Starting phenix.real_space_refine on Wed Mar 4 17:51:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xtg_33448/03_2026/7xtg_33448_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xtg_33448/03_2026/7xtg_33448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xtg_33448/03_2026/7xtg_33448_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xtg_33448/03_2026/7xtg_33448_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xtg_33448/03_2026/7xtg_33448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xtg_33448/03_2026/7xtg_33448.map" } resolution = 2.2 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= 0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10110 2.51 5 N 2544 2.21 5 O 2697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15435 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 307 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "C" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 307 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "D" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1784 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 239} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2322 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "G" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 307 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "H" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1784 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 239} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2322 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "Y" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1784 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 239} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2322 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.61, per 1000 atoms: 0.23 Number of scatterers: 15435 At special positions: 0 Unit cell: (129.868, 127.338, 101.196, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2697 8.00 N 2544 7.00 C 10110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 15 " distance=2.04 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS C 15 " distance=2.04 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 15 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 532.7 milliseconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 3 sheets defined 75.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.822A pdb=" N MET A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 21 through 27 removed outlier: 3.774A pdb=" N ASP B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.628A pdb=" N LEU B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.742A pdb=" N VAL B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 40 removed outlier: 3.846A pdb=" N MET C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.550A pdb=" N ILE D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 44 removed outlier: 3.856A pdb=" N THR D 37 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 60 removed outlier: 3.747A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.660A pdb=" N SER D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.845A pdb=" N ILE D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 134 removed outlier: 3.561A pdb=" N ILE D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 129 " --> pdb=" O HIS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 164 removed outlier: 3.737A pdb=" N ILE D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 165 through 175 removed outlier: 3.692A pdb=" N GLU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 removed outlier: 3.580A pdb=" N LEU D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.856A pdb=" N GLY D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 225 through 249 removed outlier: 3.582A pdb=" N GLN D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 32 through 40 Processing helix chain 'E' and resid 40 through 48 removed outlier: 4.311A pdb=" N LYS E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 72 through 88 Processing helix chain 'E' and resid 95 through 117 removed outlier: 3.588A pdb=" N LYS E 101 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY E 106 " --> pdb=" O VAL E 102 " (cutoff:3.500A) Proline residue: E 107 - end of helix Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 119 through 134 removed outlier: 3.610A pdb=" N LEU E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 166 removed outlier: 3.798A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 201 removed outlier: 4.000A pdb=" N LYS E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 253 through 261 removed outlier: 3.934A pdb=" N LEU E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 279 Processing helix chain 'E' and resid 282 through 300 removed outlier: 3.653A pdb=" N GLY E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 19 removed outlier: 3.507A pdb=" N ASN F 9 " --> pdb=" O TYR F 5 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 10 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 27 removed outlier: 3.677A pdb=" N ILE F 25 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 21 through 27' Processing helix chain 'F' and resid 27 through 42 removed outlier: 3.627A pdb=" N LEU F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'F' and resid 70 through 76 removed outlier: 3.766A pdb=" N VAL F 74 " --> pdb=" O PRO F 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 41 Processing helix chain 'H' and resid 4 through 25 removed outlier: 3.569A pdb=" N ILE H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 24 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 44 removed outlier: 3.681A pdb=" N THR H 37 " --> pdb=" O VAL H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 60 removed outlier: 3.832A pdb=" N CYS H 49 " --> pdb=" O ASN H 45 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET H 58 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.529A pdb=" N ALA H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 134 removed outlier: 3.581A pdb=" N ILE H 101 " --> pdb=" O SER H 97 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL H 103 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Proline residue: H 104 - end of helix removed outlier: 4.250A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 129 " --> pdb=" O HIS H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 164 removed outlier: 3.829A pdb=" N TRP H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET H 149 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Proline residue: H 157 - end of helix Processing helix chain 'H' and resid 165 through 175 removed outlier: 3.579A pdb=" N VAL H 169 " --> pdb=" O GLY H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 189 removed outlier: 3.740A pdb=" N LEU H 184 " --> pdb=" O LEU H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 204 removed outlier: 3.805A pdb=" N GLY H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 225 through 249 Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 40 through 48 removed outlier: 3.660A pdb=" N LYS I 46 " --> pdb=" O PRO I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 62 Processing helix chain 'I' and resid 72 through 88 Processing helix chain 'I' and resid 95 through 117 removed outlier: 3.754A pdb=" N LYS I 101 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY I 106 " --> pdb=" O VAL I 102 " (cutoff:3.500A) Proline residue: I 107 - end of helix Proline residue: I 114 - end of helix Processing helix chain 'I' and resid 119 through 134 removed outlier: 3.549A pdb=" N LEU I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER I 134 " --> pdb=" O SER I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 166 removed outlier: 3.860A pdb=" N ILE I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA I 153 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN I 159 " --> pdb=" O THR I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 173 removed outlier: 4.374A pdb=" N THR I 170 " --> pdb=" O SER I 167 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU I 171 " --> pdb=" O LYS I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 201 removed outlier: 4.128A pdb=" N LEU I 178 " --> pdb=" O SER I 174 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 182 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL I 201 " --> pdb=" O VAL I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 241 removed outlier: 3.541A pdb=" N SER I 234 " --> pdb=" O LYS I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 261 removed outlier: 3.556A pdb=" N LEU I 260 " --> pdb=" O ASN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 279 removed outlier: 3.508A pdb=" N LEU I 269 " --> pdb=" O ALA I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 300 Processing helix chain 'J' and resid 4 through 19 Processing helix chain 'J' and resid 21 through 27 removed outlier: 3.508A pdb=" N LYS J 26 " --> pdb=" O PRO J 22 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 43 Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'J' and resid 70 through 76 removed outlier: 3.768A pdb=" N VAL J 74 " --> pdb=" O PRO J 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 25 removed outlier: 4.185A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 Processing helix chain 'Y' and resid 45 through 60 removed outlier: 3.911A pdb=" N CYS Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 88 Processing helix chain 'Y' and resid 94 through 134 removed outlier: 4.100A pdb=" N VAL Y 103 " --> pdb=" O ILE Y 99 " (cutoff:3.500A) Proline residue: Y 104 - end of helix removed outlier: 4.225A pdb=" N THR Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY Y 122 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE Y 123 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 164 removed outlier: 3.791A pdb=" N ILE Y 139 " --> pdb=" O ASN Y 135 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) Proline residue: Y 157 - end of helix Processing helix chain 'Y' and resid 165 through 175 Processing helix chain 'Y' and resid 177 through 189 removed outlier: 3.589A pdb=" N THR Y 181 " --> pdb=" O PRO Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 204 removed outlier: 3.951A pdb=" N GLY Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 219 Processing helix chain 'Y' and resid 225 through 249 Processing helix chain 'Z' and resid 8 through 19 Processing helix chain 'Z' and resid 20 through 22 No H-bonds generated for 'chain 'Z' and resid 20 through 22' Processing helix chain 'Z' and resid 32 through 40 Processing helix chain 'Z' and resid 40 through 48 Processing helix chain 'Z' and resid 50 through 62 Processing helix chain 'Z' and resid 72 through 89 Processing helix chain 'Z' and resid 95 through 117 removed outlier: 4.009A pdb=" N GLY Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) Proline residue: Z 107 - end of helix Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 134 removed outlier: 3.920A pdb=" N ILE Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 166 removed outlier: 3.970A pdb=" N ILE Z 141 " --> pdb=" O ILE Z 137 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY Z 166 " --> pdb=" O GLY Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 201 removed outlier: 3.885A pdb=" N VAL Z 201 " --> pdb=" O VAL Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 241 Processing helix chain 'Z' and resid 253 through 261 removed outlier: 3.728A pdb=" N LEU Z 260 " --> pdb=" O ASN Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 300 Processing sheet with id=AA1, first strand: chain 'E' and resid 208 through 210 removed outlier: 7.177A pdb=" N THR E 251 " --> pdb=" O VAL E 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 208 through 210 removed outlier: 6.756A pdb=" N THR I 251 " --> pdb=" O VAL I 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 208 through 210 removed outlier: 6.661A pdb=" N THR Z 251 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 3084 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: 2.36 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4779 1.35 - 1.47: 3660 1.47 - 1.59: 7157 1.59 - 1.71: 1 1.71 - 1.83: 150 Bond restraints: 15747 Sorted by residual: bond pdb=" CG PRO Z 122 " pdb=" CD PRO Z 122 " ideal model delta sigma weight residual 1.503 1.331 0.172 3.40e-02 8.65e+02 2.56e+01 bond pdb=" CB PRO Z 122 " pdb=" CG PRO Z 122 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CG PRO E 122 " pdb=" CD PRO E 122 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.56e+00 bond pdb=" N PRO E 122 " pdb=" CD PRO E 122 " ideal model delta sigma weight residual 1.473 1.497 -0.024 1.40e-02 5.10e+03 2.86e+00 bond pdb=" CB PRO I 107 " pdb=" CG PRO I 107 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.10e+00 ... (remaining 15742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 21073 2.56 - 5.11: 261 5.11 - 7.67: 33 7.67 - 10.22: 6 10.22 - 12.78: 5 Bond angle restraints: 21378 Sorted by residual: angle pdb=" CA PRO Z 122 " pdb=" N PRO Z 122 " pdb=" CD PRO Z 122 " ideal model delta sigma weight residual 112.00 101.26 10.74 1.40e+00 5.10e-01 5.88e+01 angle pdb=" N PRO Z 122 " pdb=" CD PRO Z 122 " pdb=" CG PRO Z 122 " ideal model delta sigma weight residual 103.20 92.04 11.16 1.50e+00 4.44e-01 5.54e+01 angle pdb=" N VAL E 95 " pdb=" CA VAL E 95 " pdb=" C VAL E 95 " ideal model delta sigma weight residual 111.90 107.77 4.13 8.10e-01 1.52e+00 2.60e+01 angle pdb=" N VAL I 95 " pdb=" CA VAL I 95 " pdb=" C VAL I 95 " ideal model delta sigma weight residual 111.90 107.80 4.10 8.10e-01 1.52e+00 2.56e+01 angle pdb=" N PRO E 122 " pdb=" CD PRO E 122 " pdb=" CG PRO E 122 " ideal model delta sigma weight residual 103.20 95.64 7.56 1.50e+00 4.44e-01 2.54e+01 ... (remaining 21373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7875 17.94 - 35.87: 1039 35.87 - 53.81: 302 53.81 - 71.74: 64 71.74 - 89.68: 20 Dihedral angle restraints: 9300 sinusoidal: 3564 harmonic: 5736 Sorted by residual: dihedral pdb=" CA ARG Z 30 " pdb=" C ARG Z 30 " pdb=" N MET Z 31 " pdb=" CA MET Z 31 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA CYS G 10 " pdb=" C CYS G 10 " pdb=" N ASN G 11 " pdb=" CA ASN G 11 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA CYS A 10 " pdb=" C CYS A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 9297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1505 0.034 - 0.068: 757 0.068 - 0.102: 233 0.102 - 0.136: 62 0.136 - 0.171: 8 Chirality restraints: 2565 Sorted by residual: chirality pdb=" CG LEU Z 22 " pdb=" CB LEU Z 22 " pdb=" CD1 LEU Z 22 " pdb=" CD2 LEU Z 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA MET Y 149 " pdb=" N MET Y 149 " pdb=" C MET Y 149 " pdb=" CB MET Y 149 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2562 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 71 " -0.090 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO D 72 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO D 72 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 72 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Z 121 " -0.068 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO Z 122 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO Z 122 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO Z 122 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP Y 209 " 0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO Y 210 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO Y 210 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO Y 210 " 0.048 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 185 2.65 - 3.22: 15110 3.22 - 3.78: 25234 3.78 - 4.34: 34216 4.34 - 4.90: 54928 Nonbonded interactions: 129673 Sorted by model distance: nonbonded pdb=" OG SER E 234 " pdb=" OE1 GLN E 238 " model vdw 2.094 3.040 nonbonded pdb=" O PHE Z 154 " pdb=" OG1 THR Z 158 " model vdw 2.145 3.040 nonbonded pdb=" ND2 ASN G 6 " pdb=" O MET H 58 " model vdw 2.208 3.120 nonbonded pdb=" OG1 THR Z 206 " pdb=" O LEU Z 302 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLU E 84 " pdb=" OH TYR E 163 " model vdw 2.222 3.040 ... (remaining 129668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.004 0.172 15750 Z= 0.175 Angle : 0.764 12.779 21384 Z= 0.413 Chirality : 0.044 0.171 2565 Planarity : 0.007 0.136 2610 Dihedral : 18.198 89.676 5625 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Rotamer: Outliers : 2.55 % Allowed : 30.66 % Favored : 66.79 % 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: -0.48 (0.18), residues: 2010 helix: 0.28 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 52 TYR 0.018 0.002 TYR F 48 PHE 0.018 0.002 PHE Z 21 TRP 0.023 0.002 TRP Z 16 HIS 0.006 0.002 HIS E 298 Details of bonding type rmsd covalent geometry : bond 0.00404 (15747) covalent geometry : angle 0.76350 (21378) SS BOND : bond 0.00753 ( 3) SS BOND : angle 1.25340 ( 6) hydrogen bonds : bond 0.22714 ( 1030) hydrogen bonds : angle 7.11750 ( 3084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 570 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: B 11 ILE cc_start: 0.8038 (mt) cc_final: 0.7837 (mt) REVERT: E 10 LYS cc_start: 0.7110 (ttmt) cc_final: 0.6862 (tptt) REVERT: E 122 PRO cc_start: 0.7699 (OUTLIER) cc_final: 0.7450 (Cg_exo) REVERT: E 247 ASP cc_start: 0.7816 (p0) cc_final: 0.7495 (p0) REVERT: Y 124 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7673 (p) REVERT: Z 10 LYS cc_start: 0.7322 (ttmt) cc_final: 0.7069 (tptt) outliers start: 41 outliers final: 8 residues processed: 597 average time/residue: 0.5319 time to fit residues: 351.1954 Evaluate side-chains 300 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 290 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain E residue 122 PRO Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Z residue 50 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN C 6 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN E 238 GLN E 248 HIS H 150 GLN H 223 GLN I 23 GLN ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN I 159 GLN I 179 GLN I 198 ASN I 239 GLN I 241 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 GLN Z 23 GLN Z 66 ASN Z 68 HIS Z 179 GLN Z 198 ASN Z 239 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107578 restraints weight = 16915.497| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.38 r_work: 0.3194 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15750 Z= 0.215 Angle : 0.738 9.038 21384 Z= 0.387 Chirality : 0.047 0.196 2565 Planarity : 0.006 0.099 2610 Dihedral : 5.273 54.119 2204 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.32 % Rotamer: Outliers : 6.47 % Allowed : 23.13 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 2010 helix: 1.40 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 60 TYR 0.019 0.002 TYR H 144 PHE 0.018 0.002 PHE B 47 TRP 0.022 0.002 TRP I 26 HIS 0.010 0.002 HIS Y 30 Details of bonding type rmsd covalent geometry : bond 0.00449 (15747) covalent geometry : angle 0.73686 (21378) SS BOND : bond 0.01272 ( 3) SS BOND : angle 2.57067 ( 6) hydrogen bonds : bond 0.05204 ( 1030) hydrogen bonds : angle 4.22909 ( 3084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 375 time to evaluate : 0.402 Fit side-chains REVERT: B 39 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7242 (mm-30) REVERT: D 92 LYS cc_start: 0.8310 (mtpt) cc_final: 0.8083 (mttt) REVERT: E 10 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7366 (tptt) REVERT: E 157 TYR cc_start: 0.8102 (m-80) cc_final: 0.7833 (m-80) REVERT: E 159 GLN cc_start: 0.8753 (tt0) cc_final: 0.8363 (tt0) REVERT: E 302 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 42 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7773 (mtmm) REVERT: F 44 ASN cc_start: 0.7879 (m-40) cc_final: 0.7560 (m110) REVERT: F 45 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7387 (mtm-85) REVERT: G 19 ARG cc_start: 0.7988 (mpt90) cc_final: 0.7059 (mmm160) REVERT: H 137 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7404 (ttt180) REVERT: I 10 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7055 (tptp) REVERT: I 31 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7859 (mtt) REVERT: I 63 GLU cc_start: 0.8081 (tp30) cc_final: 0.7814 (mm-30) REVERT: I 159 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: I 241 GLN cc_start: 0.7407 (mt0) cc_final: 0.7201 (mp10) REVERT: I 247 ASP cc_start: 0.7906 (p0) cc_final: 0.7433 (p0) REVERT: J 7 LYS cc_start: 0.7783 (tttt) cc_final: 0.7488 (tttm) REVERT: J 65 ASN cc_start: 0.7795 (m-40) cc_final: 0.7210 (t0) REVERT: J 68 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8116 (tt0) REVERT: Y 17 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8554 (mp) REVERT: Y 97 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8205 (p) REVERT: Z 6 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7101 (tmmt) REVERT: Z 10 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7462 (mptt) REVERT: Z 84 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7745 (tt0) REVERT: Z 86 ARG cc_start: 0.7959 (ttt-90) cc_final: 0.7722 (ttt-90) REVERT: Z 173 LEU cc_start: 0.4549 (OUTLIER) cc_final: 0.4012 (tm) REVERT: Z 183 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8562 (tptm) REVERT: Z 230 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7768 (mppt) REVERT: Z 237 GLN cc_start: 0.8548 (mt0) cc_final: 0.8314 (mt0) outliers start: 104 outliers final: 27 residues processed: 442 average time/residue: 0.5716 time to fit residues: 278.6509 Evaluate side-chains 337 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 300 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 31 MET Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 210 SER Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 179 GLN I 179 GLN I 237 GLN J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 159 GLN Z 179 GLN Z 238 GLN Z 248 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097957 restraints weight = 16906.243| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.35 r_work: 0.3052 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15750 Z= 0.170 Angle : 0.642 9.316 21384 Z= 0.339 Chirality : 0.045 0.218 2565 Planarity : 0.005 0.075 2610 Dihedral : 4.761 36.872 2192 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.93 % Favored : 95.87 % Rotamer: Outliers : 5.16 % Allowed : 21.83 % Favored : 73.01 % 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: 1.50 (0.19), residues: 2010 helix: 1.91 (0.13), residues: 1479 sheet: None (None), residues: 0 loop : -1.74 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 164 TYR 0.010 0.002 TYR I 70 PHE 0.013 0.002 PHE E 161 TRP 0.019 0.002 TRP I 26 HIS 0.008 0.001 HIS Y 28 Details of bonding type rmsd covalent geometry : bond 0.00382 (15747) covalent geometry : angle 0.63746 (21378) SS BOND : bond 0.01265 ( 3) SS BOND : angle 4.79286 ( 6) hydrogen bonds : bond 0.05389 ( 1030) hydrogen bonds : angle 4.02419 ( 3084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 307 time to evaluate : 0.459 Fit side-chains REVERT: B 7 LYS cc_start: 0.7881 (tttt) cc_final: 0.7608 (tttp) REVERT: B 40 GLU cc_start: 0.7979 (tp30) cc_final: 0.7584 (mm-30) REVERT: B 42 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7935 (mttm) REVERT: B 65 ASN cc_start: 0.7757 (t0) cc_final: 0.7495 (t0) REVERT: D 92 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8141 (mttt) REVERT: E 11 ASP cc_start: 0.7832 (m-30) cc_final: 0.7369 (m-30) REVERT: E 84 GLU cc_start: 0.8340 (tt0) cc_final: 0.8122 (tt0) REVERT: E 157 TYR cc_start: 0.8089 (m-80) cc_final: 0.7827 (m-80) REVERT: F 44 ASN cc_start: 0.7817 (m-40) cc_final: 0.7570 (m-40) REVERT: F 65 ASN cc_start: 0.7676 (t0) cc_final: 0.7358 (t0) REVERT: G 19 ARG cc_start: 0.8034 (mpt90) cc_final: 0.7079 (mmm160) REVERT: I 10 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7063 (tptp) REVERT: I 31 MET cc_start: 0.8344 (mtt) cc_final: 0.7970 (mtt) REVERT: I 63 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: I 234 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8066 (t) REVERT: I 237 GLN cc_start: 0.8319 (mt0) cc_final: 0.8014 (mt0) REVERT: I 303 MET cc_start: 0.8564 (mtt) cc_final: 0.8156 (mtt) REVERT: J 65 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7364 (t0) REVERT: J 68 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8346 (mt-10) REVERT: Y 17 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8666 (mp) REVERT: Y 97 SER cc_start: 0.8610 (m) cc_final: 0.8351 (p) REVERT: Z 6 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7166 (tmmt) REVERT: Z 10 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7592 (mptt) REVERT: Z 84 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7887 (tt0) REVERT: Z 173 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.4065 (tm) REVERT: Z 183 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8508 (tptm) REVERT: Z 230 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7832 (mppt) REVERT: Z 255 ASP cc_start: 0.8451 (m-30) cc_final: 0.8245 (m-30) outliers start: 83 outliers final: 31 residues processed: 361 average time/residue: 0.6374 time to fit residues: 251.4885 Evaluate side-chains 331 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 86 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 185 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN I 61 HIS I 179 GLN J 65 ASN Y 28 HIS ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 GLN Z 98 GLN Z 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.094488 restraints weight = 16822.045| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.36 r_work: 0.3001 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15750 Z= 0.199 Angle : 0.681 10.698 21384 Z= 0.360 Chirality : 0.046 0.240 2565 Planarity : 0.005 0.070 2610 Dihedral : 5.068 50.942 2192 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.13 % Favored : 95.57 % Rotamer: Outliers : 5.35 % Allowed : 21.33 % Favored : 73.32 % 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: 1.51 (0.19), residues: 2010 helix: 1.86 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.70 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 164 TYR 0.021 0.002 TYR C 9 PHE 0.013 0.002 PHE D 211 TRP 0.023 0.002 TRP I 26 HIS 0.007 0.002 HIS Y 28 Details of bonding type rmsd covalent geometry : bond 0.00460 (15747) covalent geometry : angle 0.67665 (21378) SS BOND : bond 0.01741 ( 3) SS BOND : angle 4.60588 ( 6) hydrogen bonds : bond 0.05479 ( 1030) hydrogen bonds : angle 4.08952 ( 3084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 307 time to evaluate : 0.594 Fit side-chains REVERT: A 41 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8201 (ptt) REVERT: B 7 LYS cc_start: 0.7989 (tttt) cc_final: 0.7761 (tttp) REVERT: B 39 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7307 (mm-30) REVERT: B 40 GLU cc_start: 0.7951 (tp30) cc_final: 0.7552 (mm-30) REVERT: B 65 ASN cc_start: 0.7827 (t0) cc_final: 0.7387 (t0) REVERT: C 41 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8120 (ptt) REVERT: D 92 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8210 (ttmt) REVERT: D 97 SER cc_start: 0.8920 (t) cc_final: 0.8698 (p) REVERT: E 11 ASP cc_start: 0.7930 (m-30) cc_final: 0.7496 (m-30) REVERT: E 152 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8809 (mtt) REVERT: E 157 TYR cc_start: 0.8166 (m-80) cc_final: 0.7948 (m-80) REVERT: E 169 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6924 (pp) REVERT: F 44 ASN cc_start: 0.7741 (m-40) cc_final: 0.7517 (m-40) REVERT: G 19 ARG cc_start: 0.7992 (mpt90) cc_final: 0.7167 (mmm160) REVERT: H 137 ARG cc_start: 0.7673 (ttp-110) cc_final: 0.7419 (ttt180) REVERT: I 10 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7063 (tptp) REVERT: I 31 MET cc_start: 0.8484 (mtt) cc_final: 0.8125 (mtt) REVERT: I 84 GLU cc_start: 0.8459 (tt0) cc_final: 0.8155 (tt0) REVERT: I 234 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.8054 (t) REVERT: J 7 LYS cc_start: 0.8280 (tttp) cc_final: 0.8032 (tttp) REVERT: J 38 GLN cc_start: 0.8447 (tt0) cc_final: 0.8193 (tt0) REVERT: J 40 GLU cc_start: 0.7943 (tp30) cc_final: 0.7404 (mm-30) REVERT: J 65 ASN cc_start: 0.7601 (m-40) cc_final: 0.7214 (t0) REVERT: J 68 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8424 (mt-10) REVERT: Y 17 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8727 (mp) REVERT: Y 25 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8796 (t70) REVERT: Y 97 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8445 (p) REVERT: Z 6 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7349 (tmmt) REVERT: Z 10 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7550 (tptt) REVERT: Z 98 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8542 (mm-40) REVERT: Z 173 LEU cc_start: 0.4638 (OUTLIER) cc_final: 0.4138 (tm) REVERT: Z 230 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7920 (mppt) REVERT: Z 250 ILE cc_start: 0.8793 (mm) cc_final: 0.8557 (mm) outliers start: 86 outliers final: 43 residues processed: 364 average time/residue: 0.6293 time to fit residues: 250.6442 Evaluate side-chains 346 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain J residue 86 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 98 GLN Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 134 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 115 optimal weight: 0.0770 chunk 91 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 65 ASN I 179 GLN I 237 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN Z 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098104 restraints weight = 16906.872| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.35 r_work: 0.3058 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 15750 Z= 0.133 Angle : 0.580 8.851 21384 Z= 0.306 Chirality : 0.042 0.241 2565 Planarity : 0.005 0.062 2610 Dihedral : 4.722 40.114 2192 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.68 % Favored : 96.17 % Rotamer: Outliers : 4.10 % Allowed : 21.83 % Favored : 74.07 % 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: 1.83 (0.19), residues: 2010 helix: 2.17 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.69 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 164 TYR 0.008 0.001 TYR B 14 PHE 0.008 0.001 PHE E 161 TRP 0.017 0.002 TRP I 26 HIS 0.003 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00287 (15747) covalent geometry : angle 0.57557 (21378) SS BOND : bond 0.01625 ( 3) SS BOND : angle 4.31237 ( 6) hydrogen bonds : bond 0.04436 ( 1030) hydrogen bonds : angle 3.85659 ( 3084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 0.667 Fit side-chains REVERT: A 41 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8206 (ptt) REVERT: B 7 LYS cc_start: 0.7947 (tttt) cc_final: 0.7669 (tttp) REVERT: B 39 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 40 GLU cc_start: 0.7905 (tp30) cc_final: 0.7580 (mm-30) REVERT: B 65 ASN cc_start: 0.7814 (t0) cc_final: 0.7284 (t0) REVERT: D 92 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8178 (ttmt) REVERT: D 97 SER cc_start: 0.8883 (t) cc_final: 0.8681 (p) REVERT: E 11 ASP cc_start: 0.7920 (m-30) cc_final: 0.7551 (m-30) REVERT: E 152 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8782 (mtt) REVERT: E 157 TYR cc_start: 0.8098 (m-80) cc_final: 0.7829 (m-80) REVERT: E 169 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7026 (pp) REVERT: E 249 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8215 (tptt) REVERT: F 44 ASN cc_start: 0.7830 (m-40) cc_final: 0.7581 (m-40) REVERT: G 19 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7013 (mmm160) REVERT: H 137 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.7387 (ttt180) REVERT: I 31 MET cc_start: 0.8393 (mtt) cc_final: 0.8028 (mtt) REVERT: I 84 GLU cc_start: 0.8435 (tt0) cc_final: 0.8044 (tt0) REVERT: I 237 GLN cc_start: 0.8279 (mt0) cc_final: 0.7798 (mt0) REVERT: I 241 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: J 38 GLN cc_start: 0.8476 (tt0) cc_final: 0.8191 (tt0) REVERT: J 39 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7446 (mm-30) REVERT: J 40 GLU cc_start: 0.7928 (tp30) cc_final: 0.7478 (mm-30) REVERT: J 60 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7879 (ttp-110) REVERT: J 68 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8393 (mt-10) REVERT: Z 6 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7565 (tptp) REVERT: Z 10 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7562 (mptt) REVERT: Z 98 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8337 (mm-40) REVERT: Z 142 ILE cc_start: 0.8745 (pp) cc_final: 0.8535 (mt) REVERT: Z 173 LEU cc_start: 0.4671 (OUTLIER) cc_final: 0.4223 (tm) REVERT: Z 183 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8490 (tptm) REVERT: Z 230 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7882 (mppt) REVERT: Z 250 ILE cc_start: 0.8676 (mm) cc_final: 0.8430 (mm) outliers start: 66 outliers final: 27 residues processed: 338 average time/residue: 0.6696 time to fit residues: 246.8417 Evaluate side-chains 324 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 98 GLN Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 115 optimal weight: 0.0670 chunk 76 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 65 ASN I 179 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN Z 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097508 restraints weight = 16730.578| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.36 r_work: 0.3058 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 15750 Z= 0.143 Angle : 0.593 9.186 21384 Z= 0.313 Chirality : 0.042 0.250 2565 Planarity : 0.005 0.060 2610 Dihedral : 4.722 36.543 2192 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.88 % Favored : 95.97 % Rotamer: Outliers : 4.17 % Allowed : 21.39 % Favored : 74.44 % 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: 1.91 (0.19), residues: 2010 helix: 2.21 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.62 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 164 TYR 0.010 0.001 TYR B 14 PHE 0.009 0.001 PHE E 161 TRP 0.018 0.002 TRP I 26 HIS 0.004 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00317 (15747) covalent geometry : angle 0.58772 (21378) SS BOND : bond 0.02285 ( 3) SS BOND : angle 4.67566 ( 6) hydrogen bonds : bond 0.04589 ( 1030) hydrogen bonds : angle 3.86749 ( 3084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 0.594 Fit side-chains REVERT: A 41 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8187 (ptt) REVERT: B 7 LYS cc_start: 0.7988 (tttt) cc_final: 0.7699 (tttp) REVERT: B 40 GLU cc_start: 0.7985 (tp30) cc_final: 0.7704 (mm-30) REVERT: D 92 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8223 (mttt) REVERT: D 97 SER cc_start: 0.8920 (t) cc_final: 0.8701 (p) REVERT: E 11 ASP cc_start: 0.7931 (m-30) cc_final: 0.7566 (m-30) REVERT: E 152 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8801 (mtt) REVERT: E 157 TYR cc_start: 0.8120 (m-80) cc_final: 0.7911 (m-80) REVERT: E 169 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7067 (pp) REVERT: E 249 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8196 (tptt) REVERT: F 44 ASN cc_start: 0.7854 (m-40) cc_final: 0.7431 (t0) REVERT: G 19 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7078 (mmm160) REVERT: H 137 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7388 (ttt180) REVERT: I 31 MET cc_start: 0.8452 (mtt) cc_final: 0.8092 (mtt) REVERT: I 84 GLU cc_start: 0.8489 (tt0) cc_final: 0.8162 (tt0) REVERT: I 237 GLN cc_start: 0.8309 (mt0) cc_final: 0.7885 (mt0) REVERT: I 241 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6940 (mp10) REVERT: J 38 GLN cc_start: 0.8456 (tt0) cc_final: 0.8196 (tt0) REVERT: J 40 GLU cc_start: 0.7990 (tp30) cc_final: 0.7769 (mm-30) REVERT: J 68 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8386 (mt-10) REVERT: Y 97 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8329 (p) REVERT: Z 6 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7612 (tptp) REVERT: Z 173 LEU cc_start: 0.4801 (OUTLIER) cc_final: 0.4317 (tm) REVERT: Z 183 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8503 (tptm) REVERT: Z 223 ASP cc_start: 0.7522 (m-30) cc_final: 0.7255 (m-30) REVERT: Z 230 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7892 (mppt) outliers start: 67 outliers final: 35 residues processed: 338 average time/residue: 0.6473 time to fit residues: 239.1159 Evaluate side-chains 336 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 132 LYS Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 153 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 53 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 238 GLN F 65 ASN I 179 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098650 restraints weight = 16784.581| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.37 r_work: 0.3077 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 15750 Z= 0.133 Angle : 0.578 9.613 21384 Z= 0.305 Chirality : 0.042 0.257 2565 Planarity : 0.005 0.057 2610 Dihedral : 4.625 29.179 2192 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.88 % Favored : 95.97 % Rotamer: Outliers : 3.92 % Allowed : 21.70 % Favored : 74.38 % 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: 2.03 (0.19), residues: 2010 helix: 2.30 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.56 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Z 164 TYR 0.010 0.001 TYR B 14 PHE 0.010 0.001 PHE E 161 TRP 0.017 0.002 TRP I 26 HIS 0.003 0.001 HIS Y 28 Details of bonding type rmsd covalent geometry : bond 0.00291 (15747) covalent geometry : angle 0.57308 (21378) SS BOND : bond 0.02133 ( 3) SS BOND : angle 4.64400 ( 6) hydrogen bonds : bond 0.04330 ( 1030) hydrogen bonds : angle 3.80000 ( 3084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 295 time to evaluate : 0.520 Fit side-chains REVERT: A 41 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8182 (ptt) REVERT: B 7 LYS cc_start: 0.7963 (tttt) cc_final: 0.7745 (tttp) REVERT: B 39 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7365 (mm-30) REVERT: B 40 GLU cc_start: 0.7923 (tp30) cc_final: 0.7627 (mm-30) REVERT: B 42 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7891 (mttm) REVERT: D 92 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8205 (mttt) REVERT: D 97 SER cc_start: 0.8916 (t) cc_final: 0.8692 (p) REVERT: E 11 ASP cc_start: 0.7915 (m-30) cc_final: 0.7585 (m-30) REVERT: E 152 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8804 (mtt) REVERT: E 157 TYR cc_start: 0.8117 (m-80) cc_final: 0.7904 (m-80) REVERT: E 169 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7098 (pp) REVERT: E 249 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8185 (tptt) REVERT: F 44 ASN cc_start: 0.7874 (m-40) cc_final: 0.7472 (t0) REVERT: G 19 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7056 (mmm160) REVERT: H 137 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7365 (ttt180) REVERT: I 31 MET cc_start: 0.8420 (mtt) cc_final: 0.8064 (mtt) REVERT: I 84 GLU cc_start: 0.8487 (tt0) cc_final: 0.8091 (tt0) REVERT: I 237 GLN cc_start: 0.8297 (mt0) cc_final: 0.7851 (mt0) REVERT: I 241 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: J 38 GLN cc_start: 0.8442 (tt0) cc_final: 0.8209 (tt0) REVERT: J 40 GLU cc_start: 0.7976 (tp30) cc_final: 0.7770 (mm-30) REVERT: J 68 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8383 (mt-10) REVERT: Z 173 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4294 (tm) REVERT: Z 183 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8466 (tptm) REVERT: Z 223 ASP cc_start: 0.7549 (m-30) cc_final: 0.7275 (m-30) REVERT: Z 230 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7821 (mppt) outliers start: 63 outliers final: 34 residues processed: 338 average time/residue: 0.6697 time to fit residues: 246.6722 Evaluate side-chains 329 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN D 30 HIS D 31 GLN E 179 GLN I 179 GLN J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096706 restraints weight = 16812.788| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.35 r_work: 0.3045 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 15750 Z= 0.156 Angle : 0.622 11.432 21384 Z= 0.328 Chirality : 0.043 0.268 2565 Planarity : 0.005 0.062 2610 Dihedral : 4.742 33.784 2191 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.08 % Favored : 95.77 % Rotamer: Outliers : 3.67 % Allowed : 21.89 % Favored : 74.44 % 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: 1.97 (0.19), residues: 2010 helix: 2.19 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Z 164 TYR 0.013 0.002 TYR B 14 PHE 0.010 0.001 PHE E 161 TRP 0.020 0.002 TRP I 26 HIS 0.005 0.001 HIS Z 61 Details of bonding type rmsd covalent geometry : bond 0.00354 (15747) covalent geometry : angle 0.61640 (21378) SS BOND : bond 0.02298 ( 3) SS BOND : angle 5.21762 ( 6) hydrogen bonds : bond 0.04814 ( 1030) hydrogen bonds : angle 3.90922 ( 3084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.571 Fit side-chains REVERT: A 41 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8205 (ptt) REVERT: B 7 LYS cc_start: 0.8027 (tttt) cc_final: 0.7794 (tttp) REVERT: B 39 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 40 GLU cc_start: 0.7989 (tp30) cc_final: 0.7696 (mm-30) REVERT: B 42 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7963 (mttm) REVERT: D 92 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8254 (mttt) REVERT: D 97 SER cc_start: 0.8941 (t) cc_final: 0.8727 (p) REVERT: E 11 ASP cc_start: 0.7940 (m-30) cc_final: 0.7592 (m-30) REVERT: E 52 GLU cc_start: 0.7476 (mp0) cc_final: 0.7147 (mp0) REVERT: E 152 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8816 (mtt) REVERT: E 157 TYR cc_start: 0.8174 (m-80) cc_final: 0.7970 (m-80) REVERT: E 169 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7233 (pp) REVERT: E 249 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8214 (tptt) REVERT: F 44 ASN cc_start: 0.7771 (m-40) cc_final: 0.7396 (t0) REVERT: G 19 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7207 (mmm160) REVERT: H 137 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7413 (ttt180) REVERT: I 31 MET cc_start: 0.8453 (mtt) cc_final: 0.8087 (mtt) REVERT: I 84 GLU cc_start: 0.8521 (tt0) cc_final: 0.8177 (tt0) REVERT: I 237 GLN cc_start: 0.8350 (mt0) cc_final: 0.7881 (mt0) REVERT: I 241 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: J 38 GLN cc_start: 0.8441 (tt0) cc_final: 0.8207 (tt0) REVERT: J 40 GLU cc_start: 0.7995 (tp30) cc_final: 0.7768 (mm-30) REVERT: J 65 ASN cc_start: 0.7882 (t0) cc_final: 0.7615 (t0) REVERT: Y 97 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8398 (p) REVERT: Z 173 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.4183 (tm) REVERT: Z 183 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8543 (tptm) REVERT: Z 223 ASP cc_start: 0.7602 (m-30) cc_final: 0.7335 (m-30) REVERT: Z 230 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7824 (mppt) outliers start: 59 outliers final: 40 residues processed: 334 average time/residue: 0.6729 time to fit residues: 245.2702 Evaluate side-chains 336 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 132 LYS Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 147 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN E 179 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095442 restraints weight = 16683.671| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.34 r_work: 0.3027 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 15750 Z= 0.176 Angle : 0.660 11.526 21384 Z= 0.347 Chirality : 0.045 0.268 2565 Planarity : 0.005 0.065 2610 Dihedral : 4.885 39.929 2191 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.68 % Favored : 96.02 % Rotamer: Outliers : 3.98 % Allowed : 21.64 % Favored : 74.38 % 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: 1.88 (0.19), residues: 2010 helix: 2.11 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 164 TYR 0.015 0.002 TYR B 14 PHE 0.011 0.002 PHE E 65 TRP 0.021 0.002 TRP I 26 HIS 0.005 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00406 (15747) covalent geometry : angle 0.65390 (21378) SS BOND : bond 0.02436 ( 3) SS BOND : angle 5.32765 ( 6) hydrogen bonds : bond 0.05094 ( 1030) hydrogen bonds : angle 4.00185 ( 3084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.593 Fit side-chains REVERT: A 41 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8284 (ptt) REVERT: B 7 LYS cc_start: 0.8037 (tttt) cc_final: 0.7796 (tttp) REVERT: B 39 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7384 (mm-30) REVERT: B 40 GLU cc_start: 0.7982 (tp30) cc_final: 0.7686 (mm-30) REVERT: D 92 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8256 (ttmt) REVERT: D 97 SER cc_start: 0.8951 (t) cc_final: 0.8746 (p) REVERT: E 11 ASP cc_start: 0.7991 (m-30) cc_final: 0.7653 (m-30) REVERT: E 52 GLU cc_start: 0.7565 (mp0) cc_final: 0.7183 (mp0) REVERT: E 152 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8817 (mtt) REVERT: E 169 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7417 (pp) REVERT: E 249 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8188 (tptt) REVERT: E 251 THR cc_start: 0.8899 (m) cc_final: 0.8591 (t) REVERT: G 19 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7207 (mmm160) REVERT: G 41 MET cc_start: 0.7803 (ppp) cc_final: 0.7553 (ptt) REVERT: H 137 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7406 (ttt180) REVERT: H 176 MET cc_start: 0.8682 (tpp) cc_final: 0.8412 (mmm) REVERT: I 31 MET cc_start: 0.8559 (mtt) cc_final: 0.8199 (mtt) REVERT: I 84 GLU cc_start: 0.8550 (tt0) cc_final: 0.8185 (tt0) REVERT: I 237 GLN cc_start: 0.8377 (mt0) cc_final: 0.7950 (mt0) REVERT: I 241 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: J 38 GLN cc_start: 0.8418 (tt0) cc_final: 0.8190 (tt0) REVERT: J 68 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8324 (mt-10) REVERT: Y 97 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8476 (p) REVERT: Z 173 LEU cc_start: 0.4828 (OUTLIER) cc_final: 0.4254 (tm) REVERT: Z 223 ASP cc_start: 0.7634 (m-30) cc_final: 0.7358 (m-30) REVERT: Z 230 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7900 (mppt) outliers start: 64 outliers final: 41 residues processed: 334 average time/residue: 0.6632 time to fit residues: 241.6142 Evaluate side-chains 334 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 86 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 132 LYS Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN I 238 GLN I 239 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094941 restraints weight = 16763.476| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.35 r_work: 0.3021 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.7438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 15750 Z= 0.187 Angle : 0.682 11.972 21384 Z= 0.360 Chirality : 0.046 0.283 2565 Planarity : 0.005 0.066 2610 Dihedral : 4.963 44.547 2191 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.08 % Favored : 95.62 % Rotamer: Outliers : 3.54 % Allowed : 22.20 % Favored : 74.25 % 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: 1.80 (0.19), residues: 2010 helix: 2.05 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 164 TYR 0.019 0.002 TYR B 14 PHE 0.011 0.002 PHE D 211 TRP 0.021 0.002 TRP I 26 HIS 0.005 0.002 HIS Z 61 Details of bonding type rmsd covalent geometry : bond 0.00436 (15747) covalent geometry : angle 0.67552 (21378) SS BOND : bond 0.02601 ( 3) SS BOND : angle 5.78208 ( 6) hydrogen bonds : bond 0.05210 ( 1030) hydrogen bonds : angle 4.04247 ( 3084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 296 time to evaluate : 0.629 Fit side-chains REVERT: A 41 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8296 (ptt) REVERT: B 7 LYS cc_start: 0.8029 (tttt) cc_final: 0.7782 (tttp) REVERT: B 39 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7309 (mm-30) REVERT: B 40 GLU cc_start: 0.7986 (tp30) cc_final: 0.7671 (mm-30) REVERT: B 42 LYS cc_start: 0.8286 (mtmm) cc_final: 0.8014 (mttm) REVERT: D 92 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8288 (ttmt) REVERT: E 11 ASP cc_start: 0.8018 (m-30) cc_final: 0.7689 (m-30) REVERT: E 52 GLU cc_start: 0.7567 (mp0) cc_final: 0.7208 (mp0) REVERT: E 169 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7501 (pp) REVERT: E 249 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8190 (tptt) REVERT: E 251 THR cc_start: 0.8921 (m) cc_final: 0.8608 (t) REVERT: G 19 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7228 (mmm160) REVERT: H 137 ARG cc_start: 0.7653 (ttp-110) cc_final: 0.7392 (ttt180) REVERT: H 176 MET cc_start: 0.8697 (tpp) cc_final: 0.8435 (mmm) REVERT: I 31 MET cc_start: 0.8561 (mtt) cc_final: 0.8179 (mtt) REVERT: I 84 GLU cc_start: 0.8566 (tt0) cc_final: 0.8198 (tt0) REVERT: I 237 GLN cc_start: 0.8262 (mt0) cc_final: 0.7873 (mt0) REVERT: I 241 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: J 38 GLN cc_start: 0.8454 (tt0) cc_final: 0.8207 (tt0) REVERT: J 40 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7720 (mm-30) REVERT: J 60 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7888 (ttp-110) REVERT: J 65 ASN cc_start: 0.7813 (t0) cc_final: 0.7609 (t0) REVERT: Z 142 ILE cc_start: 0.8808 (pp) cc_final: 0.8565 (mt) REVERT: Z 173 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.4322 (tm) REVERT: Z 223 ASP cc_start: 0.7677 (m-30) cc_final: 0.7326 (m-30) REVERT: Z 230 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7957 (mppt) outliers start: 57 outliers final: 43 residues processed: 337 average time/residue: 0.6768 time to fit residues: 248.4665 Evaluate side-chains 332 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 86 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 132 LYS Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 76 optimal weight: 0.0170 chunk 155 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN E 179 GLN I 179 GLN I 238 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099404 restraints weight = 16774.440| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.36 r_work: 0.3089 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 15750 Z= 0.129 Angle : 0.589 10.625 21384 Z= 0.310 Chirality : 0.042 0.230 2565 Planarity : 0.005 0.057 2610 Dihedral : 4.635 29.787 2191 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.78 % Favored : 96.07 % Rotamer: Outliers : 2.36 % Allowed : 23.69 % Favored : 73.94 % 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: 2.06 (0.19), residues: 2010 helix: 2.31 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.51 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Z 164 TYR 0.015 0.001 TYR J 14 PHE 0.011 0.001 PHE E 161 TRP 0.018 0.002 TRP Z 26 HIS 0.003 0.001 HIS Y 28 Details of bonding type rmsd covalent geometry : bond 0.00277 (15747) covalent geometry : angle 0.58437 (21378) SS BOND : bond 0.02237 ( 3) SS BOND : angle 4.55733 ( 6) hydrogen bonds : bond 0.04154 ( 1030) hydrogen bonds : angle 3.80412 ( 3084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7908.86 seconds wall clock time: 134 minutes 39.67 seconds (8079.67 seconds total)