Starting phenix.real_space_refine on Fri Feb 6 00:23:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8a_62166/02_2026/9k8a_62166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8a_62166/02_2026/9k8a_62166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8a_62166/02_2026/9k8a_62166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8a_62166/02_2026/9k8a_62166.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8a_62166/02_2026/9k8a_62166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8a_62166/02_2026/9k8a_62166.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.070 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 Zn 24 6.06 5 S 24 5.16 5 C 13764 2.51 5 N 3576 2.21 5 O 4104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 179 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21492 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "G" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "J" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "H" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "K" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "F" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "I" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "L" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.26, per 1000 atoms: 0.24 Number of scatterers: 21492 At special positions: 0 Unit cell: (149.745, 157.286, 131.431, 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) Zn 24 29.99 S 24 16.00 O 4104 8.00 N 3576 7.00 C 13764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 58 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS C 15 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 166 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS J 220 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS B 58 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 15 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 166 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS F 220 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS C 58 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 15 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 166 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS E 220 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 58 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS J 15 " pdb=" ZN D 302 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 166 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS K 220 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS G 58 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 15 " pdb=" ZN D 304 " pdb="ZN ZN D 304 " - pdb=" NE2 HIS K 166 " pdb="ZN ZN D 304 " - pdb=" NE2 HIS D 220 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 58 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS K 15 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS E 166 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS C 220 " pdb=" ZN E 303 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS H 58 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 15 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 58 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS L 15 " pdb=" ZN F 302 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS F 166 " pdb=" ZN F 303 " pdb="ZN ZN F 303 " - pdb=" NE2 HIS I 58 " pdb="ZN ZN F 303 " - pdb=" NE2 HIS F 15 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 166 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS I 220 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 166 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS L 220 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS K 58 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 15 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 166 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 58 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS G 15 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS J 166 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS A 220 " pdb=" ZN L 301 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS L 58 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS I 15 " pdb=" ZN L 302 " pdb="ZN ZN L 302 " - pdb=" NE2 HIS L 166 " pdb="ZN ZN L 302 " - pdb=" NE2 HIS H 220 " 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 Processing helix chain 'A' and resid 27 through 43 removed outlier: 3.607A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 67 removed outlier: 4.100A pdb=" N ILE A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.677A pdb=" N ILE A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.623A pdb=" N ARG A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'A' and resid 135 through 157 removed outlier: 3.932A pdb=" N VAL A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.825A pdb=" N LYS A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.501A pdb=" N ALA A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.647A pdb=" N ALA B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 67 removed outlier: 4.026A pdb=" N ILE B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.621A pdb=" N ILE B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 113 removed outlier: 3.580A pdb=" N ARG B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.665A pdb=" N ALA B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 157 Processing helix chain 'B' and resid 160 through 179 removed outlier: 3.959A pdb=" N LYS B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 201 removed outlier: 4.008A pdb=" N LEU B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 224 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 27 through 43 removed outlier: 3.651A pdb=" N ALA C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 67 removed outlier: 4.046A pdb=" N ILE C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.634A pdb=" N ILE C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 113 removed outlier: 3.898A pdb=" N ARG C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Processing helix chain 'C' and resid 135 through 157 removed outlier: 4.019A pdb=" N VAL C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 179 removed outlier: 3.836A pdb=" N LYS C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 201 removed outlier: 3.551A pdb=" N GLU C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 224 Processing helix chain 'D' and resid 7 through 24 Processing helix chain 'D' and resid 27 through 43 removed outlier: 3.645A pdb=" N ALA D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 67 removed outlier: 4.108A pdb=" N ILE D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 86 removed outlier: 3.719A pdb=" N ILE D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.676A pdb=" N ARG D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 131 removed outlier: 3.541A pdb=" N ALA D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 157 removed outlier: 4.046A pdb=" N VAL D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 179 removed outlier: 3.796A pdb=" N LYS D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.527A pdb=" N ALA D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 224 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 27 through 43 removed outlier: 3.678A pdb=" N ALA G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 65 removed outlier: 4.252A pdb=" N ILE G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 86 removed outlier: 3.590A pdb=" N ILE G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 113 removed outlier: 3.938A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.522A pdb=" N ALA G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 157 removed outlier: 3.952A pdb=" N VAL G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 179 removed outlier: 3.806A pdb=" N LYS G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 201 Processing helix chain 'G' and resid 206 through 224 Processing helix chain 'J' and resid 7 through 24 Processing helix chain 'J' and resid 27 through 43 removed outlier: 3.646A pdb=" N ALA J 31 " --> pdb=" O LYS J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 65 removed outlier: 3.990A pdb=" N ILE J 53 " --> pdb=" O ALA J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 86 removed outlier: 3.654A pdb=" N ILE J 76 " --> pdb=" O GLU J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 113 removed outlier: 3.679A pdb=" N ARG J 96 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU J 97 " --> pdb=" O GLU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 130 removed outlier: 3.659A pdb=" N ALA J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 157 removed outlier: 3.932A pdb=" N VAL J 140 " --> pdb=" O LYS J 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU J 157 " --> pdb=" O ARG J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 179 removed outlier: 3.871A pdb=" N LYS J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 201 removed outlier: 4.005A pdb=" N LEU J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 224 Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 27 through 43 removed outlier: 3.647A pdb=" N ALA E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 67 removed outlier: 4.117A pdb=" N ILE E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.699A pdb=" N ILE E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 113 removed outlier: 3.682A pdb=" N ARG E 96 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 130 removed outlier: 3.501A pdb=" N ALA E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 157 removed outlier: 3.870A pdb=" N VAL E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 179 removed outlier: 3.763A pdb=" N LYS E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 201 removed outlier: 3.999A pdb=" N LEU E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 224 Processing helix chain 'H' and resid 7 through 24 Processing helix chain 'H' and resid 27 through 43 removed outlier: 3.619A pdb=" N ALA H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 67 removed outlier: 3.971A pdb=" N ILE H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG H 66 " --> pdb=" O ASP H 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 86 removed outlier: 3.683A pdb=" N ILE H 76 " --> pdb=" O GLU H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 113 removed outlier: 3.610A pdb=" N ARG H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 130 removed outlier: 3.679A pdb=" N ALA H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 157 removed outlier: 4.100A pdb=" N VAL H 140 " --> pdb=" O LYS H 136 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU H 141 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU H 157 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 179 removed outlier: 3.765A pdb=" N LYS H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 201 removed outlier: 4.049A pdb=" N LEU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 224 Processing helix chain 'K' and resid 7 through 24 Processing helix chain 'K' and resid 27 through 43 removed outlier: 3.582A pdb=" N ALA K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 67 removed outlier: 4.031A pdb=" N ILE K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG K 66 " --> pdb=" O ASP K 62 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 86 removed outlier: 3.711A pdb=" N ILE K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 113 removed outlier: 3.576A pdb=" N ARG K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 130 removed outlier: 3.516A pdb=" N ALA K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 157 removed outlier: 4.029A pdb=" N VAL K 140 " --> pdb=" O LYS K 136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU K 141 " --> pdb=" O SER K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 179 removed outlier: 3.836A pdb=" N LYS K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 201 removed outlier: 4.052A pdb=" N LEU K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 224 Processing helix chain 'F' and resid 7 through 24 Processing helix chain 'F' and resid 27 through 43 removed outlier: 3.638A pdb=" N ALA F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 removed outlier: 3.925A pdb=" N ILE F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.611A pdb=" N ILE F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 113 removed outlier: 3.616A pdb=" N ARG F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 removed outlier: 3.552A pdb=" N ALA F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 157 Processing helix chain 'F' and resid 160 through 179 removed outlier: 3.821A pdb=" N LYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 201 removed outlier: 4.136A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 224 Processing helix chain 'I' and resid 7 through 24 Processing helix chain 'I' and resid 27 through 43 removed outlier: 3.660A pdb=" N ALA I 31 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 65 removed outlier: 4.042A pdb=" N ILE I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 86 removed outlier: 3.663A pdb=" N ILE I 76 " --> pdb=" O GLU I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 113 removed outlier: 3.867A pdb=" N ARG I 96 " --> pdb=" O ARG I 92 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 130 Processing helix chain 'I' and resid 138 through 157 removed outlier: 3.813A pdb=" N GLU I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 179 removed outlier: 3.789A pdb=" N LYS I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 201 Processing helix chain 'I' and resid 206 through 224 Processing helix chain 'L' and resid 7 through 24 Processing helix chain 'L' and resid 27 through 43 removed outlier: 3.647A pdb=" N ALA L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 67 removed outlier: 4.077A pdb=" N ILE L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG L 66 " --> pdb=" O ASP L 62 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 86 removed outlier: 3.574A pdb=" N ILE L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 113 removed outlier: 3.687A pdb=" N ARG L 96 " --> pdb=" O ARG L 92 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 130 removed outlier: 3.628A pdb=" N ALA L 120 " --> pdb=" O GLU L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 157 removed outlier: 4.166A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU L 157 " --> pdb=" O ARG L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 179 removed outlier: 3.850A pdb=" N LYS L 164 " --> pdb=" O SER L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 201 Processing helix chain 'L' and resid 206 through 224 1625 hydrogen bonds defined for protein. 4875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7076 1.34 - 1.46: 1321 1.46 - 1.57: 13191 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 21636 Sorted by residual: bond pdb=" CA HIS K 166 " pdb=" C HIS K 166 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.29e-02 6.01e+03 4.22e+00 bond pdb=" C HIS K 166 " pdb=" N LEU K 167 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.25e-02 6.40e+03 3.99e+00 bond pdb=" N HIS K 166 " pdb=" CA HIS K 166 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.23e-02 6.61e+03 3.87e+00 bond pdb=" C LYS K 104 " pdb=" N ASP K 105 " ideal model delta sigma weight residual 1.334 1.308 0.026 1.46e-02 4.69e+03 3.27e+00 bond pdb=" C LEU K 165 " pdb=" N HIS K 166 " ideal model delta sigma weight residual 1.335 1.311 0.024 1.36e-02 5.41e+03 3.17e+00 ... (remaining 21631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 28445 2.09 - 4.19: 304 4.19 - 6.28: 47 6.28 - 8.38: 10 8.38 - 10.47: 6 Bond angle restraints: 28812 Sorted by residual: angle pdb=" N LYS G 48 " pdb=" CA LYS G 48 " pdb=" C LYS G 48 " ideal model delta sigma weight residual 113.56 107.39 6.17 1.39e+00 5.18e-01 1.97e+01 angle pdb=" N HIS K 166 " pdb=" CA HIS K 166 " pdb=" C HIS K 166 " ideal model delta sigma weight residual 111.36 106.82 4.54 1.09e+00 8.42e-01 1.74e+01 angle pdb=" C GLU H 25 " pdb=" N GLY H 26 " pdb=" CA GLY H 26 " ideal model delta sigma weight residual 123.08 119.55 3.53 1.12e+00 7.97e-01 9.96e+00 angle pdb=" C GLU K 25 " pdb=" N GLY K 26 " pdb=" CA GLY K 26 " ideal model delta sigma weight residual 123.08 119.63 3.45 1.12e+00 7.97e-01 9.51e+00 angle pdb=" C GLU A 25 " pdb=" N GLY A 26 " pdb=" CA GLY A 26 " ideal model delta sigma weight residual 123.08 119.66 3.42 1.12e+00 7.97e-01 9.32e+00 ... (remaining 28807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11038 17.99 - 35.98: 1951 35.98 - 53.97: 608 53.97 - 71.95: 103 71.95 - 89.94: 52 Dihedral angle restraints: 13752 sinusoidal: 5988 harmonic: 7764 Sorted by residual: dihedral pdb=" CB GLU B 7 " pdb=" CG GLU B 7 " pdb=" CD GLU B 7 " pdb=" OE1 GLU B 7 " ideal model delta sinusoidal sigma weight residual 0.00 89.94 -89.94 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU I 7 " pdb=" CG GLU I 7 " pdb=" CD GLU I 7 " pdb=" OE1 GLU I 7 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU K 7 " pdb=" CG GLU K 7 " pdb=" CD GLU K 7 " pdb=" OE1 GLU K 7 " ideal model delta sinusoidal sigma weight residual 0.00 89.90 -89.90 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 13749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2629 0.042 - 0.084: 661 0.084 - 0.125: 17 0.125 - 0.167: 4 0.167 - 0.209: 13 Chirality restraints: 3324 Sorted by residual: chirality pdb=" CA PRO I 2 " pdb=" N PRO I 2 " pdb=" C PRO I 2 " pdb=" CB PRO I 2 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA PRO J 2 " pdb=" N PRO J 2 " pdb=" C PRO J 2 " pdb=" CB PRO J 2 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA PRO E 2 " pdb=" N PRO E 2 " pdb=" C PRO E 2 " pdb=" CB PRO E 2 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 3321 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 1 " 0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO I 2 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO I 2 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO I 2 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 1 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO C 2 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 2 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 2 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 1 " -0.059 5.00e-02 4.00e+02 8.96e-02 1.29e+01 pdb=" N PRO H 2 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO H 2 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 2 " -0.048 5.00e-02 4.00e+02 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 155 2.57 - 3.16: 16628 3.16 - 3.74: 34195 3.74 - 4.32: 42997 4.32 - 4.90: 74714 Nonbonded interactions: 168689 Sorted by model distance: nonbonded pdb=" OD2 ASP I 37 " pdb="ZN ZN L 301 " model vdw 1.993 2.230 nonbonded pdb=" OD2 ASP G 37 " pdb="ZN ZN J 301 " model vdw 2.002 2.230 nonbonded pdb=" OD2 ASP K 37 " pdb="ZN ZN E 301 " model vdw 2.010 2.230 nonbonded pdb=" OD2 ASP A 37 " pdb="ZN ZN A 303 " model vdw 2.011 2.230 nonbonded pdb=" OD2 ASP H 37 " pdb="ZN ZN H 302 " model vdw 2.012 2.230 ... (remaining 168684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 224) selection = (chain 'B' and resid 1 through 224) selection = (chain 'C' and resid 1 through 224) selection = (chain 'D' and resid 1 through 224) selection = (chain 'E' and resid 1 through 224) selection = (chain 'F' and resid 1 through 224) selection = (chain 'G' and resid 1 through 224) selection = (chain 'H' and resid 1 through 224) selection = (chain 'I' and resid 1 through 224) selection = (chain 'J' and resid 1 through 224) selection = chain 'K' selection = (chain 'L' and resid 1 through 224) } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.240 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 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 : 0.015 0.691 21682 Z= 0.500 Angle : 0.583 10.475 28812 Z= 0.328 Chirality : 0.034 0.209 3324 Planarity : 0.006 0.094 3612 Dihedral : 20.142 89.943 8712 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.90 % Allowed : 2.06 % Favored : 97.03 % Rotamer: Outliers : 0.13 % Allowed : 26.78 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.16), residues: 2664 helix: 2.35 (0.11), residues: 2208 sheet: None (None), residues: 0 loop : -2.79 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 92 TYR 0.007 0.001 TYR G 118 PHE 0.008 0.001 PHE D 117 TRP 0.022 0.003 TRP H 151 HIS 0.002 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00306 (21636) covalent geometry : angle 0.58265 (28812) hydrogen bonds : bond 0.09932 ( 1625) hydrogen bonds : angle 4.04495 ( 4875) metal coordination : bond 0.31404 ( 46) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 349 time to evaluate : 0.761 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: A 126 ARG cc_start: 0.6314 (ttm110) cc_final: 0.5798 (ttm110) REVERT: D 126 ARG cc_start: 0.6431 (ttm110) cc_final: 0.6021 (ttm110) REVERT: J 126 ARG cc_start: 0.6739 (ttm110) cc_final: 0.6165 (ttm110) REVERT: E 126 ARG cc_start: 0.6485 (ttm110) cc_final: 0.6062 (ttm110) REVERT: K 126 ARG cc_start: 0.6568 (ttm110) cc_final: 0.6339 (ttm110) outliers start: 3 outliers final: 1 residues processed: 351 average time/residue: 0.2546 time to fit residues: 120.3368 Evaluate side-chains 223 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS D 15 HIS J 15 HIS E 15 HIS F 15 HIS I 15 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.075699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.056556 restraints weight = 90944.952| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 5.60 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 21682 Z= 0.200 Angle : 0.588 8.560 28812 Z= 0.312 Chirality : 0.036 0.209 3324 Planarity : 0.006 0.092 3612 Dihedral : 3.734 51.853 2845 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.90 % Allowed : 1.01 % Favored : 98.09 % Rotamer: Outliers : 2.90 % Allowed : 25.53 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.17), residues: 2664 helix: 2.36 (0.11), residues: 2256 sheet: None (None), residues: 0 loop : -2.94 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 126 TYR 0.024 0.002 TYR D 118 PHE 0.013 0.002 PHE D 148 TRP 0.011 0.002 TRP A 151 HIS 0.004 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00426 (21636) covalent geometry : angle 0.58756 (28812) hydrogen bonds : bond 0.03671 ( 1625) hydrogen bonds : angle 3.70083 ( 4875) metal coordination : bond 0.06017 ( 46) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 0.877 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: A 105 ASP cc_start: 0.8870 (m-30) cc_final: 0.8546 (m-30) REVERT: A 145 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8771 (mm-30) REVERT: B 48 LYS cc_start: 0.9138 (tppt) cc_final: 0.8732 (tppt) REVERT: B 105 ASP cc_start: 0.9296 (m-30) cc_final: 0.8604 (m-30) REVERT: B 126 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8319 (ttm110) REVERT: C 40 GLU cc_start: 0.8860 (tp30) cc_final: 0.8653 (tp30) REVERT: C 48 LYS cc_start: 0.9143 (tppt) cc_final: 0.8740 (tppt) REVERT: C 92 ARG cc_start: 0.9005 (mtp-110) cc_final: 0.8776 (ttm110) REVERT: C 105 ASP cc_start: 0.8900 (m-30) cc_final: 0.8489 (m-30) REVERT: C 118 TYR cc_start: 0.9127 (t80) cc_final: 0.8412 (t80) REVERT: C 145 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8477 (mm-30) REVERT: D 62 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: G 48 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8761 (mmtm) REVERT: J 48 LYS cc_start: 0.9236 (tppt) cc_final: 0.8928 (tppt) REVERT: J 105 ASP cc_start: 0.8806 (m-30) cc_final: 0.8513 (m-30) REVERT: K 40 GLU cc_start: 0.8819 (tp30) cc_final: 0.8575 (tp30) REVERT: K 48 LYS cc_start: 0.9265 (tppt) cc_final: 0.9025 (tppt) REVERT: K 105 ASP cc_start: 0.9237 (m-30) cc_final: 0.8586 (m-30) REVERT: K 174 ARG cc_start: 0.9321 (mmm160) cc_final: 0.8449 (mmm160) REVERT: K 177 GLU cc_start: 0.8955 (tt0) cc_final: 0.8492 (tt0) REVERT: F 40 GLU cc_start: 0.9097 (tp30) cc_final: 0.8773 (tp30) REVERT: F 48 LYS cc_start: 0.9288 (tppt) cc_final: 0.9008 (tppt) REVERT: F 105 ASP cc_start: 0.8958 (m-30) cc_final: 0.8598 (m-30) REVERT: F 145 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8741 (mm-30) REVERT: F 177 GLU cc_start: 0.9288 (tt0) cc_final: 0.9055 (tt0) REVERT: I 178 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8812 (mm) REVERT: L 48 LYS cc_start: 0.9401 (tppt) cc_final: 0.9118 (tppt) REVERT: L 105 ASP cc_start: 0.9286 (m-30) cc_final: 0.8673 (m-30) outliers start: 65 outliers final: 23 residues processed: 300 average time/residue: 0.2504 time to fit residues: 101.5087 Evaluate side-chains 222 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 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 15 HIS K 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.075560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.057486 restraints weight = 90588.554| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 5.50 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 21682 Z= 0.145 Angle : 0.513 8.008 28812 Z= 0.277 Chirality : 0.034 0.205 3324 Planarity : 0.006 0.091 3612 Dihedral : 3.507 13.353 2844 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.79 % Allowed : 1.91 % Favored : 97.30 % Rotamer: Outliers : 2.50 % Allowed : 25.22 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.17), residues: 2664 helix: 2.54 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -2.80 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 126 TYR 0.027 0.002 TYR I 118 PHE 0.015 0.001 PHE D 148 TRP 0.010 0.002 TRP K 151 HIS 0.002 0.001 HIS I 15 Details of bonding type rmsd covalent geometry : bond 0.00336 (21636) covalent geometry : angle 0.51258 (28812) hydrogen bonds : bond 0.03260 ( 1625) hydrogen bonds : angle 3.47065 ( 4875) metal coordination : bond 0.03563 ( 46) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.942 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: A 40 GLU cc_start: 0.8862 (tp30) cc_final: 0.8456 (tp30) REVERT: A 105 ASP cc_start: 0.8842 (m-30) cc_final: 0.8496 (m-30) REVERT: A 130 GLU cc_start: 0.8463 (mp0) cc_final: 0.8246 (pm20) REVERT: A 145 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8742 (mm-30) REVERT: B 48 LYS cc_start: 0.9176 (tppt) cc_final: 0.8747 (tppt) REVERT: B 105 ASP cc_start: 0.9247 (m-30) cc_final: 0.8554 (m-30) REVERT: B 126 ARG cc_start: 0.8777 (ttm110) cc_final: 0.8391 (ttm110) REVERT: B 191 LEU cc_start: 0.9770 (mt) cc_final: 0.9510 (mt) REVERT: C 40 GLU cc_start: 0.8782 (tp30) cc_final: 0.8550 (tp30) REVERT: C 105 ASP cc_start: 0.8884 (m-30) cc_final: 0.8460 (m-30) REVERT: C 118 TYR cc_start: 0.9077 (t80) cc_final: 0.8368 (t80) REVERT: C 130 GLU cc_start: 0.8492 (mp0) cc_final: 0.8199 (pm20) REVERT: C 145 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8451 (mm-30) REVERT: C 153 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8807 (ttp80) REVERT: C 191 LEU cc_start: 0.9735 (mt) cc_final: 0.9508 (mt) REVERT: D 62 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: D 96 ARG cc_start: 0.9018 (mtt-85) cc_final: 0.8763 (ptp90) REVERT: D 126 ARG cc_start: 0.8758 (ttm110) cc_final: 0.8475 (ttm110) REVERT: D 142 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8871 (mm-30) REVERT: G 48 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8705 (mmtm) REVERT: G 105 ASP cc_start: 0.9074 (m-30) cc_final: 0.8594 (m-30) REVERT: J 40 GLU cc_start: 0.8930 (tp30) cc_final: 0.8564 (tp30) REVERT: J 48 LYS cc_start: 0.9242 (tppt) cc_final: 0.8820 (tppt) REVERT: J 105 ASP cc_start: 0.8747 (m-30) cc_final: 0.8439 (m-30) REVERT: J 145 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8382 (mm-30) REVERT: H 118 TYR cc_start: 0.9005 (t80) cc_final: 0.8556 (t80) REVERT: H 126 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8497 (ttm110) REVERT: H 145 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8698 (mm-30) REVERT: K 40 GLU cc_start: 0.8773 (tp30) cc_final: 0.8499 (tp30) REVERT: K 48 LYS cc_start: 0.9312 (tppt) cc_final: 0.8949 (tppt) REVERT: K 96 ARG cc_start: 0.9147 (mmt180) cc_final: 0.8712 (mmt90) REVERT: K 105 ASP cc_start: 0.9173 (m-30) cc_final: 0.8515 (m-30) REVERT: K 118 TYR cc_start: 0.8998 (t80) cc_final: 0.8794 (t80) REVERT: K 174 ARG cc_start: 0.9349 (mmm160) cc_final: 0.8740 (mmm160) REVERT: F 40 GLU cc_start: 0.9036 (tp30) cc_final: 0.8668 (tp30) REVERT: F 48 LYS cc_start: 0.9259 (tppt) cc_final: 0.8915 (tppt) REVERT: F 145 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8728 (mm-30) REVERT: I 105 ASP cc_start: 0.9171 (m-30) cc_final: 0.8556 (m-30) REVERT: I 130 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8445 (pt0) REVERT: L 40 GLU cc_start: 0.9003 (tp30) cc_final: 0.8584 (tp30) REVERT: L 153 ARG cc_start: 0.9293 (tmm-80) cc_final: 0.8634 (tmm-80) outliers start: 56 outliers final: 25 residues processed: 285 average time/residue: 0.2452 time to fit residues: 95.3754 Evaluate side-chains 225 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 242 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 253 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.074741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.056462 restraints weight = 90369.313| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 5.54 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 21682 Z= 0.143 Angle : 0.503 7.073 28812 Z= 0.274 Chirality : 0.034 0.206 3324 Planarity : 0.006 0.090 3612 Dihedral : 3.486 13.227 2844 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.75 % Allowed : 1.76 % Favored : 97.48 % Rotamer: Outliers : 2.50 % Allowed : 26.11 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.17), residues: 2664 helix: 2.57 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -2.72 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 126 TYR 0.029 0.002 TYR I 118 PHE 0.015 0.001 PHE D 148 TRP 0.009 0.001 TRP E 151 HIS 0.002 0.001 HIS K 15 Details of bonding type rmsd covalent geometry : bond 0.00347 (21636) covalent geometry : angle 0.50294 (28812) hydrogen bonds : bond 0.03272 ( 1625) hydrogen bonds : angle 3.46231 ( 4875) metal coordination : bond 0.02056 ( 46) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.947 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: A 40 GLU cc_start: 0.8901 (tp30) cc_final: 0.8468 (tp30) REVERT: A 105 ASP cc_start: 0.8850 (m-30) cc_final: 0.8502 (m-30) REVERT: A 145 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8716 (mm-30) REVERT: B 48 LYS cc_start: 0.9218 (tppt) cc_final: 0.8777 (tppt) REVERT: B 96 ARG cc_start: 0.9002 (mtt-85) cc_final: 0.8425 (mtt90) REVERT: B 126 ARG cc_start: 0.8772 (ttm110) cc_final: 0.8470 (ttm110) REVERT: C 40 GLU cc_start: 0.8800 (tp30) cc_final: 0.8559 (tp30) REVERT: C 105 ASP cc_start: 0.8892 (m-30) cc_final: 0.8519 (m-30) REVERT: C 118 TYR cc_start: 0.9092 (t80) cc_final: 0.8689 (t80) REVERT: C 145 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8628 (mm-30) REVERT: C 153 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8835 (ttp80) REVERT: D 62 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: D 96 ARG cc_start: 0.9051 (mtt-85) cc_final: 0.8789 (ptp90) REVERT: D 105 ASP cc_start: 0.8369 (m-30) cc_final: 0.8153 (m-30) REVERT: D 126 ARG cc_start: 0.8742 (ttm110) cc_final: 0.8486 (ttm110) REVERT: D 142 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8868 (mm-30) REVERT: J 48 LYS cc_start: 0.9154 (tppt) cc_final: 0.8716 (tppt) REVERT: J 98 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8850 (tp) REVERT: J 105 ASP cc_start: 0.8774 (m-30) cc_final: 0.8535 (m-30) REVERT: J 145 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8415 (mm-30) REVERT: E 130 GLU cc_start: 0.8542 (mp0) cc_final: 0.8260 (mp0) REVERT: E 145 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: H 105 ASP cc_start: 0.8844 (m-30) cc_final: 0.8641 (m-30) REVERT: H 118 TYR cc_start: 0.9058 (t80) cc_final: 0.8454 (t80) REVERT: H 145 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8431 (mm-30) REVERT: H 153 ARG cc_start: 0.9299 (tmm-80) cc_final: 0.8976 (tmm-80) REVERT: K 40 GLU cc_start: 0.8788 (tp30) cc_final: 0.8508 (tp30) REVERT: K 48 LYS cc_start: 0.9310 (tppt) cc_final: 0.8836 (tppt) REVERT: K 153 ARG cc_start: 0.9372 (tmm-80) cc_final: 0.9006 (tmm-80) REVERT: K 174 ARG cc_start: 0.9330 (mmm160) cc_final: 0.8679 (mmm160) REVERT: F 40 GLU cc_start: 0.9067 (tp30) cc_final: 0.8693 (tp30) REVERT: F 48 LYS cc_start: 0.9297 (tppt) cc_final: 0.8874 (tppt) REVERT: F 96 ARG cc_start: 0.9088 (mtt-85) cc_final: 0.8694 (mtt90) REVERT: F 105 ASP cc_start: 0.8934 (m-30) cc_final: 0.8560 (m-30) REVERT: F 139 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9231 (mtmm) REVERT: F 145 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8751 (mm-30) REVERT: I 105 ASP cc_start: 0.9159 (m-30) cc_final: 0.8571 (m-30) REVERT: I 130 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8522 (pt0) REVERT: L 118 TYR cc_start: 0.9119 (t80) cc_final: 0.8666 (t80) REVERT: L 145 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8626 (mm-30) REVERT: L 153 ARG cc_start: 0.9375 (tmm-80) cc_final: 0.8818 (tmm-80) outliers start: 56 outliers final: 34 residues processed: 269 average time/residue: 0.2202 time to fit residues: 81.2816 Evaluate side-chains 230 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain L residue 22 TYR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 215 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 141 optimal weight: 0.0670 chunk 120 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 155 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 HIS H 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.076095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.057863 restraints weight = 90160.021| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 5.57 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.201 21682 Z= 0.122 Angle : 0.484 10.494 28812 Z= 0.260 Chirality : 0.034 0.284 3324 Planarity : 0.006 0.088 3612 Dihedral : 3.433 11.929 2844 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.18 % Favored : 97.15 % Rotamer: Outliers : 2.54 % Allowed : 27.63 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.16), residues: 2664 helix: 2.77 (0.11), residues: 2232 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 126 TYR 0.025 0.002 TYR K 118 PHE 0.014 0.001 PHE D 148 TRP 0.011 0.001 TRP E 151 HIS 0.001 0.000 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00269 (21636) covalent geometry : angle 0.48391 (28812) hydrogen bonds : bond 0.02935 ( 1625) hydrogen bonds : angle 3.27477 ( 4875) metal coordination : bond 0.04168 ( 46) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.994 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: A 40 GLU cc_start: 0.8856 (tp30) cc_final: 0.8420 (tp30) REVERT: A 105 ASP cc_start: 0.8788 (m-30) cc_final: 0.8425 (m-30) REVERT: A 145 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8777 (mm-30) REVERT: B 48 LYS cc_start: 0.9216 (tppt) cc_final: 0.8853 (tppt) REVERT: B 96 ARG cc_start: 0.9018 (mtt-85) cc_final: 0.8462 (mtt90) REVERT: B 105 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8558 (m-30) REVERT: B 126 ARG cc_start: 0.8715 (ttm110) cc_final: 0.8412 (ttm110) REVERT: B 145 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8543 (mm-30) REVERT: B 191 LEU cc_start: 0.9749 (mt) cc_final: 0.9498 (mt) REVERT: C 6 MET cc_start: 0.8501 (mmm) cc_final: 0.8195 (mmm) REVERT: C 92 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8763 (mtp-110) REVERT: C 105 ASP cc_start: 0.8833 (m-30) cc_final: 0.8401 (m-30) REVERT: C 118 TYR cc_start: 0.9107 (t80) cc_final: 0.8672 (t80) REVERT: C 145 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8609 (mm-30) REVERT: C 150 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8752 (mm-30) REVERT: C 168 PHE cc_start: 0.9525 (m-10) cc_final: 0.9322 (m-80) REVERT: D 62 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: D 96 ARG cc_start: 0.9059 (mtt-85) cc_final: 0.8787 (ptp90) REVERT: D 105 ASP cc_start: 0.8251 (m-30) cc_final: 0.7967 (m-30) REVERT: D 126 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8495 (ttm110) REVERT: D 142 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8851 (mm-30) REVERT: J 48 LYS cc_start: 0.9174 (tppt) cc_final: 0.8699 (tppt) REVERT: J 105 ASP cc_start: 0.8702 (m-30) cc_final: 0.8370 (m-30) REVERT: J 145 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: J 174 ARG cc_start: 0.9466 (mmm-85) cc_final: 0.9214 (mmm160) REVERT: E 130 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: E 145 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8422 (mm-30) REVERT: H 105 ASP cc_start: 0.8812 (m-30) cc_final: 0.8579 (m-30) REVERT: H 118 TYR cc_start: 0.9054 (t80) cc_final: 0.8633 (t80) REVERT: H 145 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8511 (mm-30) REVERT: H 153 ARG cc_start: 0.9297 (tmm-80) cc_final: 0.8944 (tmm-80) REVERT: K 40 GLU cc_start: 0.8833 (tp30) cc_final: 0.8615 (tp30) REVERT: K 48 LYS cc_start: 0.9336 (tppt) cc_final: 0.8822 (tppt) REVERT: K 105 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: K 118 TYR cc_start: 0.8895 (t80) cc_final: 0.8655 (t80) REVERT: K 174 ARG cc_start: 0.9323 (mmm160) cc_final: 0.8577 (mmm160) REVERT: F 6 MET cc_start: 0.8725 (mmm) cc_final: 0.8485 (mmm) REVERT: F 40 GLU cc_start: 0.9045 (tp30) cc_final: 0.8683 (tp30) REVERT: F 48 LYS cc_start: 0.9291 (tppt) cc_final: 0.8880 (tppt) REVERT: F 105 ASP cc_start: 0.8863 (m-30) cc_final: 0.8469 (m-30) REVERT: F 145 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8734 (mm-30) REVERT: F 168 PHE cc_start: 0.9173 (m-10) cc_final: 0.8942 (m-80) REVERT: F 174 ARG cc_start: 0.9427 (mmm160) cc_final: 0.9150 (mmm160) REVERT: F 176 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9147 (mt) REVERT: F 177 GLU cc_start: 0.9261 (tt0) cc_final: 0.8755 (tt0) REVERT: I 48 LYS cc_start: 0.9128 (tppt) cc_final: 0.8876 (tppt) REVERT: I 105 ASP cc_start: 0.9123 (m-30) cc_final: 0.8594 (m-30) REVERT: I 130 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8404 (pt0) REVERT: I 174 ARG cc_start: 0.9396 (mmm160) cc_final: 0.9153 (mmm160) REVERT: L 145 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: L 153 ARG cc_start: 0.9398 (tmm-80) cc_final: 0.8884 (tmm-80) outliers start: 57 outliers final: 30 residues processed: 277 average time/residue: 0.2244 time to fit residues: 86.5719 Evaluate side-chains 244 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 108 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.072621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.053988 restraints weight = 90977.134| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 5.47 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21682 Z= 0.223 Angle : 0.599 16.265 28812 Z= 0.320 Chirality : 0.037 0.354 3324 Planarity : 0.006 0.086 3612 Dihedral : 3.517 14.599 2844 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.56 % Allowed : 1.73 % Favored : 97.71 % Rotamer: Outliers : 2.90 % Allowed : 28.16 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.16), residues: 2664 helix: 2.45 (0.11), residues: 2256 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 126 TYR 0.032 0.003 TYR A 118 PHE 0.022 0.002 PHE F 148 TRP 0.004 0.001 TRP E 151 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00509 (21636) covalent geometry : angle 0.59934 (28812) hydrogen bonds : bond 0.03784 ( 1625) hydrogen bonds : angle 3.73994 ( 4875) metal coordination : bond 0.00304 ( 46) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 0.966 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: A 40 GLU cc_start: 0.8907 (tp30) cc_final: 0.8470 (tp30) REVERT: A 48 LYS cc_start: 0.9110 (tppt) cc_final: 0.8852 (tppt) REVERT: A 105 ASP cc_start: 0.8992 (m-30) cc_final: 0.8646 (m-30) REVERT: A 126 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8333 (ttm110) REVERT: A 130 GLU cc_start: 0.8428 (mp0) cc_final: 0.8190 (mp0) REVERT: A 145 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8758 (mm-30) REVERT: B 48 LYS cc_start: 0.9258 (tppt) cc_final: 0.8928 (tppt) REVERT: B 96 ARG cc_start: 0.9007 (mtt-85) cc_final: 0.8437 (mtt90) REVERT: B 126 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8477 (ttm110) REVERT: B 145 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8586 (mm-30) REVERT: C 40 GLU cc_start: 0.8848 (tp30) cc_final: 0.8630 (tp30) REVERT: C 92 ARG cc_start: 0.9103 (ttm110) cc_final: 0.8723 (mtp-110) REVERT: C 105 ASP cc_start: 0.8938 (m-30) cc_final: 0.8548 (m-30) REVERT: C 118 TYR cc_start: 0.9174 (t80) cc_final: 0.8685 (t80) REVERT: C 130 GLU cc_start: 0.8569 (mp0) cc_final: 0.8330 (mp0) REVERT: C 145 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8659 (mm-30) REVERT: C 153 ARG cc_start: 0.9229 (ttp80) cc_final: 0.8891 (ttp80) REVERT: C 168 PHE cc_start: 0.9575 (m-10) cc_final: 0.9340 (m-80) REVERT: C 186 MET cc_start: 0.9107 (ppp) cc_final: 0.8655 (ppp) REVERT: D 62 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: D 96 ARG cc_start: 0.9097 (mtt-85) cc_final: 0.8544 (mtt90) REVERT: D 105 ASP cc_start: 0.8443 (m-30) cc_final: 0.8135 (m-30) REVERT: D 126 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8449 (ttm110) REVERT: D 142 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8817 (mm-30) REVERT: J 48 LYS cc_start: 0.9187 (tppt) cc_final: 0.8722 (tppt) REVERT: J 105 ASP cc_start: 0.8916 (m-30) cc_final: 0.8500 (m-30) REVERT: J 145 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8427 (mm-30) REVERT: J 174 ARG cc_start: 0.9482 (mmm-85) cc_final: 0.9205 (mmm160) REVERT: E 145 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8395 (mm-30) REVERT: H 105 ASP cc_start: 0.8906 (m-30) cc_final: 0.8654 (m-30) REVERT: H 118 TYR cc_start: 0.9155 (t80) cc_final: 0.8598 (t80) REVERT: H 145 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8469 (mm-30) REVERT: H 153 ARG cc_start: 0.9344 (tmm-80) cc_final: 0.9006 (tmm-80) REVERT: K 40 GLU cc_start: 0.8802 (tp30) cc_final: 0.8518 (tp30) REVERT: K 48 LYS cc_start: 0.9307 (tppt) cc_final: 0.8865 (tppt) REVERT: F 40 GLU cc_start: 0.9061 (tp30) cc_final: 0.8675 (tp30) REVERT: F 48 LYS cc_start: 0.9296 (tppt) cc_final: 0.8871 (tppt) REVERT: F 105 ASP cc_start: 0.9053 (m-30) cc_final: 0.8635 (m-30) REVERT: F 130 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: F 145 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8839 (mm-30) REVERT: F 168 PHE cc_start: 0.9401 (m-10) cc_final: 0.9176 (m-80) REVERT: F 174 ARG cc_start: 0.9446 (mmm160) cc_final: 0.9227 (mmm160) REVERT: F 176 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9197 (mt) REVERT: F 177 GLU cc_start: 0.9316 (tt0) cc_final: 0.8964 (tt0) REVERT: I 48 LYS cc_start: 0.9239 (tppt) cc_final: 0.8951 (tppt) REVERT: I 105 ASP cc_start: 0.9192 (m-30) cc_final: 0.8678 (m-30) REVERT: I 130 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8654 (pt0) REVERT: I 145 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8758 (mm-30) REVERT: L 145 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8464 (mm-30) outliers start: 65 outliers final: 36 residues processed: 260 average time/residue: 0.2416 time to fit residues: 86.4027 Evaluate side-chains 226 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain L residue 22 TYR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 213 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 31 optimal weight: 0.0470 chunk 186 optimal weight: 6.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.074307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.055986 restraints weight = 90292.413| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 5.48 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21682 Z= 0.119 Angle : 0.516 13.242 28812 Z= 0.276 Chirality : 0.035 0.315 3324 Planarity : 0.005 0.083 3612 Dihedral : 3.479 15.679 2844 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.25 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 29.10 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.16), residues: 2664 helix: 2.74 (0.11), residues: 2232 sheet: None (None), residues: 0 loop : -2.51 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 126 TYR 0.029 0.002 TYR A 118 PHE 0.020 0.002 PHE K 148 TRP 0.010 0.001 TRP E 151 HIS 0.002 0.000 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00299 (21636) covalent geometry : angle 0.51595 (28812) hydrogen bonds : bond 0.03177 ( 1625) hydrogen bonds : angle 3.42899 ( 4875) metal coordination : bond 0.00134 ( 46) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 0.944 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: A 40 GLU cc_start: 0.8847 (tp30) cc_final: 0.8416 (tp30) REVERT: A 48 LYS cc_start: 0.9146 (tppt) cc_final: 0.8884 (tppt) REVERT: A 105 ASP cc_start: 0.8836 (m-30) cc_final: 0.8471 (m-30) REVERT: A 126 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8557 (ttm110) REVERT: A 130 GLU cc_start: 0.8416 (mp0) cc_final: 0.8211 (mp0) REVERT: B 6 MET cc_start: 0.8358 (mmm) cc_final: 0.8021 (mmm) REVERT: B 48 LYS cc_start: 0.9249 (tppt) cc_final: 0.8886 (tppt) REVERT: B 96 ARG cc_start: 0.9048 (mtt-85) cc_final: 0.8451 (mtt90) REVERT: B 126 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8407 (ttm110) REVERT: B 145 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8596 (mm-30) REVERT: C 6 MET cc_start: 0.8578 (mmm) cc_final: 0.8299 (mmm) REVERT: C 40 GLU cc_start: 0.8873 (tp30) cc_final: 0.8637 (tp30) REVERT: C 105 ASP cc_start: 0.8855 (m-30) cc_final: 0.8473 (m-30) REVERT: C 118 TYR cc_start: 0.9149 (t80) cc_final: 0.8652 (t80) REVERT: C 130 GLU cc_start: 0.8593 (mp0) cc_final: 0.8360 (mp0) REVERT: C 145 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8651 (mm-30) REVERT: C 153 ARG cc_start: 0.9234 (ttp80) cc_final: 0.8869 (ttp80) REVERT: C 168 PHE cc_start: 0.9572 (m-10) cc_final: 0.9347 (m-80) REVERT: C 186 MET cc_start: 0.9120 (ppp) cc_final: 0.8634 (ppp) REVERT: D 62 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: D 105 ASP cc_start: 0.8422 (m-30) cc_final: 0.8097 (m-30) REVERT: D 126 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8409 (ttm110) REVERT: D 142 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8819 (mm-30) REVERT: G 130 GLU cc_start: 0.8341 (mp0) cc_final: 0.8098 (mp0) REVERT: J 48 LYS cc_start: 0.9150 (tppt) cc_final: 0.8636 (tppt) REVERT: J 105 ASP cc_start: 0.8800 (m-30) cc_final: 0.8370 (m-30) REVERT: J 145 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: J 153 ARG cc_start: 0.9422 (tmm-80) cc_final: 0.9120 (tmm-80) REVERT: J 174 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.9195 (mmm160) REVERT: E 130 GLU cc_start: 0.8395 (mp0) cc_final: 0.8106 (mp0) REVERT: E 145 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: H 105 ASP cc_start: 0.8876 (m-30) cc_final: 0.8607 (m-30) REVERT: H 118 TYR cc_start: 0.9137 (t80) cc_final: 0.8619 (t80) REVERT: H 145 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8428 (mm-30) REVERT: K 40 GLU cc_start: 0.8830 (tp30) cc_final: 0.8597 (tp30) REVERT: K 48 LYS cc_start: 0.9298 (tppt) cc_final: 0.8838 (tppt) REVERT: K 105 ASP cc_start: 0.9163 (m-30) cc_final: 0.8545 (m-30) REVERT: K 130 GLU cc_start: 0.8619 (mp0) cc_final: 0.8367 (mp0) REVERT: F 40 GLU cc_start: 0.9044 (tp30) cc_final: 0.8674 (tp30) REVERT: F 48 LYS cc_start: 0.9303 (tppt) cc_final: 0.8864 (tppt) REVERT: F 105 ASP cc_start: 0.8927 (m-30) cc_final: 0.8558 (m-30) REVERT: F 130 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: F 145 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8716 (mm-30) REVERT: F 168 PHE cc_start: 0.9371 (m-10) cc_final: 0.9104 (m-80) REVERT: F 176 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9137 (mt) REVERT: F 177 GLU cc_start: 0.9302 (tt0) cc_final: 0.8939 (tt0) REVERT: I 48 LYS cc_start: 0.9218 (tppt) cc_final: 0.8844 (tppt) REVERT: I 105 ASP cc_start: 0.9132 (m-30) cc_final: 0.8622 (m-30) REVERT: I 126 ARG cc_start: 0.8952 (ttm110) cc_final: 0.8566 (ttm110) REVERT: I 130 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8568 (pt0) REVERT: I 174 ARG cc_start: 0.9411 (mmm160) cc_final: 0.9170 (mmm160) REVERT: L 145 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8448 (mm-30) REVERT: L 153 ARG cc_start: 0.9347 (tmm-80) cc_final: 0.9111 (tmm-80) outliers start: 51 outliers final: 32 residues processed: 240 average time/residue: 0.2335 time to fit residues: 77.8527 Evaluate side-chains 213 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 22 TYR Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain L residue 22 TYR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 176 optimal weight: 0.0170 chunk 207 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 237 optimal weight: 0.3980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.075667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.057060 restraints weight = 90637.467| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 5.48 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.294 21682 Z= 0.124 Angle : 0.508 11.045 28812 Z= 0.272 Chirality : 0.036 0.355 3324 Planarity : 0.005 0.081 3612 Dihedral : 3.417 22.554 2844 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.18 % Favored : 97.37 % Rotamer: Outliers : 2.27 % Allowed : 29.01 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.16), residues: 2664 helix: 2.86 (0.11), residues: 2232 sheet: None (None), residues: 0 loop : -2.51 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 126 TYR 0.024 0.002 TYR A 118 PHE 0.018 0.001 PHE K 168 TRP 0.011 0.001 TRP E 151 HIS 0.001 0.000 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00267 (21636) covalent geometry : angle 0.50842 (28812) hydrogen bonds : bond 0.02951 ( 1625) hydrogen bonds : angle 3.29421 ( 4875) metal coordination : bond 0.04331 ( 46) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.987 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: A 40 GLU cc_start: 0.8808 (tp30) cc_final: 0.8400 (tp30) REVERT: A 48 LYS cc_start: 0.9166 (tppt) cc_final: 0.8869 (tppt) REVERT: A 105 ASP cc_start: 0.8812 (m-30) cc_final: 0.8471 (m-30) REVERT: A 145 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8723 (mm-30) REVERT: B 6 MET cc_start: 0.8392 (mmm) cc_final: 0.8074 (mmm) REVERT: B 48 LYS cc_start: 0.9277 (tppt) cc_final: 0.8924 (tppt) REVERT: B 126 ARG cc_start: 0.8678 (ttm110) cc_final: 0.8269 (ttm110) REVERT: B 145 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: C 6 MET cc_start: 0.8668 (mmm) cc_final: 0.8392 (mmm) REVERT: C 40 GLU cc_start: 0.8862 (tp30) cc_final: 0.8655 (tp30) REVERT: C 105 ASP cc_start: 0.8868 (m-30) cc_final: 0.8464 (m-30) REVERT: C 118 TYR cc_start: 0.9149 (t80) cc_final: 0.8706 (t80) REVERT: C 145 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8596 (mm-30) REVERT: C 153 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8860 (ttp80) REVERT: C 168 PHE cc_start: 0.9561 (m-10) cc_final: 0.9313 (m-80) REVERT: D 96 ARG cc_start: 0.9109 (mtt-85) cc_final: 0.8421 (mtt90) REVERT: D 105 ASP cc_start: 0.8358 (m-30) cc_final: 0.8031 (m-30) REVERT: D 126 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8442 (ttm110) REVERT: D 142 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8804 (mm-30) REVERT: G 105 ASP cc_start: 0.9016 (m-30) cc_final: 0.8514 (m-30) REVERT: J 48 LYS cc_start: 0.9187 (tppt) cc_final: 0.8701 (tppt) REVERT: J 105 ASP cc_start: 0.8763 (m-30) cc_final: 0.8360 (m-30) REVERT: J 118 TYR cc_start: 0.8881 (t80) cc_final: 0.8201 (t80) REVERT: J 145 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8489 (mm-30) REVERT: J 153 ARG cc_start: 0.9446 (tmm-80) cc_final: 0.9124 (tmm-80) REVERT: J 174 ARG cc_start: 0.9488 (mmm-85) cc_final: 0.9195 (mmm160) REVERT: E 6 MET cc_start: 0.8666 (mmt) cc_final: 0.8212 (mmm) REVERT: E 145 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8352 (mm-30) REVERT: H 105 ASP cc_start: 0.8837 (m-30) cc_final: 0.8560 (m-30) REVERT: H 118 TYR cc_start: 0.9123 (t80) cc_final: 0.8877 (t80) REVERT: H 145 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8688 (mm-30) REVERT: K 22 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.7030 (m-10) REVERT: K 40 GLU cc_start: 0.8825 (tp30) cc_final: 0.8596 (tp30) REVERT: K 48 LYS cc_start: 0.9287 (tppt) cc_final: 0.8825 (tppt) REVERT: K 105 ASP cc_start: 0.9067 (m-30) cc_final: 0.8451 (m-30) REVERT: F 6 MET cc_start: 0.8712 (mmm) cc_final: 0.8474 (mmm) REVERT: F 40 GLU cc_start: 0.9021 (tp30) cc_final: 0.8602 (tp30) REVERT: F 48 LYS cc_start: 0.9342 (tppt) cc_final: 0.8926 (tppt) REVERT: F 105 ASP cc_start: 0.8808 (m-30) cc_final: 0.8416 (m-30) REVERT: F 130 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: F 168 PHE cc_start: 0.9050 (m-10) cc_final: 0.8781 (m-80) REVERT: F 176 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9137 (mt) REVERT: I 48 LYS cc_start: 0.9293 (tppt) cc_final: 0.8932 (tppt) REVERT: I 96 ARG cc_start: 0.8748 (mtt90) cc_final: 0.8230 (mpt-90) REVERT: I 105 ASP cc_start: 0.9040 (m-30) cc_final: 0.8499 (m-30) REVERT: I 126 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8553 (ttm110) REVERT: I 130 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8494 (pt0) REVERT: I 174 ARG cc_start: 0.9413 (mmm160) cc_final: 0.9175 (mmm160) REVERT: L 6 MET cc_start: 0.8498 (mmm) cc_final: 0.8201 (mmm) REVERT: L 145 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: L 153 ARG cc_start: 0.9387 (tmm-80) cc_final: 0.8861 (tmm-80) outliers start: 51 outliers final: 27 residues processed: 233 average time/residue: 0.2260 time to fit residues: 73.7141 Evaluate side-chains 212 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 244 optimal weight: 0.1980 chunk 174 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.075043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.056480 restraints weight = 90590.819| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 5.46 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.244 21682 Z= 0.129 Angle : 0.532 14.684 28812 Z= 0.285 Chirality : 0.035 0.357 3324 Planarity : 0.005 0.078 3612 Dihedral : 3.397 27.133 2844 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.10 % Favored : 97.45 % Rotamer: Outliers : 2.09 % Allowed : 29.46 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.16), residues: 2664 helix: 2.84 (0.11), residues: 2232 sheet: None (None), residues: 0 loop : -2.46 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 126 TYR 0.022 0.002 TYR A 118 PHE 0.017 0.001 PHE K 148 TRP 0.008 0.001 TRP E 151 HIS 0.003 0.000 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00295 (21636) covalent geometry : angle 0.53174 (28812) hydrogen bonds : bond 0.03052 ( 1625) hydrogen bonds : angle 3.36484 ( 4875) metal coordination : bond 0.03605 ( 46) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.796 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: A 40 GLU cc_start: 0.8848 (tp30) cc_final: 0.8417 (tp30) REVERT: A 48 LYS cc_start: 0.9179 (tppt) cc_final: 0.8882 (tppt) REVERT: A 105 ASP cc_start: 0.8851 (m-30) cc_final: 0.8505 (m-30) REVERT: A 145 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8798 (mm-30) REVERT: B 6 MET cc_start: 0.8391 (mmm) cc_final: 0.8070 (mmm) REVERT: B 48 LYS cc_start: 0.9278 (tppt) cc_final: 0.8876 (tppt) REVERT: B 126 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8240 (ttm110) REVERT: B 145 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: C 6 MET cc_start: 0.8664 (mmm) cc_final: 0.8421 (mmm) REVERT: C 40 GLU cc_start: 0.8844 (tp30) cc_final: 0.8594 (tp30) REVERT: C 105 ASP cc_start: 0.8870 (m-30) cc_final: 0.8471 (m-30) REVERT: C 118 TYR cc_start: 0.9151 (t80) cc_final: 0.8715 (t80) REVERT: C 145 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: C 168 PHE cc_start: 0.9557 (m-10) cc_final: 0.9300 (m-80) REVERT: D 96 ARG cc_start: 0.9104 (mtt-85) cc_final: 0.8412 (mtt90) REVERT: D 105 ASP cc_start: 0.8402 (m-30) cc_final: 0.8070 (m-30) REVERT: G 62 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: G 105 ASP cc_start: 0.9009 (m-30) cc_final: 0.8545 (m-30) REVERT: G 186 MET cc_start: 0.9231 (ppp) cc_final: 0.8902 (ppp) REVERT: J 48 LYS cc_start: 0.9193 (tppt) cc_final: 0.8715 (tppt) REVERT: J 96 ARG cc_start: 0.9109 (mmt90) cc_final: 0.8887 (mmt90) REVERT: J 105 ASP cc_start: 0.8840 (m-30) cc_final: 0.8446 (m-30) REVERT: J 118 TYR cc_start: 0.8868 (t80) cc_final: 0.8105 (t80) REVERT: J 126 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8354 (ttm110) REVERT: J 145 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8450 (mm-30) REVERT: J 174 ARG cc_start: 0.9482 (mmm-85) cc_final: 0.9187 (mmm160) REVERT: E 6 MET cc_start: 0.8693 (mmt) cc_final: 0.8237 (mmm) REVERT: E 130 GLU cc_start: 0.8351 (mp0) cc_final: 0.8120 (mp0) REVERT: E 145 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: H 105 ASP cc_start: 0.8858 (m-30) cc_final: 0.8580 (m-30) REVERT: H 118 TYR cc_start: 0.9131 (t80) cc_final: 0.8905 (t80) REVERT: H 145 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8663 (mm-30) REVERT: K 22 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.7210 (m-10) REVERT: K 40 GLU cc_start: 0.8813 (tp30) cc_final: 0.8589 (tp30) REVERT: K 48 LYS cc_start: 0.9276 (tppt) cc_final: 0.8798 (tppt) REVERT: K 105 ASP cc_start: 0.9023 (m-30) cc_final: 0.8413 (m-30) REVERT: F 6 MET cc_start: 0.8699 (mmm) cc_final: 0.8471 (mmm) REVERT: F 40 GLU cc_start: 0.9027 (tp30) cc_final: 0.8608 (tp30) REVERT: F 48 LYS cc_start: 0.9350 (tppt) cc_final: 0.8927 (tppt) REVERT: F 105 ASP cc_start: 0.8839 (m-30) cc_final: 0.8409 (m-30) REVERT: F 130 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: F 168 PHE cc_start: 0.9150 (m-10) cc_final: 0.8879 (m-80) REVERT: F 176 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9143 (mt) REVERT: I 48 LYS cc_start: 0.9288 (tppt) cc_final: 0.8909 (tppt) REVERT: I 96 ARG cc_start: 0.8713 (mtt90) cc_final: 0.8173 (mpt-90) REVERT: I 105 ASP cc_start: 0.9026 (m-30) cc_final: 0.8497 (m-30) REVERT: I 130 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8513 (pt0) REVERT: I 174 ARG cc_start: 0.9408 (mmm160) cc_final: 0.9184 (mmm160) REVERT: L 6 MET cc_start: 0.8533 (mmm) cc_final: 0.8207 (mmm) REVERT: L 145 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8510 (mm-30) REVERT: L 153 ARG cc_start: 0.9403 (tmm-80) cc_final: 0.8893 (tmm-80) outliers start: 47 outliers final: 27 residues processed: 224 average time/residue: 0.2127 time to fit residues: 66.6926 Evaluate side-chains 205 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 36 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 18 optimal weight: 0.0040 chunk 200 optimal weight: 0.3980 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.075426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.056710 restraints weight = 90756.370| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 5.49 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.243 21682 Z= 0.127 Angle : 0.554 17.615 28812 Z= 0.293 Chirality : 0.036 0.394 3324 Planarity : 0.006 0.075 3612 Dihedral : 3.415 32.319 2844 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.06 % Favored : 97.48 % Rotamer: Outliers : 1.83 % Allowed : 30.04 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.16), residues: 2664 helix: 2.78 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 126 TYR 0.019 0.001 TYR I 118 PHE 0.015 0.001 PHE K 148 TRP 0.009 0.001 TRP E 151 HIS 0.002 0.000 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00289 (21636) covalent geometry : angle 0.55429 (28812) hydrogen bonds : bond 0.02994 ( 1625) hydrogen bonds : angle 3.38284 ( 4875) metal coordination : bond 0.03583 ( 46) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 1.054 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: A 40 GLU cc_start: 0.8824 (tp30) cc_final: 0.8411 (tp30) REVERT: A 48 LYS cc_start: 0.9192 (tppt) cc_final: 0.8891 (tppt) REVERT: A 105 ASP cc_start: 0.8902 (m-30) cc_final: 0.8540 (m-30) REVERT: B 6 MET cc_start: 0.8355 (mmm) cc_final: 0.8045 (mmm) REVERT: B 48 LYS cc_start: 0.9278 (tppt) cc_final: 0.8821 (tppt) REVERT: B 126 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8223 (ttm110) REVERT: B 145 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8613 (mm-30) REVERT: C 6 MET cc_start: 0.8720 (mmm) cc_final: 0.8448 (mmm) REVERT: C 40 GLU cc_start: 0.8860 (tp30) cc_final: 0.8618 (tp30) REVERT: C 105 ASP cc_start: 0.8882 (m-30) cc_final: 0.8488 (m-30) REVERT: C 118 TYR cc_start: 0.9143 (t80) cc_final: 0.8720 (t80) REVERT: C 145 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8575 (mm-30) REVERT: C 150 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8840 (mm-30) REVERT: C 168 PHE cc_start: 0.9536 (m-10) cc_final: 0.9283 (m-80) REVERT: C 186 MET cc_start: 0.9107 (ppp) cc_final: 0.8732 (ppp) REVERT: D 96 ARG cc_start: 0.9094 (mtt-85) cc_final: 0.8619 (mpt-90) REVERT: D 105 ASP cc_start: 0.8365 (m-30) cc_final: 0.8044 (m-30) REVERT: D 126 ARG cc_start: 0.8693 (ttm110) cc_final: 0.8427 (ttm110) REVERT: G 105 ASP cc_start: 0.9035 (m-30) cc_final: 0.8553 (m-30) REVERT: G 186 MET cc_start: 0.9257 (ppp) cc_final: 0.8935 (ppp) REVERT: J 48 LYS cc_start: 0.9202 (tppt) cc_final: 0.8721 (tppt) REVERT: J 105 ASP cc_start: 0.8862 (m-30) cc_final: 0.8452 (m-30) REVERT: J 118 TYR cc_start: 0.8871 (t80) cc_final: 0.8130 (t80) REVERT: J 145 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8453 (mm-30) REVERT: J 174 ARG cc_start: 0.9486 (mmm-85) cc_final: 0.9189 (mmm160) REVERT: E 6 MET cc_start: 0.8685 (mmt) cc_final: 0.8226 (mmm) REVERT: E 130 GLU cc_start: 0.8278 (mp0) cc_final: 0.8053 (mp0) REVERT: E 145 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8360 (mm-30) REVERT: H 105 ASP cc_start: 0.8866 (m-30) cc_final: 0.8585 (m-30) REVERT: H 118 TYR cc_start: 0.9133 (t80) cc_final: 0.8919 (t80) REVERT: H 145 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8630 (mm-30) REVERT: K 48 LYS cc_start: 0.9288 (tppt) cc_final: 0.8887 (tppt) REVERT: K 105 ASP cc_start: 0.9000 (m-30) cc_final: 0.8402 (m-30) REVERT: K 174 ARG cc_start: 0.9355 (mmm160) cc_final: 0.9076 (mmm160) REVERT: F 6 MET cc_start: 0.8701 (mmm) cc_final: 0.8483 (mmm) REVERT: F 40 GLU cc_start: 0.9029 (tp30) cc_final: 0.8608 (tp30) REVERT: F 48 LYS cc_start: 0.9352 (tppt) cc_final: 0.8933 (tppt) REVERT: F 105 ASP cc_start: 0.8855 (m-30) cc_final: 0.8494 (m-30) REVERT: F 130 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8592 (mp0) REVERT: F 168 PHE cc_start: 0.9164 (m-10) cc_final: 0.8897 (m-80) REVERT: F 176 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9142 (mt) REVERT: I 6 MET cc_start: 0.8428 (mmt) cc_final: 0.8169 (mmm) REVERT: I 48 LYS cc_start: 0.9313 (tppt) cc_final: 0.8959 (tppt) REVERT: I 96 ARG cc_start: 0.8722 (mtt90) cc_final: 0.8167 (mpt-90) REVERT: I 105 ASP cc_start: 0.9006 (m-30) cc_final: 0.8479 (m-30) REVERT: I 126 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8566 (ttm110) REVERT: I 130 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8521 (pt0) REVERT: I 174 ARG cc_start: 0.9404 (mmm160) cc_final: 0.9186 (mmm160) REVERT: L 6 MET cc_start: 0.8598 (mmm) cc_final: 0.8290 (mmm) REVERT: L 105 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: L 145 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8522 (mm-30) REVERT: L 153 ARG cc_start: 0.9401 (tmm-80) cc_final: 0.8895 (tmm-80) outliers start: 41 outliers final: 27 residues processed: 214 average time/residue: 0.2291 time to fit residues: 68.7626 Evaluate side-chains 206 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 89 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.075523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.057161 restraints weight = 91301.642| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 5.47 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.323 21682 Z= 0.134 Angle : 0.552 16.936 28812 Z= 0.293 Chirality : 0.036 0.368 3324 Planarity : 0.005 0.072 3612 Dihedral : 3.401 39.390 2844 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.14 % Favored : 97.41 % Rotamer: Outliers : 1.74 % Allowed : 30.17 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.16), residues: 2664 helix: 2.91 (0.11), residues: 2220 sheet: None (None), residues: 0 loop : -2.32 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 126 TYR 0.016 0.001 TYR D 118 PHE 0.017 0.001 PHE E 168 TRP 0.010 0.001 TRP E 151 HIS 0.001 0.000 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00282 (21636) covalent geometry : angle 0.55200 (28812) hydrogen bonds : bond 0.02936 ( 1625) hydrogen bonds : angle 3.33712 ( 4875) metal coordination : bond 0.04767 ( 46) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.62 seconds wall clock time: 79 minutes 9.01 seconds (4749.01 seconds total)