Starting phenix.real_space_refine on Sun Jun 29 14:07:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxz_29549/06_2025/8fxz_29549_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxz_29549/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxz_29549/06_2025/8fxz_29549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxz_29549/06_2025/8fxz_29549.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxz_29549/06_2025/8fxz_29549_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxz_29549/06_2025/8fxz_29549_trim.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.97, per 1000 atoms: 0.43 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: 7.52 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.70 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: 13.65 Time building geometry restraints manager: 9.20 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.550 Extract box with map and model: 1.100 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 66.490 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.140 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP C 32 HIS 0.007 0.001 HIS K 176 PHE 0.007 0.001 PHE I 89 TYR 0.015 0.002 TYR I 46 ARG 0.003 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.14439 ( 665) hydrogen bonds : angle 6.52780 ( 1914) SS BOND : bond 0.00579 ( 28) SS BOND : angle 1.64415 ( 56) covalent geometry : bond 0.00601 (18011) covalent geometry : angle 0.55700 (24388) *********************** 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 : 2.813 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: 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: 0.6805 (p90) REVERT: B 182 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8586 (tt) REVERT: C 33 GLN cc_start: 0.7773 (pt0) cc_final: 0.7503 (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: 0.5829 (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: 0.8216 (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: 0.6617 (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: 2.4114 time to fit residues: 1495.1417 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 : 2.978 ------------------------------------------------------------------------------- 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 177 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 100 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132023 restraints weight = 67790.309| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.13 r_work: 0.3427 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18039 Z= 0.204 Angle : 0.559 5.453 24444 Z= 0.299 Chirality : 0.045 0.138 2800 Planarity : 0.004 0.043 3066 Dihedral : 10.109 59.852 2924 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.40 % Favored : 95.27 % Rotamer: Outliers : 4.10 % Allowed : 11.85 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2135 helix: -3.05 (0.79), residues: 42 sheet: 0.68 (0.16), residues: 1071 loop : -1.13 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 32 HIS 0.006 0.001 HIS M 176 PHE 0.009 0.001 PHE E 59 TYR 0.016 0.002 TYR D 174 ARG 0.005 0.000 ARG J 29 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 665) hydrogen bonds : angle 5.45652 ( 1914) SS BOND : bond 0.00455 ( 28) SS BOND : angle 1.42725 ( 56) covalent geometry : bond 0.00471 (18011) covalent geometry : angle 0.55534 (24388) *********************** 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 550 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 469 time to evaluate : 2.475 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 152 THR cc_start: 0.8664 (m) cc_final: 0.8462 (t) REVERT: A 204 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.6086 (pp30) REVERT: H 42 MET cc_start: 0.6266 (ttp) cc_final: 0.5420 (tmt) REVERT: B 30 ASP cc_start: 0.7549 (m-30) cc_final: 0.7279 (m-30) REVERT: B 119 ILE cc_start: 0.8419 (mm) cc_final: 0.8142 (mp) REVERT: B 152 THR cc_start: 0.8578 (m) cc_final: 0.8330 (t) REVERT: B 182 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8509 (tt) REVERT: C 33 GLN cc_start: 0.7819 (pt0) cc_final: 0.7474 (pt0) REVERT: C 42 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.4788 (tmt) REVERT: C 43 MET cc_start: 0.5841 (mtp) cc_final: 0.5548 (mtp) REVERT: C 57 THR cc_start: 0.8135 (m) cc_final: 0.7894 (p) REVERT: C 66 SER cc_start: 0.7943 (p) cc_final: 0.7678 (m) REVERT: D 53 MET cc_start: 0.7788 (mtp) cc_final: 0.7582 (mtp) REVERT: D 113 ASP cc_start: 0.7991 (p0) cc_final: 0.7704 (p0) REVERT: D 156 SER cc_start: 0.8076 (p) cc_final: 0.7740 (t) REVERT: D 190 MET cc_start: 0.8284 (mmp) cc_final: 0.7968 (mmp) REVERT: D 204 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6185 (pp30) REVERT: E 42 MET cc_start: 0.6938 (ttp) cc_final: 0.5861 (tmt) REVERT: F 164 GLU cc_start: 0.7616 (tp30) cc_final: 0.7393 (tp30) REVERT: F 202 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.6021 (pp) REVERT: G 42 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.4988 (tmt) REVERT: G 57 THR cc_start: 0.7935 (m) cc_final: 0.7628 (p) REVERT: G 65 LEU cc_start: 0.7885 (mt) cc_final: 0.7642 (mt) REVERT: I 204 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6602 (pp30) REVERT: L 42 MET cc_start: 0.5925 (tmt) cc_final: 0.5725 (tmt) REVERT: M 102 LEU cc_start: 0.8725 (tp) cc_final: 0.8509 (tt) REVERT: M 113 ASP cc_start: 0.7480 (p0) cc_final: 0.7221 (p0) REVERT: M 151 ILE cc_start: 0.7730 (tp) cc_final: 0.7498 (tt) REVERT: M 175 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5577 (pt) REVERT: M 182 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8472 (tt) REVERT: M 204 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6676 (pp30) REVERT: N 42 MET cc_start: 0.6831 (ttp) cc_final: 0.5549 (tmt) outliers start: 81 outliers final: 61 residues processed: 521 average time/residue: 2.5176 time to fit residues: 1495.2543 Evaluate side-chains 522 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 451 time to evaluate : 3.397 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 197 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.167608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132815 restraints weight = 67779.775| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.14 r_work: 0.3442 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1462 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= 0.160 Angle : 0.521 4.988 24444 Z= 0.279 Chirality : 0.044 0.135 2800 Planarity : 0.003 0.033 3066 Dihedral : 9.789 59.625 2916 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.54 % Favored : 95.13 % Rotamer: Outliers : 4.76 % Allowed : 12.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 2135 helix: -3.11 (0.79), residues: 42 sheet: 0.72 (0.16), residues: 1071 loop : -1.12 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 32 HIS 0.006 0.001 HIS M 176 PHE 0.008 0.001 PHE E 59 TYR 0.019 0.001 TYR B 174 ARG 0.004 0.000 ARG I 184 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 665) hydrogen bonds : angle 5.20239 ( 1914) SS BOND : bond 0.00414 ( 28) SS BOND : angle 1.27064 ( 56) covalent geometry : bond 0.00368 (18011) covalent geometry : angle 0.51843 (24388) *********************** 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 550 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 456 time to evaluate : 2.951 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: 0.8322 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: A 204 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6023 (pp30) REVERT: A 210 LYS cc_start: 0.6631 (mmtt) cc_final: 0.4648 (mmtt) REVERT: H 42 MET cc_start: 0.6240 (ttp) cc_final: 0.5437 (tmt) REVERT: B 30 ASP cc_start: 0.7532 (m-30) cc_final: 0.7259 (m-30) REVERT: B 119 ILE cc_start: 0.8421 (mm) cc_final: 0.8142 (mp) REVERT: B 152 THR cc_start: 0.8562 (m) cc_final: 0.8326 (t) REVERT: B 182 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8506 (tt) REVERT: C 33 GLN cc_start: 0.7836 (pt0) cc_final: 0.7490 (pt0) REVERT: C 66 SER cc_start: 0.7959 (p) cc_final: 0.7699 (m) REVERT: D 53 MET cc_start: 0.7809 (mtp) cc_final: 0.7603 (mtp) REVERT: D 113 ASP cc_start: 0.7935 (p0) cc_final: 0.7664 (p0) REVERT: D 156 SER cc_start: 0.8082 (p) cc_final: 0.7743 (t) REVERT: D 190 MET cc_start: 0.8261 (mmp) cc_final: 0.7961 (mmp) REVERT: D 204 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6169 (pp30) REVERT: E 42 MET cc_start: 0.6932 (ttp) cc_final: 0.5845 (tmt) REVERT: F 164 GLU cc_start: 0.7620 (tp30) cc_final: 0.7396 (tp30) REVERT: F 171 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7570 (m110) REVERT: F 204 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6127 (pp30) REVERT: F 219 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7459 (mmm-85) REVERT: G 42 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.4946 (tmt) REVERT: G 57 THR cc_start: 0.7930 (m) cc_final: 0.7640 (p) REVERT: G 65 LEU cc_start: 0.7871 (mt) cc_final: 0.7639 (mt) REVERT: I 204 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6593 (pp30) REVERT: J 83 VAL cc_start: 0.7729 (p) cc_final: 0.7431 (t) REVERT: K 64 ASP cc_start: 0.8134 (t70) cc_final: 0.7894 (m-30) REVERT: K 182 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8469 (tt) REVERT: K 204 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6334 (pp30) REVERT: L 42 MET cc_start: 0.5982 (tmt) cc_final: 0.5675 (tmt) REVERT: M 102 LEU cc_start: 0.8687 (tp) cc_final: 0.8453 (tt) REVERT: M 113 ASP cc_start: 0.7446 (p0) cc_final: 0.7199 (p0) REVERT: M 182 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8497 (tt) REVERT: M 204 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6593 (pp30) REVERT: N 42 MET cc_start: 0.6794 (ttp) cc_final: 0.5554 (tmt) outliers start: 94 outliers final: 64 residues processed: 517 average time/residue: 2.4762 time to fit residues: 1461.5017 Evaluate side-chains 524 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 448 time to evaluate : 2.564 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 131 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.166881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132155 restraints weight = 67232.718| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.12 r_work: 0.3417 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.066 18039 Z= 0.409 Angle : 0.652 6.811 24444 Z= 0.342 Chirality : 0.050 0.155 2800 Planarity : 0.004 0.042 3066 Dihedral : 9.903 59.735 2912 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.57 % Favored : 94.10 % Rotamer: Outliers : 5.32 % Allowed : 13.78 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2135 helix: -3.12 (0.79), residues: 42 sheet: 0.63 (0.16), residues: 1071 loop : -1.41 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 32 HIS 0.014 0.002 HIS B 176 PHE 0.013 0.002 PHE K 107 TYR 0.023 0.003 TYR M 35 ARG 0.004 0.001 ARG I 184 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 665) hydrogen bonds : angle 5.34688 ( 1914) SS BOND : bond 0.00839 ( 28) SS BOND : angle 2.15981 ( 56) covalent geometry : bond 0.00969 (18011) covalent geometry : angle 0.64460 (24388) *********************** 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 563 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 458 time to evaluate : 4.548 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: 0.8362 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: A 204 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6068 (pp30) REVERT: A 210 LYS cc_start: 0.6760 (mmtt) cc_final: 0.4785 (mmtt) REVERT: H 42 MET cc_start: 0.6161 (ttp) cc_final: 0.5335 (tmt) REVERT: B 30 ASP cc_start: 0.7541 (m-30) cc_final: 0.7263 (m-30) REVERT: B 98 LYS cc_start: 0.8288 (mmtm) cc_final: 0.8056 (mmtm) REVERT: B 119 ILE cc_start: 0.8443 (mm) cc_final: 0.8184 (mp) REVERT: B 152 THR cc_start: 0.8611 (m) cc_final: 0.8339 (t) REVERT: C 33 GLN cc_start: 0.7824 (pt0) cc_final: 0.7510 (pt0) REVERT: C 66 SER cc_start: 0.8013 (p) cc_final: 0.7750 (m) REVERT: D 53 MET cc_start: 0.7826 (mtp) cc_final: 0.7607 (mtp) REVERT: D 113 ASP cc_start: 0.8022 (p0) cc_final: 0.7768 (p0) REVERT: D 156 SER cc_start: 0.8085 (p) cc_final: 0.7749 (t) REVERT: D 190 MET cc_start: 0.8285 (mmp) cc_final: 0.8014 (mmp) REVERT: D 204 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6223 (pp30) REVERT: E 42 MET cc_start: 0.6912 (ttp) cc_final: 0.5794 (tmt) REVERT: F 164 GLU cc_start: 0.7575 (tp30) cc_final: 0.7332 (tp30) REVERT: F 204 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6141 (pp30) REVERT: F 219 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7581 (ttm-80) REVERT: G 42 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.5078 (tmt) REVERT: G 57 THR cc_start: 0.7920 (m) cc_final: 0.7640 (p) REVERT: G 65 LEU cc_start: 0.7919 (mt) cc_final: 0.7680 (mt) REVERT: I 204 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6634 (pp30) REVERT: K 204 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6415 (pp30) REVERT: K 211 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7110 (mm-30) REVERT: L 42 MET cc_start: 0.6009 (tmt) cc_final: 0.5648 (tmt) REVERT: M 102 LEU cc_start: 0.8718 (tp) cc_final: 0.8486 (tt) REVERT: M 113 ASP cc_start: 0.7485 (p0) cc_final: 0.7226 (p0) REVERT: M 151 ILE cc_start: 0.7738 (tp) cc_final: 0.7473 (tt) REVERT: M 182 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8464 (tt) REVERT: M 204 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6732 (pp30) outliers start: 105 outliers final: 78 residues processed: 530 average time/residue: 2.5899 time to fit residues: 1585.0775 Evaluate side-chains 545 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 458 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 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 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 D residue 58 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 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 204 GLN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 83 VAL 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 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 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 58 MET 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 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 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 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 32 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.167116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132959 restraints weight = 67470.355| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.02 r_work: 0.3445 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18039 Z= 0.171 Angle : 0.537 5.093 24444 Z= 0.287 Chirality : 0.045 0.134 2800 Planarity : 0.003 0.036 3066 Dihedral : 9.566 58.607 2912 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.64 % Favored : 95.04 % Rotamer: Outliers : 4.61 % Allowed : 14.64 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 2135 helix: -3.15 (0.76), residues: 42 sheet: 0.65 (0.16), residues: 1071 loop : -1.26 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 32 HIS 0.006 0.001 HIS M 176 PHE 0.006 0.001 PHE I 89 TYR 0.015 0.001 TYR D 188 ARG 0.003 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 665) hydrogen bonds : angle 5.08125 ( 1914) SS BOND : bond 0.00452 ( 28) SS BOND : angle 1.33808 ( 56) covalent geometry : bond 0.00396 (18011) covalent geometry : angle 0.53421 (24388) *********************** 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 551 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 460 time to evaluate : 2.757 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: A 204 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.5980 (pp30) REVERT: A 210 LYS cc_start: 0.6834 (mmtt) cc_final: 0.4817 (mmtt) REVERT: H 42 MET cc_start: 0.6413 (ttp) cc_final: 0.5526 (tmt) REVERT: B 30 ASP cc_start: 0.7514 (m-30) cc_final: 0.7243 (m-30) REVERT: B 119 ILE cc_start: 0.8416 (mm) cc_final: 0.8135 (mp) REVERT: B 152 THR cc_start: 0.8552 (m) cc_final: 0.8297 (t) REVERT: C 33 GLN cc_start: 0.7854 (pt0) cc_final: 0.7556 (pt0) REVERT: C 66 SER cc_start: 0.7969 (p) cc_final: 0.7706 (m) REVERT: D 53 MET cc_start: 0.7760 (mtp) cc_final: 0.7541 (mtp) REVERT: D 113 ASP cc_start: 0.7930 (p0) cc_final: 0.7655 (p0) REVERT: D 156 SER cc_start: 0.8057 (p) cc_final: 0.7702 (t) REVERT: D 204 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6225 (pp30) REVERT: E 42 MET cc_start: 0.6909 (ttp) cc_final: 0.5746 (tmt) REVERT: F 164 GLU cc_start: 0.7555 (tp30) cc_final: 0.7287 (tp30) REVERT: F 171 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7619 (m110) REVERT: F 204 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6097 (pp30) REVERT: G 42 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5046 (tmt) REVERT: G 57 THR cc_start: 0.7913 (m) cc_final: 0.7651 (p) REVERT: I 204 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6573 (pp30) REVERT: J 52 GLU cc_start: 0.7870 (tp30) cc_final: 0.7283 (tp30) REVERT: J 83 VAL cc_start: 0.7647 (p) cc_final: 0.7395 (t) REVERT: K 64 ASP cc_start: 0.8138 (t70) cc_final: 0.7891 (m-30) REVERT: K 182 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8466 (tt) REVERT: K 204 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6338 (pp30) REVERT: K 211 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7073 (mm-30) REVERT: L 42 MET cc_start: 0.6056 (tmt) cc_final: 0.5681 (tmt) REVERT: M 102 LEU cc_start: 0.8665 (tp) cc_final: 0.8440 (tt) REVERT: M 113 ASP cc_start: 0.7457 (p0) cc_final: 0.7185 (p0) REVERT: M 175 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5543 (pt) REVERT: M 182 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8487 (tt) REVERT: M 204 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6584 (pp30) REVERT: N 42 MET cc_start: 0.6721 (ttp) cc_final: 0.5581 (tmt) outliers start: 91 outliers final: 65 residues processed: 522 average time/residue: 2.3426 time to fit residues: 1393.3396 Evaluate side-chains 529 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 453 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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 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 C residue 81 GLU 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 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 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 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 M residue 58 MET Chi-restraints excluded: chain M residue 90 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS I 68 ASN I 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130637 restraints weight = 67371.769| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.13 r_work: 0.3413 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 18039 Z= 0.323 Angle : 0.607 6.381 24444 Z= 0.319 Chirality : 0.047 0.185 2800 Planarity : 0.003 0.041 3066 Dihedral : 9.473 59.912 2901 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.95 % Favored : 93.72 % Rotamer: Outliers : 5.07 % Allowed : 14.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2135 helix: -3.12 (0.77), residues: 42 sheet: 0.59 (0.16), residues: 1071 loop : -1.38 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 32 HIS 0.011 0.002 HIS B 176 PHE 0.011 0.002 PHE K 107 TYR 0.028 0.002 TYR D 174 ARG 0.003 0.000 ARG G 94 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 665) hydrogen bonds : angle 5.16664 ( 1914) SS BOND : bond 0.00705 ( 28) SS BOND : angle 1.93473 ( 56) covalent geometry : bond 0.00765 (18011) covalent geometry : angle 0.60096 (24388) *********************** 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 558 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 458 time to evaluate : 2.536 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 204 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6056 (pp30) REVERT: A 210 LYS cc_start: 0.6792 (mmtt) cc_final: 0.4740 (mmtt) REVERT: H 42 MET cc_start: 0.6411 (ttp) cc_final: 0.5510 (tmt) REVERT: H 83 VAL cc_start: 0.7088 (p) cc_final: 0.6874 (t) REVERT: B 30 ASP cc_start: 0.7555 (m-30) cc_final: 0.7279 (m-30) REVERT: B 98 LYS cc_start: 0.8281 (mmtm) cc_final: 0.8038 (mmtm) REVERT: B 119 ILE cc_start: 0.8419 (mm) cc_final: 0.8144 (mp) REVERT: B 152 THR cc_start: 0.8598 (m) cc_final: 0.8335 (t) REVERT: C 33 GLN cc_start: 0.7845 (pt0) cc_final: 0.7532 (pt0) REVERT: C 42 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.4721 (tmt) REVERT: C 66 SER cc_start: 0.7997 (p) cc_final: 0.7732 (m) REVERT: D 53 MET cc_start: 0.7828 (mtp) cc_final: 0.7607 (mtp) REVERT: D 113 ASP cc_start: 0.7994 (p0) cc_final: 0.7741 (p0) REVERT: D 156 SER cc_start: 0.8113 (p) cc_final: 0.7744 (t) REVERT: D 204 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6235 (pp30) REVERT: E 42 MET cc_start: 0.6868 (ttp) cc_final: 0.5749 (tmt) REVERT: F 164 GLU cc_start: 0.7601 (tp30) cc_final: 0.7325 (tp30) REVERT: F 204 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6090 (pp30) REVERT: G 42 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.5052 (tmt) REVERT: G 57 THR cc_start: 0.7932 (m) cc_final: 0.7651 (p) REVERT: I 204 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6652 (pp30) REVERT: J 52 GLU cc_start: 0.7918 (tp30) cc_final: 0.7313 (tp30) REVERT: J 83 VAL cc_start: 0.7693 (p) cc_final: 0.7424 (t) REVERT: K 204 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6455 (pp30) REVERT: K 211 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7091 (mm-30) REVERT: L 42 MET cc_start: 0.6048 (tmt) cc_final: 0.5651 (tmt) REVERT: M 102 LEU cc_start: 0.8700 (tp) cc_final: 0.8470 (tt) REVERT: M 113 ASP cc_start: 0.7509 (p0) cc_final: 0.7278 (p0) REVERT: M 175 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.5813 (pt) REVERT: M 182 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8464 (tt) REVERT: M 204 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6674 (pp30) REVERT: N 42 MET cc_start: 0.6666 (ttp) cc_final: 0.5494 (tmt) outliers start: 100 outliers final: 74 residues processed: 527 average time/residue: 2.3422 time to fit residues: 1403.9381 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 : 2.883 ------------------------------------------------------------------------------- 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 174 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU 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 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 D residue 63 ILE 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 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 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 72 THR 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 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 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 72 THR 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 67 ILE 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 92 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.167310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132373 restraints weight = 67467.598| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.14 r_work: 0.3436 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18039 Z= 0.162 Angle : 0.532 5.855 24444 Z= 0.283 Chirality : 0.044 0.134 2800 Planarity : 0.003 0.037 3066 Dihedral : 9.180 59.013 2900 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.68 % Favored : 94.99 % Rotamer: Outliers : 4.61 % Allowed : 15.91 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2135 helix: -3.09 (0.76), residues: 42 sheet: 0.63 (0.16), residues: 1078 loop : -1.28 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 32 HIS 0.006 0.001 HIS D 176 PHE 0.008 0.001 PHE I 89 TYR 0.038 0.001 TYR I 174 ARG 0.002 0.000 ARG J 29 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 665) hydrogen bonds : angle 4.96456 ( 1914) SS BOND : bond 0.00399 ( 28) SS BOND : angle 1.26935 ( 56) covalent geometry : bond 0.00376 (18011) covalent geometry : angle 0.52929 (24388) *********************** 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 551 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 460 time to evaluate : 2.653 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: 0.6449 (OUTLIER) cc_final: 0.5985 (pp30) REVERT: A 210 LYS cc_start: 0.6783 (mmtt) cc_final: 0.4740 (mmtt) REVERT: H 42 MET cc_start: 0.6347 (ttp) cc_final: 0.5510 (tmt) REVERT: H 83 VAL cc_start: 0.7071 (p) cc_final: 0.6838 (t) REVERT: B 30 ASP cc_start: 0.7562 (m-30) cc_final: 0.7286 (m-30) REVERT: B 98 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8016 (mmtm) REVERT: B 119 ILE cc_start: 0.8399 (mm) cc_final: 0.8111 (mp) REVERT: B 152 THR cc_start: 0.8580 (m) cc_final: 0.8324 (t) REVERT: C 33 GLN cc_start: 0.7860 (pt0) cc_final: 0.7557 (pt0) REVERT: C 42 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.4725 (tmt) REVERT: C 66 SER cc_start: 0.7961 (p) cc_final: 0.7697 (m) REVERT: D 53 MET cc_start: 0.7799 (mtp) cc_final: 0.7572 (mtp) REVERT: D 113 ASP cc_start: 0.7953 (p0) cc_final: 0.7670 (p0) REVERT: D 156 SER cc_start: 0.8120 (p) cc_final: 0.7779 (t) REVERT: D 204 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6225 (pp30) REVERT: E 42 MET cc_start: 0.6911 (ttp) cc_final: 0.5737 (tmt) REVERT: F 164 GLU cc_start: 0.7590 (tp30) cc_final: 0.7302 (tp30) REVERT: F 171 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7637 (m110) REVERT: F 204 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6071 (pp30) REVERT: G 42 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.4999 (tmt) REVERT: G 57 THR cc_start: 0.7942 (m) cc_final: 0.7659 (p) REVERT: I 204 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6595 (pp30) REVERT: I 218 TYR cc_start: 0.7074 (m-80) cc_final: 0.6761 (m-80) REVERT: J 52 GLU cc_start: 0.7908 (tp30) cc_final: 0.7281 (tp30) REVERT: J 83 VAL cc_start: 0.7671 (p) cc_final: 0.7413 (t) REVERT: K 147 SER cc_start: 0.8488 (p) cc_final: 0.8196 (p) REVERT: K 182 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8504 (tt) REVERT: K 204 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6376 (pp30) REVERT: L 33 GLN cc_start: 0.7843 (pt0) cc_final: 0.7486 (pt0) REVERT: L 42 MET cc_start: 0.5984 (tmt) cc_final: 0.5584 (tmt) REVERT: M 102 LEU cc_start: 0.8661 (tp) cc_final: 0.8425 (tt) REVERT: M 113 ASP cc_start: 0.7504 (p0) cc_final: 0.7262 (p0) REVERT: M 182 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8472 (tt) REVERT: M 204 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6642 (pp30) REVERT: N 42 MET cc_start: 0.6619 (ttp) cc_final: 0.5447 (tmt) outliers start: 91 outliers final: 72 residues processed: 524 average time/residue: 2.3861 time to fit residues: 1423.1421 Evaluate side-chains 540 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 457 time to evaluate : 2.933 ------------------------------------------------------------------------------- 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 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 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 81 GLU Chi-restraints excluded: chain D residue 63 ILE 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 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 64 ASP Chi-restraints excluded: chain I residue 72 THR 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 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 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 L residue 67 ILE Chi-restraints excluded: chain M residue 58 MET 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 81 GLU 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 28 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.166491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131536 restraints weight = 67506.670| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.13 r_work: 0.3427 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18039 Z= 0.234 Angle : 0.562 5.877 24444 Z= 0.296 Chirality : 0.045 0.139 2800 Planarity : 0.003 0.038 3066 Dihedral : 9.014 59.612 2891 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.43 % Favored : 94.24 % Rotamer: Outliers : 4.56 % Allowed : 15.70 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2135 helix: -2.96 (0.79), residues: 42 sheet: 0.61 (0.16), residues: 1078 loop : -1.32 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 32 HIS 0.007 0.001 HIS B 176 PHE 0.010 0.001 PHE I 89 TYR 0.048 0.002 TYR M 174 ARG 0.003 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 665) hydrogen bonds : angle 4.98502 ( 1914) SS BOND : bond 0.00569 ( 28) SS BOND : angle 1.59991 ( 56) covalent geometry : bond 0.00550 (18011) covalent geometry : angle 0.55750 (24388) *********************** 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 549 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 459 time to evaluate : 2.909 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: 0.6461 (OUTLIER) cc_final: 0.5999 (pp30) REVERT: A 210 LYS cc_start: 0.6769 (mmtt) cc_final: 0.4724 (mmtt) REVERT: H 42 MET cc_start: 0.6333 (ttp) cc_final: 0.5475 (tmt) REVERT: H 83 VAL cc_start: 0.7108 (p) cc_final: 0.6871 (t) REVERT: B 30 ASP cc_start: 0.7564 (m-30) cc_final: 0.7288 (m-30) REVERT: B 98 LYS cc_start: 0.8276 (mmtm) cc_final: 0.8024 (mmtm) REVERT: B 119 ILE cc_start: 0.8412 (mm) cc_final: 0.8127 (mp) REVERT: B 152 THR cc_start: 0.8587 (m) cc_final: 0.8325 (t) REVERT: C 33 GLN cc_start: 0.7893 (pt0) cc_final: 0.7604 (pt0) REVERT: C 42 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.4758 (tmt) REVERT: C 66 SER cc_start: 0.7974 (p) cc_final: 0.7708 (m) REVERT: D 53 MET cc_start: 0.7778 (mtp) cc_final: 0.7555 (mtp) REVERT: D 113 ASP cc_start: 0.7965 (p0) cc_final: 0.7705 (p0) REVERT: D 156 SER cc_start: 0.8136 (p) cc_final: 0.7758 (t) REVERT: D 204 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6238 (pp30) REVERT: E 42 MET cc_start: 0.6839 (ttp) cc_final: 0.5729 (tmt) REVERT: F 164 GLU cc_start: 0.7603 (tp30) cc_final: 0.7315 (tp30) REVERT: F 171 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7724 (m-40) REVERT: F 204 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6069 (pp30) REVERT: G 42 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.4929 (tmt) REVERT: G 57 THR cc_start: 0.7907 (m) cc_final: 0.7650 (p) REVERT: I 204 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6567 (pp30) REVERT: I 218 TYR cc_start: 0.7086 (m-80) cc_final: 0.6774 (m-80) REVERT: J 52 GLU cc_start: 0.7895 (tp30) cc_final: 0.7281 (tp30) REVERT: J 83 VAL cc_start: 0.7684 (p) cc_final: 0.7432 (t) REVERT: K 147 SER cc_start: 0.8507 (p) cc_final: 0.8215 (p) REVERT: K 182 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8505 (tt) REVERT: K 204 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6415 (pp30) REVERT: L 33 GLN cc_start: 0.7862 (pt0) cc_final: 0.7518 (pt0) REVERT: L 42 MET cc_start: 0.6024 (tmt) cc_final: 0.5625 (tmt) REVERT: M 102 LEU cc_start: 0.8684 (tp) cc_final: 0.8455 (tt) REVERT: M 113 ASP cc_start: 0.7530 (p0) cc_final: 0.7303 (p0) REVERT: M 182 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8451 (tt) REVERT: M 204 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6677 (pp30) REVERT: N 42 MET cc_start: 0.6651 (ttp) cc_final: 0.5469 (tmt) outliers start: 90 outliers final: 78 residues processed: 520 average time/residue: 2.3355 time to fit residues: 1382.5799 Evaluate side-chains 544 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 455 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 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 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 171 ASN 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 64 ASP Chi-restraints excluded: chain I residue 72 THR 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 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 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 L residue 67 ILE Chi-restraints excluded: chain M residue 58 MET 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 139 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 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 D 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131676 restraints weight = 67462.910| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.13 r_work: 0.3427 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 18039 Z= 0.242 Angle : 0.565 6.425 24444 Z= 0.298 Chirality : 0.045 0.136 2800 Planarity : 0.003 0.040 3066 Dihedral : 8.962 59.785 2891 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.20 % Favored : 94.47 % Rotamer: Outliers : 4.86 % Allowed : 15.60 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2135 helix: -2.95 (0.80), residues: 42 sheet: 0.55 (0.16), residues: 1078 loop : -1.33 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 32 HIS 0.008 0.001 HIS B 176 PHE 0.010 0.001 PHE I 89 TYR 0.031 0.002 TYR M 174 ARG 0.003 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 665) hydrogen bonds : angle 4.97613 ( 1914) SS BOND : bond 0.00547 ( 28) SS BOND : angle 1.60589 ( 56) covalent geometry : bond 0.00570 (18011) covalent geometry : angle 0.56083 (24388) *********************** 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 557 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 461 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8347 (mtpt) cc_final: 0.8116 (mtmm) REVERT: A 204 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5910 (pp30) REVERT: A 210 LYS cc_start: 0.6745 (mmtt) cc_final: 0.4681 (mmtt) REVERT: H 42 MET cc_start: 0.6342 (ttp) cc_final: 0.5532 (tmt) REVERT: H 83 VAL cc_start: 0.7135 (p) cc_final: 0.6887 (t) REVERT: B 30 ASP cc_start: 0.7560 (m-30) cc_final: 0.7286 (m-30) REVERT: B 98 LYS cc_start: 0.8272 (mmtm) cc_final: 0.8030 (mmtm) REVERT: B 119 ILE cc_start: 0.8411 (mm) cc_final: 0.8129 (mp) REVERT: B 152 THR cc_start: 0.8575 (m) cc_final: 0.8316 (t) REVERT: C 33 GLN cc_start: 0.7877 (pt0) cc_final: 0.7586 (pt0) REVERT: C 42 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.4782 (tmt) REVERT: C 66 SER cc_start: 0.7998 (p) cc_final: 0.7734 (m) REVERT: D 53 MET cc_start: 0.7762 (mtp) cc_final: 0.7546 (mtp) REVERT: D 113 ASP cc_start: 0.7982 (p0) cc_final: 0.7710 (p0) REVERT: D 156 SER cc_start: 0.8118 (p) cc_final: 0.7754 (t) REVERT: D 204 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6253 (pp30) REVERT: E 42 MET cc_start: 0.6856 (ttp) cc_final: 0.5692 (tmt) REVERT: F 164 GLU cc_start: 0.7582 (tp30) cc_final: 0.7314 (tp30) REVERT: F 171 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: F 204 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6083 (pp30) REVERT: G 42 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.4922 (tmt) REVERT: G 57 THR cc_start: 0.7945 (m) cc_final: 0.7667 (p) REVERT: I 204 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6583 (pp30) REVERT: I 218 TYR cc_start: 0.7106 (m-80) cc_final: 0.6803 (m-80) REVERT: J 52 GLU cc_start: 0.7883 (tp30) cc_final: 0.7268 (tp30) REVERT: J 83 VAL cc_start: 0.7702 (p) cc_final: 0.7449 (t) REVERT: K 147 SER cc_start: 0.8505 (p) cc_final: 0.8212 (p) REVERT: K 204 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6415 (pp30) REVERT: L 33 GLN cc_start: 0.7870 (pt0) cc_final: 0.7523 (pt0) REVERT: L 42 MET cc_start: 0.6060 (tmt) cc_final: 0.5661 (tmt) REVERT: M 102 LEU cc_start: 0.8685 (tp) cc_final: 0.8463 (tt) REVERT: M 113 ASP cc_start: 0.7526 (p0) cc_final: 0.7303 (p0) REVERT: M 204 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6682 (pp30) REVERT: N 42 MET cc_start: 0.6701 (ttp) cc_final: 0.5545 (tmt) outliers start: 96 outliers final: 79 residues processed: 527 average time/residue: 2.4097 time to fit residues: 1469.1680 Evaluate side-chains 549 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 461 time to evaluate : 2.932 ------------------------------------------------------------------------------- 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 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 48 ILE 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 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 64 ASP Chi-restraints excluded: chain I residue 72 THR 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 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 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 L residue 67 ILE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 72 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 202 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS D 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132409 restraints weight = 66931.421| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.12 r_work: 0.3432 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18039 Z= 0.168 Angle : 0.534 6.481 24444 Z= 0.284 Chirality : 0.044 0.131 2800 Planarity : 0.003 0.037 3066 Dihedral : 8.754 59.816 2888 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.96 % Favored : 94.71 % Rotamer: Outliers : 4.26 % Allowed : 16.16 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 2135 helix: -2.90 (0.81), residues: 42 sheet: 0.56 (0.16), residues: 1078 loop : -1.24 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 32 HIS 0.006 0.001 HIS I 176 PHE 0.010 0.001 PHE N 59 TYR 0.036 0.001 TYR M 174 ARG 0.002 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 665) hydrogen bonds : angle 4.89286 ( 1914) SS BOND : bond 0.00405 ( 28) SS BOND : angle 1.42061 ( 56) covalent geometry : bond 0.00391 (18011) covalent geometry : angle 0.53019 (24388) ********************** 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 543 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 459 time to evaluate : 2.477 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: A 114 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8110 (mtmm) REVERT: A 204 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.5936 (pp30) REVERT: A 210 LYS cc_start: 0.6747 (mmtt) cc_final: 0.4709 (mmtt) REVERT: H 42 MET cc_start: 0.6363 (ttp) cc_final: 0.5459 (tmt) REVERT: B 30 ASP cc_start: 0.7529 (m-30) cc_final: 0.7255 (m-30) REVERT: B 98 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8019 (mmtm) REVERT: B 152 THR cc_start: 0.8574 (m) cc_final: 0.8321 (t) REVERT: C 33 GLN cc_start: 0.7903 (pt0) cc_final: 0.7618 (pt0) REVERT: C 42 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.4803 (tmt) REVERT: C 66 SER cc_start: 0.7938 (p) cc_final: 0.7715 (m) REVERT: D 53 MET cc_start: 0.7800 (mtp) cc_final: 0.7579 (mtp) REVERT: D 113 ASP cc_start: 0.7957 (p0) cc_final: 0.7667 (p0) REVERT: D 156 SER cc_start: 0.8130 (p) cc_final: 0.7754 (t) REVERT: D 204 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6265 (pp30) REVERT: E 42 MET cc_start: 0.6827 (ttp) cc_final: 0.5712 (tmt) REVERT: F 164 GLU cc_start: 0.7587 (tp30) cc_final: 0.7311 (tp30) REVERT: F 171 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7629 (m110) REVERT: F 204 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6087 (pp30) REVERT: G 42 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.4970 (tmt) REVERT: G 57 THR cc_start: 0.7949 (m) cc_final: 0.7678 (p) REVERT: I 204 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6558 (pp30) REVERT: I 218 TYR cc_start: 0.7112 (m-80) cc_final: 0.6819 (m-80) REVERT: J 52 GLU cc_start: 0.7878 (tp30) cc_final: 0.7251 (tp30) REVERT: J 83 VAL cc_start: 0.7707 (p) cc_final: 0.7454 (t) REVERT: K 147 SER cc_start: 0.8499 (p) cc_final: 0.8216 (p) REVERT: K 162 ASN cc_start: 0.8536 (t0) cc_final: 0.8259 (t0) REVERT: K 204 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6394 (pp30) REVERT: L 33 GLN cc_start: 0.7863 (pt0) cc_final: 0.7515 (pt0) REVERT: L 42 MET cc_start: 0.6159 (tmt) cc_final: 0.5766 (tmt) REVERT: M 102 LEU cc_start: 0.8673 (tp) cc_final: 0.8443 (tt) REVERT: M 113 ASP cc_start: 0.7516 (p0) cc_final: 0.7300 (p0) REVERT: M 204 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6684 (pp30) REVERT: N 42 MET cc_start: 0.6668 (ttp) cc_final: 0.5493 (tmt) outliers start: 84 outliers final: 76 residues processed: 516 average time/residue: 2.3729 time to fit residues: 1388.4262 Evaluate side-chains 543 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 458 time to evaluate : 2.453 ------------------------------------------------------------------------------- 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 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 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 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 61 SER 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 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 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 L residue 67 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS D 185 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131850 restraints weight = 67510.076| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.13 r_work: 0.3429 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18039 Z= 0.224 Angle : 0.559 6.553 24444 Z= 0.295 Chirality : 0.045 0.137 2800 Planarity : 0.003 0.039 3066 Dihedral : 8.675 59.209 2885 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.01 % Favored : 94.66 % Rotamer: Outliers : 4.36 % Allowed : 16.21 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2135 helix: -2.86 (0.82), residues: 42 sheet: 0.54 (0.16), residues: 1078 loop : -1.28 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 32 HIS 0.008 0.001 HIS C 18 PHE 0.010 0.001 PHE A 206 TYR 0.031 0.002 TYR M 174 ARG 0.003 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 665) hydrogen bonds : angle 4.92508 ( 1914) SS BOND : bond 0.00582 ( 28) SS BOND : angle 1.70269 ( 56) covalent geometry : bond 0.00527 (18011) covalent geometry : angle 0.55355 (24388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32292.38 seconds wall clock time: 553 minutes 22.90 seconds (33202.90 seconds total)