond 0.00364 ( 28) SS BOND : angle 1.19551 ( 56) hydrogen bonds : bond 0.03838 ( 665) hydrogen bonds : angle 5.39246 ( 1914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 475 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6104 (pp30) REVERT: H 42 MET cc_start: 0.6270 (ttp) cc_final: 0.5437 (tmt) REVERT: B 30 ASP cc_start: 0.7508 (m-30) cc_final: 0.7235 (m-30) REVERT: B 119 ILE cc_start: 0.8411 (mm) cc_final: 0.8128 (mp) REVERT: B 152 THR cc_start: 0.8556 (m) cc_final: 0.8306 (t) REVERT: B 182 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8505 (tt) REVERT: C 33 GLN cc_start: 0.7852 (pt0) cc_final: 0.7503 (pt0) REVERT: C 42 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.4819 (tmt) REVERT: C 57 THR cc_start: 0.8133 (m) cc_final: 0.7893 (p) REVERT: C 66 SER cc_start: 0.7950 (p) cc_final: 0.7685 (m) REVERT: C 95 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7380 (mm-30) REVERT: D 53 MET cc_start: 0.7781 (mtp) cc_final: 0.7573 (mtp) REVERT: D 113 ASP cc_start: 0.7974 (p0) cc_final: 0.7693 (p0) REVERT: D 156 SER cc_start: 0.8057 (p) cc_final: 0.7718 (t) REVERT: D 190 MET cc_start: 0.8293 (mmp) cc_final: 0.7976 (mmp) REVERT: D 204 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6171 (pp30) REVERT: E 42 MET cc_start: 0.6947 (ttp) cc_final: 0.5897 (tmt) REVERT: F 164 GLU cc_start: 0.7612 (tp30) cc_final: 0.7397 (tp30) REVERT: F 182 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8576 (tt) REVERT: F 202 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6053 (pp) REVERT: G 42 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.5004 (tmt) REVERT: G 57 THR cc_start: 0.7926 (m) cc_final: 0.7624 (p) REVERT: G 65 LEU cc_start: 0.7893 (mt) cc_final: 0.7654 (mt) REVERT: I 204 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6596 (pp30) REVERT: K 64 ASP cc_start: 0.8123 (t70) cc_final: 0.7871 (m-30) REVERT: K 182 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8511 (tt) REVERT: L 42 MET cc_start: 0.6029 (tmt) cc_final: 0.5828 (tmt) REVERT: M 102 LEU cc_start: 0.8720 (tp) cc_final: 0.8500 (tt) REVERT: M 113 ASP cc_start: 0.7470 (p0) cc_final: 0.7216 (p0) REVERT: M 175 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5479 (pt) REVERT: M 182 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8479 (tt) REVERT: M 204 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6600 (pp30) REVERT: N 42 MET cc_start: 0.6828 (ttp) cc_final: 0.5581 (tmt) outliers start: 76 outliers final: 53 residues processed: 524 average time/residue: 0.9429 time to fit residues: 562.0998 Evaluate side-chains 523 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 458 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 64 ASP Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS I 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.166795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131912 restraints weight = 67509.705| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.13 r_work: 0.3421 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 18039 Z= 0.250 Angle : 0.565 5.545 24444 Z= 0.300 Chirality : 0.045 0.141 2800 Planarity : 0.003 0.045 3066 Dihedral : 9.906 59.833 2912 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.68 % Favored : 94.99 % Rotamer: Outliers : 4.86 % Allowed : 12.46 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.19), residues: 2135 helix: -3.10 (0.80), residues: 42 sheet: 0.71 (0.16), residues: 1071 loop : -1.21 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 32 TYR 0.015 0.002 TYR M 35 PHE 0.009 0.001 PHE K 107 TRP 0.006 0.001 TRP J 32 HIS 0.007 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00589 (18011) covalent geometry : angle 0.56025 (24388) SS BOND : bond 0.00593 ( 28) SS BOND : angle 1.67266 ( 56) hydrogen bonds : bond 0.04032 ( 665) hydrogen bonds : angle 5.31891 ( 1914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 455 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: A 204 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6024 (pp30) REVERT: A 210 LYS cc_start: 0.6696 (mmtt) cc_final: 0.4704 (mmtt) REVERT: H 42 MET cc_start: 0.6237 (ttp) cc_final: 0.5379 (tmt) REVERT: B 30 ASP cc_start: 0.7544 (m-30) cc_final: 0.7269 (m-30) REVERT: B 98 LYS cc_start: 0.8274 (mmtm) cc_final: 0.8046 (mmtm) REVERT: B 119 ILE cc_start: 0.8437 (mm) cc_final: 0.8160 (mp) REVERT: B 152 THR cc_start: 0.8574 (m) cc_final: 0.8333 (t) REVERT: B 182 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8502 (tt) REVERT: C 33 GLN cc_start: 0.7819 (pt0) cc_final: 0.7493 (pt0) REVERT: C 66 SER cc_start: 0.7969 (p) cc_final: 0.7707 (m) REVERT: C 95 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7358 (mm-30) REVERT: D 53 MET cc_start: 0.7782 (mtp) cc_final: 0.7577 (mtp) REVERT: D 113 ASP cc_start: 0.7974 (p0) cc_final: 0.7715 (p0) REVERT: D 156 SER cc_start: 0.8099 (p) cc_final: 0.7756 (t) REVERT: D 204 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6183 (pp30) REVERT: E 42 MET cc_start: 0.6876 (ttp) cc_final: 0.5807 (tmt) REVERT: F 164 GLU cc_start: 0.7606 (tp30) cc_final: 0.7389 (tp30) REVERT: F 204 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6153 (pp30) REVERT: F 219 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7469 (mmm-85) REVERT: G 42 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.4937 (tmt) REVERT: G 57 THR cc_start: 0.7916 (m) cc_final: 0.7615 (p) REVERT: G 65 LEU cc_start: 0.7868 (mt) cc_final: 0.7631 (mt) REVERT: I 139 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7986 (mt) REVERT: I 204 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6600 (pp30) REVERT: K 204 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6349 (pp30) REVERT: L 42 MET cc_start: 0.6003 (tmt) cc_final: 0.5713 (tmt) REVERT: M 102 LEU cc_start: 0.8697 (tp) cc_final: 0.8468 (tt) REVERT: M 113 ASP cc_start: 0.7459 (p0) cc_final: 0.7211 (p0) REVERT: M 182 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8484 (tt) REVERT: M 204 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6637 (pp30) REVERT: N 42 MET cc_start: 0.6782 (ttp) cc_final: 0.5537 (tmt) outliers start: 96 outliers final: 67 residues processed: 519 average time/residue: 0.9465 time to fit residues: 558.3007 Evaluate side-chains 527 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 449 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 64 ASP Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 164 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.167422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132562 restraints weight = 67524.405| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.14 r_work: 0.3457 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18039 Z= 0.154 Angle : 0.520 4.821 24444 Z= 0.278 Chirality : 0.044 0.133 2800 Planarity : 0.003 0.034 3066 Dihedral : 9.631 59.848 2910 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.45 % Favored : 95.22 % Rotamer: Outliers : 4.66 % Allowed : 13.63 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.19), residues: 2135 helix: -3.08 (0.78), residues: 42 sheet: 0.71 (0.16), residues: 1078 loop : -1.17 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 32 TYR 0.015 0.001 TYR L 80 PHE 0.011 0.001 PHE L 59 TRP 0.005 0.001 TRP J 32 HIS 0.005 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00354 (18011) covalent geometry : angle 0.51709 (24388) SS BOND : bond 0.00371 ( 28) SS BOND : angle 1.20108 ( 56) hydrogen bonds : bond 0.03449 ( 665) hydrogen bonds : angle 5.04456 ( 1914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 452 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6027 (pp30) REVERT: A 210 LYS cc_start: 0.6807 (mmtt) cc_final: 0.4794 (mmtt) REVERT: H 42 MET cc_start: 0.6387 (ttp) cc_final: 0.5536 (tmt) REVERT: B 30 ASP cc_start: 0.7544 (m-30) cc_final: 0.7271 (m-30) REVERT: B 119 ILE cc_start: 0.8421 (mm) cc_final: 0.8140 (mp) REVERT: B 152 THR cc_start: 0.8545 (m) cc_final: 0.8309 (t) REVERT: B 182 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8500 (tt) REVERT: C 33 GLN cc_start: 0.7853 (pt0) cc_final: 0.7538 (pt0) REVERT: C 66 SER cc_start: 0.7978 (p) cc_final: 0.7722 (m) REVERT: D 53 MET cc_start: 0.7794 (mtp) cc_final: 0.7585 (mtp) REVERT: D 113 ASP cc_start: 0.7955 (p0) cc_final: 0.7684 (p0) REVERT: D 156 SER cc_start: 0.8126 (p) cc_final: 0.7763 (t) REVERT: D 204 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6153 (pp30) REVERT: E 42 MET cc_start: 0.6873 (ttp) cc_final: 0.5787 (tmt) REVERT: F 164 GLU cc_start: 0.7590 (tp30) cc_final: 0.7343 (tp30) REVERT: F 204 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6094 (pp30) REVERT: G 42 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.5054 (tmt) REVERT: G 57 THR cc_start: 0.7924 (m) cc_final: 0.7642 (p) REVERT: G 65 LEU cc_start: 0.7895 (mt) cc_final: 0.7663 (mt) REVERT: I 204 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6588 (pp30) REVERT: J 83 VAL cc_start: 0.7711 (p) cc_final: 0.7445 (t) REVERT: K 182 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8470 (tt) REVERT: K 204 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6319 (pp30) REVERT: K 211 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7098 (mm-30) REVERT: L 42 MET cc_start: 0.6114 (tmt) cc_final: 0.5735 (tmt) REVERT: M 102 LEU cc_start: 0.8667 (tp) cc_final: 0.8436 (tt) REVERT: M 113 ASP cc_start: 0.7449 (p0) cc_final: 0.7213 (p0) REVERT: M 182 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8486 (tt) REVERT: M 204 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6566 (pp30) outliers start: 92 outliers final: 66 residues processed: 514 average time/residue: 0.9361 time to fit residues: 546.4346 Evaluate side-chains 525 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 449 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 64 ASP Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 205 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132032 restraints weight = 67571.418| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.15 r_work: 0.3426 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18039 Z= 0.222 Angle : 0.542 5.395 24444 Z= 0.288 Chirality : 0.045 0.140 2800 Planarity : 0.003 0.035 3066 Dihedral : 9.550 59.756 2908 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 5.02 % Allowed : 14.13 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.19), residues: 2135 helix: -3.10 (0.78), residues: 42 sheet: 0.69 (0.16), residues: 1071 loop : -1.18 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 32 TYR 0.012 0.002 TYR M 35 PHE 0.008 0.001 PHE K 107 TRP 0.006 0.001 TRP J 32 HIS 0.007 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00522 (18011) covalent geometry : angle 0.53777 (24388) SS BOND : bond 0.00529 ( 28) SS BOND : angle 1.52953 ( 56) hydrogen bonds : bond 0.03690 ( 665) hydrogen bonds : angle 5.05667 ( 1914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 455 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6032 (pp30) REVERT: A 210 LYS cc_start: 0.6801 (mmtt) cc_final: 0.4783 (mmtt) REVERT: H 42 MET cc_start: 0.6390 (ttp) cc_final: 0.5486 (tmt) REVERT: B 30 ASP cc_start: 0.7555 (m-30) cc_final: 0.7276 (m-30) REVERT: B 98 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8044 (mmtm) REVERT: B 119 ILE cc_start: 0.8427 (mm) cc_final: 0.8145 (mp) REVERT: B 152 THR cc_start: 0.8568 (m) cc_final: 0.8324 (t) REVERT: B 182 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8508 (tt) REVERT: C 33 GLN cc_start: 0.7856 (pt0) cc_final: 0.7541 (pt0) REVERT: C 42 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.4715 (tmt) REVERT: C 66 SER cc_start: 0.7952 (p) cc_final: 0.7689 (m) REVERT: D 53 MET cc_start: 0.7817 (mtp) cc_final: 0.7605 (mtp) REVERT: D 113 ASP cc_start: 0.7983 (p0) cc_final: 0.7724 (p0) REVERT: D 156 SER cc_start: 0.8127 (p) cc_final: 0.7762 (t) REVERT: D 204 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6210 (pp30) REVERT: E 42 MET cc_start: 0.6891 (ttp) cc_final: 0.5792 (tmt) REVERT: F 164 GLU cc_start: 0.7609 (tp30) cc_final: 0.7352 (tp30) REVERT: F 204 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6075 (pp30) REVERT: G 42 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5034 (tmt) REVERT: G 57 THR cc_start: 0.7926 (m) cc_final: 0.7640 (p) REVERT: G 65 LEU cc_start: 0.7899 (mt) cc_final: 0.7658 (mt) REVERT: I 138 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7417 (t0) REVERT: I 154 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8312 (m-40) REVERT: I 204 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6615 (pp30) REVERT: J 52 GLU cc_start: 0.7880 (tp30) cc_final: 0.7299 (tp30) REVERT: J 83 VAL cc_start: 0.7695 (p) cc_final: 0.7433 (t) REVERT: K 182 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8485 (tt) REVERT: K 204 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6344 (pp30) REVERT: K 211 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7104 (mm-30) REVERT: L 42 MET cc_start: 0.6034 (tmt) cc_final: 0.5643 (tmt) REVERT: M 102 LEU cc_start: 0.8679 (tp) cc_final: 0.8449 (tt) REVERT: M 113 ASP cc_start: 0.7468 (p0) cc_final: 0.7234 (p0) REVERT: M 182 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8499 (tt) REVERT: M 204 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6574 (pp30) REVERT: N 42 MET cc_start: 0.6785 (ttp) cc_final: 0.5569 (tmt) outliers start: 99 outliers final: 72 residues processed: 526 average time/residue: 0.9793 time to fit residues: 588.5929 Evaluate side-chains 537 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 452 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 64 ASP Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 137 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131542 restraints weight = 67516.656| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.13 r_work: 0.3417 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 18039 Z= 0.254 Angle : 0.565 5.668 24444 Z= 0.299 Chirality : 0.045 0.140 2800 Planarity : 0.003 0.039 3066 Dihedral : 9.438 59.901 2905 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.25 % Favored : 94.43 % Rotamer: Outliers : 4.91 % Allowed : 14.69 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.19), residues: 2135 helix: -3.08 (0.78), residues: 42 sheet: 0.66 (0.16), residues: 1071 loop : -1.25 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 32 TYR 0.015 0.002 TYR M 35 PHE 0.011 0.001 PHE L 59 TRP 0.005 0.001 TRP C 32 HIS 0.009 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00597 (18011) covalent geometry : angle 0.55927 (24388) SS BOND : bond 0.00605 ( 28) SS BOND : angle 1.72486 ( 56) hydrogen bonds : bond 0.03842 ( 665) hydrogen bonds : angle 5.04259 ( 1914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 464 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6031 (pp30) REVERT: A 210 LYS cc_start: 0.6777 (mmtt) cc_final: 0.4736 (mmtt) REVERT: H 42 MET cc_start: 0.6336 (ttp) cc_final: 0.5515 (tmt) REVERT: H 83 VAL cc_start: 0.7108 (p) cc_final: 0.6875 (t) REVERT: B 30 ASP cc_start: 0.7549 (m-30) cc_final: 0.7273 (m-30) REVERT: B 98 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8027 (mmtm) REVERT: B 119 ILE cc_start: 0.8435 (mm) cc_final: 0.8158 (mp) REVERT: B 152 THR cc_start: 0.8576 (m) cc_final: 0.8317 (t) REVERT: C 33 GLN cc_start: 0.7833 (pt0) cc_final: 0.7517 (pt0) REVERT: C 42 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.4705 (tmt) REVERT: C 66 SER cc_start: 0.7961 (p) cc_final: 0.7695 (m) REVERT: D 53 MET cc_start: 0.7805 (mtp) cc_final: 0.7591 (mtp) REVERT: D 113 ASP cc_start: 0.7985 (p0) cc_final: 0.7727 (p0) REVERT: D 156 SER cc_start: 0.8151 (p) cc_final: 0.7793 (t) REVERT: D 204 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6191 (pp30) REVERT: E 42 MET cc_start: 0.6914 (ttp) cc_final: 0.5739 (tmt) REVERT: F 164 GLU cc_start: 0.7597 (tp30) cc_final: 0.7324 (tp30) REVERT: F 204 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6070 (pp30) REVERT: G 42 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5006 (tmt) REVERT: G 57 THR cc_start: 0.7928 (m) cc_final: 0.7642 (p) REVERT: I 154 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8349 (m-40) REVERT: I 204 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6660 (pp30) REVERT: J 52 GLU cc_start: 0.7922 (tp30) cc_final: 0.7324 (tp30) REVERT: J 83 VAL cc_start: 0.7679 (p) cc_final: 0.7429 (t) REVERT: K 147 SER cc_start: 0.8480 (p) cc_final: 0.8198 (p) REVERT: K 204 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6394 (pp30) REVERT: K 211 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7103 (mm-30) REVERT: L 42 MET cc_start: 0.6013 (tmt) cc_final: 0.5605 (tmt) REVERT: M 102 LEU cc_start: 0.8684 (tp) cc_final: 0.8461 (tt) REVERT: M 113 ASP cc_start: 0.7496 (p0) cc_final: 0.7227 (p0) REVERT: M 151 ILE cc_start: 0.7749 (tp) cc_final: 0.7476 (tt) REVERT: M 175 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5695 (pt) REVERT: M 182 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8458 (tt) REVERT: M 204 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6639 (pp30) REVERT: N 42 MET cc_start: 0.6617 (ttp) cc_final: 0.5468 (tmt) outliers start: 97 outliers final: 74 residues processed: 532 average time/residue: 0.9619 time to fit residues: 581.0409 Evaluate side-chains 544 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 459 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 126 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS I 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.167083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132098 restraints weight = 67488.883| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.13 r_work: 0.3436 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18039 Z= 0.175 Angle : 0.528 5.176 24444 Z= 0.281 Chirality : 0.044 0.161 2800 Planarity : 0.003 0.037 3066 Dihedral : 9.196 59.156 2899 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.01 % Favored : 94.66 % Rotamer: Outliers : 4.91 % Allowed : 15.10 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 2135 helix: -3.05 (0.78), residues: 42 sheet: 0.68 (0.16), residues: 1071 loop : -1.16 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.011 0.001 TYR K 174 PHE 0.007 0.001 PHE I 89 TRP 0.006 0.001 TRP J 32 HIS 0.006 0.001 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00410 (18011) covalent geometry : angle 0.52446 (24388) SS BOND : bond 0.00433 ( 28) SS BOND : angle 1.34958 ( 56) hydrogen bonds : bond 0.03511 ( 665) hydrogen bonds : angle 4.91594 ( 1914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 455 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: A 204 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.6005 (pp30) REVERT: A 210 LYS cc_start: 0.6758 (mmtt) cc_final: 0.4712 (mmtt) REVERT: H 42 MET cc_start: 0.6333 (ttp) cc_final: 0.5486 (tmt) REVERT: H 83 VAL cc_start: 0.7121 (p) cc_final: 0.6881 (t) REVERT: B 30 ASP cc_start: 0.7548 (m-30) cc_final: 0.7272 (m-30) REVERT: B 98 LYS cc_start: 0.8269 (mmtm) cc_final: 0.8021 (mmtm) REVERT: B 119 ILE cc_start: 0.8405 (mm) cc_final: 0.8119 (mp) REVERT: B 152 THR cc_start: 0.8564 (m) cc_final: 0.8314 (t) REVERT: C 33 GLN cc_start: 0.7863 (pt0) cc_final: 0.7563 (pt0) REVERT: C 42 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.4751 (tmt) REVERT: C 66 SER cc_start: 0.7966 (p) cc_final: 0.7707 (m) REVERT: D 53 MET cc_start: 0.7795 (mtp) cc_final: 0.7588 (mtp) REVERT: D 113 ASP cc_start: 0.7954 (p0) cc_final: 0.7688 (p0) REVERT: D 156 SER cc_start: 0.8134 (p) cc_final: 0.7782 (t) REVERT: D 204 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6222 (pp30) REVERT: E 42 MET cc_start: 0.6890 (ttp) cc_final: 0.5793 (tmt) REVERT: F 164 GLU cc_start: 0.7594 (tp30) cc_final: 0.7320 (tp30) REVERT: F 204 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6050 (pp30) REVERT: G 42 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.5024 (tmt) REVERT: G 57 THR cc_start: 0.7931 (m) cc_final: 0.7647 (p) REVERT: I 204 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6632 (pp30) REVERT: I 218 TYR cc_start: 0.7063 (m-80) cc_final: 0.6755 (m-80) REVERT: J 52 GLU cc_start: 0.7883 (tp30) cc_final: 0.7281 (tp30) REVERT: J 83 VAL cc_start: 0.7693 (p) cc_final: 0.7446 (t) REVERT: K 147 SER cc_start: 0.8455 (p) cc_final: 0.8173 (p) REVERT: K 182 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8495 (tt) REVERT: K 204 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6362 (pp30) REVERT: L 33 GLN cc_start: 0.7821 (pt0) cc_final: 0.7480 (pt0) REVERT: L 42 MET cc_start: 0.6048 (tmt) cc_final: 0.5645 (tmt) REVERT: M 102 LEU cc_start: 0.8666 (tp) cc_final: 0.8439 (tt) REVERT: M 113 ASP cc_start: 0.7486 (p0) cc_final: 0.7223 (p0) REVERT: M 175 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5553 (pt) REVERT: M 182 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8493 (tt) REVERT: M 204 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6631 (pp30) REVERT: N 42 MET cc_start: 0.6590 (ttp) cc_final: 0.5464 (tmt) outliers start: 97 outliers final: 72 residues processed: 524 average time/residue: 0.8983 time to fit residues: 534.8798 Evaluate side-chains 538 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 454 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 PHE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 205 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS M 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131343 restraints weight = 67397.023| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.14 r_work: 0.3417 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 18039 Z= 0.253 Angle : 0.569 6.232 24444 Z= 0.299 Chirality : 0.045 0.140 2800 Planarity : 0.003 0.039 3066 Dihedral : 9.007 59.650 2887 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.71 % Favored : 93.96 % Rotamer: Outliers : 4.66 % Allowed : 15.30 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.19), residues: 2135 helix: -2.99 (0.79), residues: 42 sheet: 0.63 (0.16), residues: 1071 loop : -1.26 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 32 TYR 0.040 0.002 TYR D 174 PHE 0.014 0.001 PHE L 59 TRP 0.005 0.001 TRP C 32 HIS 0.008 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00596 (18011) covalent geometry : angle 0.56350 (24388) SS BOND : bond 0.00595 ( 28) SS BOND : angle 1.68366 ( 56) hydrogen bonds : bond 0.03815 ( 665) hydrogen bonds : angle 4.97023 ( 1914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 460 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (m-30) REVERT: A 204 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.6049 (pp30) REVERT: A 210 LYS cc_start: 0.6737 (mmtt) cc_final: 0.4684 (mmtt) REVERT: H 42 MET cc_start: 0.6344 (ttp) cc_final: 0.5461 (tmt) REVERT: H 83 VAL cc_start: 0.7104 (p) cc_final: 0.6862 (t) REVERT: B 30 ASP cc_start: 0.7543 (m-30) cc_final: 0.7267 (m-30) REVERT: B 98 LYS cc_start: 0.8268 (mmtm) cc_final: 0.8019 (mmtm) REVERT: B 119 ILE cc_start: 0.8414 (mm) cc_final: 0.8131 (mp) REVERT: B 152 THR cc_start: 0.8579 (m) cc_final: 0.8317 (t) REVERT: C 33 GLN cc_start: 0.7830 (pt0) cc_final: 0.7527 (pt0) REVERT: C 42 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.4870 (tmt) REVERT: C 66 SER cc_start: 0.7989 (p) cc_final: 0.7729 (m) REVERT: D 53 MET cc_start: 0.7813 (mtp) cc_final: 0.7591 (mtp) REVERT: D 113 ASP cc_start: 0.7965 (p0) cc_final: 0.7691 (p0) REVERT: D 156 SER cc_start: 0.8139 (p) cc_final: 0.7794 (t) REVERT: D 204 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6236 (pp30) REVERT: E 42 MET cc_start: 0.6868 (ttp) cc_final: 0.5755 (tmt) REVERT: F 164 GLU cc_start: 0.7586 (tp30) cc_final: 0.7307 (tp30) REVERT: F 171 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7753 (m-40) REVERT: F 204 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6095 (pp30) REVERT: G 42 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.4958 (tmt) REVERT: G 57 THR cc_start: 0.7938 (m) cc_final: 0.7648 (p) REVERT: I 204 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6663 (pp30) REVERT: I 218 TYR cc_start: 0.7096 (m-80) cc_final: 0.6785 (m-80) REVERT: J 52 GLU cc_start: 0.7919 (tp30) cc_final: 0.7297 (tp30) REVERT: J 83 VAL cc_start: 0.7698 (p) cc_final: 0.7446 (t) REVERT: K 147 SER cc_start: 0.8467 (p) cc_final: 0.8186 (p) REVERT: K 182 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8502 (tt) REVERT: K 204 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6380 (pp30) REVERT: L 42 MET cc_start: 0.6018 (tmt) cc_final: 0.5604 (tmt) REVERT: M 102 LEU cc_start: 0.8679 (tp) cc_final: 0.8453 (tt) REVERT: M 113 ASP cc_start: 0.7509 (p0) cc_final: 0.7280 (p0) REVERT: M 175 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5726 (pt) REVERT: M 182 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8459 (tt) REVERT: M 204 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6687 (pp30) REVERT: N 42 MET cc_start: 0.6661 (ttp) cc_final: 0.5459 (tmt) outliers start: 92 outliers final: 71 residues processed: 524 average time/residue: 1.0117 time to fit residues: 600.2459 Evaluate side-chains 542 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 458 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 PHE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 193 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132480 restraints weight = 67366.575| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.13 r_work: 0.3442 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18039 Z= 0.155 Angle : 0.521 6.306 24444 Z= 0.278 Chirality : 0.044 0.131 2800 Planarity : 0.003 0.037 3066 Dihedral : 8.766 59.617 2884 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 4.46 % Allowed : 15.70 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.19), residues: 2135 helix: -2.94 (0.80), residues: 42 sheet: 0.64 (0.16), residues: 1078 loop : -1.17 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 29 TYR 0.025 0.001 TYR D 174 PHE 0.007 0.001 PHE I 89 TRP 0.005 0.001 TRP J 32 HIS 0.006 0.001 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00360 (18011) covalent geometry : angle 0.51779 (24388) SS BOND : bond 0.00386 ( 28) SS BOND : angle 1.23410 ( 56) hydrogen bonds : bond 0.03369 ( 665) hydrogen bonds : angle 4.83321 ( 1914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 464 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.6024 (pp30) REVERT: A 210 LYS cc_start: 0.6757 (mmtt) cc_final: 0.4748 (mmtt) REVERT: H 42 MET cc_start: 0.6332 (ttp) cc_final: 0.5443 (tmt) REVERT: H 83 VAL cc_start: 0.7120 (p) cc_final: 0.6875 (t) REVERT: B 30 ASP cc_start: 0.7537 (m-30) cc_final: 0.7259 (m-30) REVERT: B 98 LYS cc_start: 0.8263 (mmtm) cc_final: 0.8005 (mmtm) REVERT: B 119 ILE cc_start: 0.8394 (mm) cc_final: 0.8098 (mp) REVERT: B 152 THR cc_start: 0.8556 (m) cc_final: 0.8299 (t) REVERT: C 33 GLN cc_start: 0.7875 (pt0) cc_final: 0.7571 (pt0) REVERT: C 42 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.4846 (tmt) REVERT: C 66 SER cc_start: 0.7975 (p) cc_final: 0.7720 (m) REVERT: D 53 MET cc_start: 0.7782 (mtp) cc_final: 0.7564 (mtp) REVERT: D 113 ASP cc_start: 0.7937 (p0) cc_final: 0.7649 (p0) REVERT: D 156 SER cc_start: 0.8145 (p) cc_final: 0.7790 (t) REVERT: D 204 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6221 (pp30) REVERT: E 42 MET cc_start: 0.6910 (ttp) cc_final: 0.5745 (tmt) REVERT: F 164 GLU cc_start: 0.7590 (tp30) cc_final: 0.7300 (tp30) REVERT: F 204 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.6091 (pp30) REVERT: G 42 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.4944 (tmt) REVERT: G 57 THR cc_start: 0.7928 (m) cc_final: 0.7637 (p) REVERT: I 204 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6555 (pp30) REVERT: I 218 TYR cc_start: 0.7093 (m-80) cc_final: 0.6795 (m-80) REVERT: J 52 GLU cc_start: 0.7902 (tp30) cc_final: 0.7265 (tp30) REVERT: J 83 VAL cc_start: 0.7687 (p) cc_final: 0.7438 (t) REVERT: K 64 ASP cc_start: 0.8184 (t70) cc_final: 0.7973 (m-30) REVERT: K 147 SER cc_start: 0.8471 (p) cc_final: 0.8192 (p) REVERT: K 182 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8497 (tt) REVERT: K 204 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6343 (pp30) REVERT: L 33 GLN cc_start: 0.7842 (pt0) cc_final: 0.7469 (pt0) REVERT: L 42 MET cc_start: 0.6003 (tmt) cc_final: 0.5593 (tmt) REVERT: M 102 LEU cc_start: 0.8651 (tp) cc_final: 0.8418 (tt) REVERT: M 113 ASP cc_start: 0.7502 (p0) cc_final: 0.7262 (p0) REVERT: M 175 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5530 (pt) REVERT: M 182 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8493 (tt) REVERT: M 204 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6652 (pp30) REVERT: N 42 MET cc_start: 0.6611 (ttp) cc_final: 0.5501 (tmt) outliers start: 88 outliers final: 70 residues processed: 524 average time/residue: 1.0498 time to fit residues: 622.6269 Evaluate side-chains 542 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 461 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 PHE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132423 restraints weight = 67559.087| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.14 r_work: 0.3440 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18039 Z= 0.156 Angle : 0.518 6.511 24444 Z= 0.276 Chirality : 0.044 0.134 2800 Planarity : 0.003 0.036 3066 Dihedral : 8.624 59.177 2884 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.29 % Favored : 94.38 % Rotamer: Outliers : 4.10 % Allowed : 16.21 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 2135 helix: -2.82 (0.82), residues: 42 sheet: 0.63 (0.16), residues: 1078 loop : -1.12 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 32 TYR 0.027 0.001 TYR D 174 PHE 0.013 0.001 PHE L 59 TRP 0.005 0.001 TRP C 32 HIS 0.005 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00362 (18011) covalent geometry : angle 0.51500 (24388) SS BOND : bond 0.00400 ( 28) SS BOND : angle 1.23112 ( 56) hydrogen bonds : bond 0.03315 ( 665) hydrogen bonds : angle 4.78525 ( 1914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 455 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8097 (mtmm) REVERT: A 204 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6032 (pp30) REVERT: A 210 LYS cc_start: 0.6719 (mmtt) cc_final: 0.4671 (mmtt) REVERT: H 42 MET cc_start: 0.6328 (ttp) cc_final: 0.5469 (tmt) REVERT: B 30 ASP cc_start: 0.7554 (m-30) cc_final: 0.7279 (m-30) REVERT: B 152 THR cc_start: 0.8563 (m) cc_final: 0.8305 (t) REVERT: B 182 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8487 (tt) REVERT: C 33 GLN cc_start: 0.7853 (pt0) cc_final: 0.7562 (pt0) REVERT: C 42 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.4826 (tmt) REVERT: C 66 SER cc_start: 0.7954 (p) cc_final: 0.7690 (m) REVERT: D 53 MET cc_start: 0.7786 (mtp) cc_final: 0.7575 (mtp) REVERT: D 113 ASP cc_start: 0.7947 (p0) cc_final: 0.7646 (p0) REVERT: D 156 SER cc_start: 0.8154 (p) cc_final: 0.7799 (t) REVERT: D 204 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6216 (pp30) REVERT: E 42 MET cc_start: 0.6860 (ttp) cc_final: 0.5742 (tmt) REVERT: F 164 GLU cc_start: 0.7590 (tp30) cc_final: 0.7301 (tp30) REVERT: F 204 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6088 (pp30) REVERT: G 42 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.4931 (tmt) REVERT: G 57 THR cc_start: 0.7924 (m) cc_final: 0.7635 (p) REVERT: I 204 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6565 (pp30) REVERT: I 218 TYR cc_start: 0.7117 (m-80) cc_final: 0.6827 (m-80) REVERT: J 42 MET cc_start: 0.6415 (tmt) cc_final: 0.5160 (tmt) REVERT: J 52 GLU cc_start: 0.7895 (tp30) cc_final: 0.7252 (tp30) REVERT: J 83 VAL cc_start: 0.7669 (p) cc_final: 0.7424 (t) REVERT: K 64 ASP cc_start: 0.8205 (t70) cc_final: 0.7990 (m-30) REVERT: K 147 SER cc_start: 0.8472 (p) cc_final: 0.8200 (p) REVERT: K 182 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8490 (tt) REVERT: K 204 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6335 (pp30) REVERT: L 33 GLN cc_start: 0.7831 (pt0) cc_final: 0.7459 (pt0) REVERT: L 42 MET cc_start: 0.6080 (tmt) cc_final: 0.5849 (tmt) REVERT: M 102 LEU cc_start: 0.8653 (tp) cc_final: 0.8415 (tt) REVERT: M 113 ASP cc_start: 0.7506 (p0) cc_final: 0.7264 (p0) REVERT: M 175 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5526 (pt) REVERT: M 182 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8439 (tt) REVERT: M 204 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6660 (pp30) REVERT: N 42 MET cc_start: 0.6572 (ttp) cc_final: 0.5459 (tmt) outliers start: 81 outliers final: 67 residues processed: 513 average time/residue: 0.9953 time to fit residues: 577.0184 Evaluate side-chains 532 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 453 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 174 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 174 TYR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 204 GLN Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 PHE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS F 118 ASN I 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131413 restraints weight = 67326.572| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.13 r_work: 0.3406 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 18039 Z= 0.311 Angle : 0.596 6.727 24444 Z= 0.313 Chirality : 0.046 0.146 2800 Planarity : 0.003 0.041 3066 Dihedral : 8.708 59.824 2881 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.71 % Favored : 93.96 % Rotamer: Outliers : 4.20 % Allowed : 16.16 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.19), residues: 2135 helix: -2.88 (0.81), residues: 42 sheet: 0.55 (0.16), residues: 1071 loop : -1.28 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 184 TYR 0.021 0.002 TYR D 174 PHE 0.012 0.002 PHE K 107 TRP 0.006 0.001 TRP C 32 HIS 0.010 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00738 (18011) covalent geometry : angle 0.58958 (24388) SS BOND : bond 0.00706 ( 28) SS BOND : angle 1.91233 ( 56) hydrogen bonds : bond 0.04046 ( 665) hydrogen bonds : angle 4.97764 ( 1914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13077.89 seconds wall clock time: 221 minutes 9.35 seconds (13269.35 seconds total)