Starting phenix.real_space_refine on Fri Jun 13 18:20:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xtg_33448/06_2025/7xtg_33448_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xtg_33448/06_2025/7xtg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xtg_33448/06_2025/7xtg_33448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xtg_33448/06_2025/7xtg_33448.map" model { file = "/net/cci-nas-00/data/ceres_data/7xtg_33448/06_2025/7xtg_33448_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xtg_33448/06_2025/7xtg_33448_neut.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.089 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.30, per 1000 atoms: 0.67 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: 4.16 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.56 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: 4.16 Time building geometry restraints manager: 4.86 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: 0.01 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.650 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- 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 : 13.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (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 TRP 0.023 0.002 TRP Z 16 HIS 0.006 0.002 HIS E 298 PHE 0.018 0.002 PHE Z 21 TYR 0.018 0.002 TYR F 48 ARG 0.007 0.001 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.22714 ( 1030) hydrogen bonds : angle 7.11750 ( 3084) SS BOND : bond 0.00753 ( 3) SS BOND : angle 1.25340 ( 6) covalent geometry : bond 0.00404 (15747) covalent geometry : angle 0.76350 (21378) *********************** 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 : 1.627 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: 1.2303 time to fit residues: 812.2338 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 : 1.782 ------------------------------------------------------------------------------- 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 167 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3712 r_free = 0.3712 target = 0.140153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108172 restraints weight = 17008.160| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.39 r_work: 0.3204 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15750 Z= 0.201 Angle : 0.726 8.833 21384 Z= 0.380 Chirality : 0.048 0.208 2565 Planarity : 0.006 0.108 2610 Dihedral : 5.206 50.773 2204 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Rotamer: Outliers : 6.53 % Allowed : 23.01 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2010 helix: 1.39 (0.13), residues: 1467 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Z 26 HIS 0.009 0.002 HIS Y 30 PHE 0.018 0.002 PHE B 47 TYR 0.022 0.002 TYR H 144 ARG 0.007 0.001 ARG Z 30 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 1030) hydrogen bonds : angle 4.22495 ( 3084) SS BOND : bond 0.00851 ( 3) SS BOND : angle 2.11641 ( 6) covalent geometry : bond 0.00443 (15747) covalent geometry : angle 0.72498 (21378) *********************** 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 476 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 371 time to evaluate : 1.685 Fit side-chains REVERT: B 9 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7625 (m-40) REVERT: B 39 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 65 ASN cc_start: 0.7556 (t0) cc_final: 0.7344 (t0) REVERT: D 92 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8062 (mttt) REVERT: E 10 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7378 (tptm) REVERT: E 157 TYR cc_start: 0.8116 (m-80) cc_final: 0.7880 (m-80) REVERT: E 159 GLN cc_start: 0.8779 (tt0) cc_final: 0.8417 (tt0) REVERT: E 302 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8027 (mp) REVERT: F 44 ASN cc_start: 0.7841 (m-40) cc_final: 0.7517 (m110) REVERT: F 45 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7361 (mtm-85) REVERT: G 19 ARG cc_start: 0.7977 (mpt90) cc_final: 0.7051 (mmm160) REVERT: H 137 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7437 (ttt180) REVERT: I 10 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7077 (tptp) REVERT: I 31 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: I 63 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7779 (mm-30) REVERT: I 159 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: I 241 GLN cc_start: 0.7391 (mt0) cc_final: 0.7071 (mp10) REVERT: J 7 LYS cc_start: 0.7770 (tttt) cc_final: 0.7473 (tttm) REVERT: J 65 ASN cc_start: 0.7794 (m-40) cc_final: 0.7240 (t0) REVERT: J 68 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8122 (tt0) REVERT: Y 17 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8554 (mp) REVERT: Y 97 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8149 (p) REVERT: Z 6 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7057 (tmmt) REVERT: Z 10 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7455 (mptt) REVERT: Z 84 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7625 (tt0) REVERT: Z 86 ARG cc_start: 0.7959 (ttt-90) cc_final: 0.7727 (ttt-90) REVERT: Z 157 TYR cc_start: 0.8292 (m-80) cc_final: 0.8079 (m-80) REVERT: Z 173 LEU cc_start: 0.4531 (OUTLIER) cc_final: 0.4013 (tm) REVERT: Z 183 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8573 (tptm) REVERT: Z 230 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7740 (mppt) REVERT: Z 237 GLN cc_start: 0.8536 (mt0) cc_final: 0.8261 (mt0) outliers start: 105 outliers final: 27 residues processed: 438 average time/residue: 1.2337 time to fit residues: 596.7764 Evaluate side-chains 337 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASN 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 20 VAL 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 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 63 GLU 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 Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 31 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 23 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 = 0.3591 r_free = 0.3591 target = 0.130294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097922 restraints weight = 16761.301| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.36 r_work: 0.3054 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15750 Z= 0.175 Angle : 0.651 9.401 21384 Z= 0.343 Chirality : 0.045 0.230 2565 Planarity : 0.005 0.079 2610 Dihedral : 4.784 37.391 2192 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.98 % Favored : 95.82 % Rotamer: Outliers : 5.16 % Allowed : 21.39 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2010 helix: 1.88 (0.13), residues: 1479 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 26 HIS 0.008 0.002 HIS Y 28 PHE 0.012 0.002 PHE F 54 TYR 0.011 0.002 TYR I 70 ARG 0.010 0.001 ARG Z 164 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 1030) hydrogen bonds : angle 4.05442 ( 3084) SS BOND : bond 0.01785 ( 3) SS BOND : angle 4.85449 ( 6) covalent geometry : bond 0.00394 (15747) covalent geometry : angle 0.64576 (21378) *********************** 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 394 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 1.790 Fit side-chains REVERT: B 39 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 40 GLU cc_start: 0.7993 (tp30) cc_final: 0.7677 (mm-30) REVERT: B 42 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7879 (mttm) REVERT: B 65 ASN cc_start: 0.7802 (t0) cc_final: 0.7326 (t0) REVERT: D 92 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8136 (mttt) REVERT: E 11 ASP cc_start: 0.7820 (m-30) cc_final: 0.7316 (m-30) REVERT: E 84 GLU cc_start: 0.8302 (tt0) cc_final: 0.8056 (tt0) REVERT: E 157 TYR cc_start: 0.8058 (m-80) cc_final: 0.7795 (m-80) REVERT: E 164 ARG cc_start: 0.7355 (mtp-110) cc_final: 0.6926 (mtm110) REVERT: F 44 ASN cc_start: 0.7813 (m-40) cc_final: 0.7544 (m-40) REVERT: F 65 ASN cc_start: 0.7617 (t0) cc_final: 0.7245 (t0) REVERT: G 19 ARG cc_start: 0.8026 (mpt90) cc_final: 0.7072 (mmm160) REVERT: I 10 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7075 (tptp) REVERT: I 31 MET cc_start: 0.8377 (mtt) cc_final: 0.7987 (mtt) REVERT: I 63 GLU cc_start: 0.8165 (tp30) cc_final: 0.7911 (mm-30) REVERT: I 159 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: I 234 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8075 (t) REVERT: I 237 GLN cc_start: 0.8341 (mt0) cc_final: 0.8044 (mt0) REVERT: I 303 MET cc_start: 0.8559 (mtt) cc_final: 0.8150 (mtt) REVERT: J 65 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7354 (t0) REVERT: J 68 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8327 (mt-10) REVERT: Y 17 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8662 (mp) REVERT: Y 97 SER cc_start: 0.8618 (m) cc_final: 0.8355 (p) REVERT: Z 6 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7370 (tppt) REVERT: Z 10 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7589 (mptt) REVERT: Z 84 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7840 (tt0) REVERT: Z 173 LEU cc_start: 0.4568 (OUTLIER) cc_final: 0.4057 (tm) REVERT: Z 183 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8542 (tptm) REVERT: Z 230 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7833 (mppt) REVERT: Z 255 ASP cc_start: 0.8444 (m-30) cc_final: 0.8241 (m-30) outliers start: 83 outliers final: 34 residues processed: 365 average time/residue: 1.8217 time to fit residues: 732.8137 Evaluate side-chains 335 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 5.558 ------------------------------------------------------------------------------- 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 28 LYS 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 6 ILE 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 113 THR Chi-restraints excluded: chain H residue 132 LYS 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 94 ASP Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 159 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 H 125 HIS 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 98 GLN Z 159 GLN Z 179 GLN Z 239 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100058 restraints weight = 16797.808| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.36 r_work: 0.3087 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 15750 Z= 0.132 Angle : 0.573 8.339 21384 Z= 0.302 Chirality : 0.041 0.209 2565 Planarity : 0.005 0.072 2610 Dihedral : 4.563 30.129 2192 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.98 % Favored : 95.87 % Rotamer: Outliers : 3.98 % Allowed : 22.89 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2010 helix: 2.16 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 26 HIS 0.003 0.001 HIS Z 298 PHE 0.009 0.001 PHE E 161 TYR 0.009 0.001 TYR B 14 ARG 0.010 0.001 ARG I 164 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 1030) hydrogen bonds : angle 3.83954 ( 3084) SS BOND : bond 0.01574 ( 3) SS BOND : angle 4.25073 ( 6) covalent geometry : bond 0.00283 (15747) covalent geometry : angle 0.56818 (21378) *********************** 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 361 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 297 time to evaluate : 1.911 Fit side-chains REVERT: B 39 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 40 GLU cc_start: 0.7925 (tp30) cc_final: 0.7530 (mm-30) REVERT: B 42 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7882 (mttm) REVERT: B 65 ASN cc_start: 0.7767 (t0) cc_final: 0.7202 (t0) REVERT: D 92 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8154 (mttt) REVERT: E 11 ASP cc_start: 0.7814 (m-30) cc_final: 0.7373 (m-30) REVERT: E 84 GLU cc_start: 0.8333 (tt0) cc_final: 0.8132 (tt0) REVERT: E 157 TYR cc_start: 0.8057 (m-80) cc_final: 0.7817 (m-80) REVERT: F 7 LYS cc_start: 0.8039 (tttm) cc_final: 0.7819 (tttm) REVERT: F 44 ASN cc_start: 0.7791 (m-40) cc_final: 0.7559 (m-40) REVERT: G 19 ARG cc_start: 0.7954 (mpt90) cc_final: 0.7044 (mmm160) REVERT: H 137 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7398 (ttt180) REVERT: I 10 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7098 (tptp) REVERT: I 31 MET cc_start: 0.8285 (mtt) cc_final: 0.7907 (mtt) REVERT: I 164 ARG cc_start: 0.7428 (mtm110) cc_final: 0.7200 (mtm110) REVERT: I 237 GLN cc_start: 0.8325 (mt0) cc_final: 0.7978 (mt0) REVERT: I 303 MET cc_start: 0.8535 (mtt) cc_final: 0.8172 (mtt) REVERT: J 40 GLU cc_start: 0.7936 (tp30) cc_final: 0.7403 (mm-30) REVERT: J 65 ASN cc_start: 0.7624 (m-40) cc_final: 0.7339 (t0) REVERT: J 68 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8244 (mt-10) REVERT: Y 17 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8671 (mp) REVERT: Y 97 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8216 (p) REVERT: Z 10 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7553 (mptt) REVERT: Z 86 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7415 (ttm-80) REVERT: Z 173 LEU cc_start: 0.4647 (OUTLIER) cc_final: 0.4179 (tm) REVERT: Z 183 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8448 (tptm) REVERT: Z 230 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7806 (mppt) REVERT: Z 255 ASP cc_start: 0.8452 (m-30) cc_final: 0.8239 (m-30) outliers start: 64 outliers final: 22 residues processed: 340 average time/residue: 1.5268 time to fit residues: 566.2890 Evaluate side-chains 316 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 C residue 8 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 241 GLN 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 H residue 97 SER Chi-restraints excluded: chain H residue 113 THR 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 117 TRP Chi-restraints excluded: chain Y residue 17 LEU 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 149 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 5 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 142 optimal weight: 0.0050 chunk 21 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 159 GLN I 179 GLN Y 28 HIS ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Z 238 GLN Z 239 GLN Z 241 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100696 restraints weight = 16950.284| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.37 r_work: 0.3097 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15750 Z= 0.124 Angle : 0.556 8.067 21384 Z= 0.291 Chirality : 0.041 0.231 2565 Planarity : 0.005 0.063 2610 Dihedral : 4.436 27.172 2191 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 3.73 % Allowed : 22.14 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2010 helix: 2.29 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.58 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 26 HIS 0.003 0.001 HIS Z 298 PHE 0.010 0.001 PHE E 161 TYR 0.009 0.001 TYR J 14 ARG 0.009 0.001 ARG Z 164 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 1030) hydrogen bonds : angle 3.74621 ( 3084) SS BOND : bond 0.01648 ( 3) SS BOND : angle 3.99402 ( 6) covalent geometry : bond 0.00262 (15747) covalent geometry : angle 0.55192 (21378) *********************** 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 362 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 1.786 Fit side-chains REVERT: A 41 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8039 (ptt) REVERT: B 40 GLU cc_start: 0.7921 (tp30) cc_final: 0.7516 (mm-30) REVERT: B 42 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7859 (mttm) REVERT: B 65 ASN cc_start: 0.7819 (t0) cc_final: 0.7239 (t0) REVERT: D 92 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8139 (mttt) REVERT: E 11 ASP cc_start: 0.7831 (m-30) cc_final: 0.7450 (m-30) REVERT: E 84 GLU cc_start: 0.8337 (tt0) cc_final: 0.8092 (tt0) REVERT: E 157 TYR cc_start: 0.8040 (m-80) cc_final: 0.7789 (m-80) REVERT: E 249 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8208 (tptt) REVERT: F 7 LYS cc_start: 0.8055 (tttm) cc_final: 0.7760 (tttm) REVERT: F 44 ASN cc_start: 0.7809 (m-40) cc_final: 0.7399 (t0) REVERT: G 19 ARG cc_start: 0.7950 (mpt90) cc_final: 0.7049 (mmm160) REVERT: G 41 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7402 (ptt) REVERT: H 17 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8675 (mp) REVERT: H 137 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7339 (ttt180) REVERT: I 31 MET cc_start: 0.8285 (mtt) cc_final: 0.7920 (mtt) REVERT: I 84 GLU cc_start: 0.8300 (tt0) cc_final: 0.8035 (tt0) REVERT: I 164 ARG cc_start: 0.7448 (mtm110) cc_final: 0.7002 (mtm110) REVERT: I 237 GLN cc_start: 0.8266 (mt0) cc_final: 0.7993 (mt0) REVERT: I 303 MET cc_start: 0.8580 (mtt) cc_final: 0.8262 (mtt) REVERT: J 39 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7385 (mm-30) REVERT: J 40 GLU cc_start: 0.8003 (tp30) cc_final: 0.7494 (mm-30) REVERT: J 60 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7920 (ttp-110) REVERT: J 65 ASN cc_start: 0.7651 (m-40) cc_final: 0.7442 (t0) REVERT: J 68 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8366 (mt-10) REVERT: Y 17 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8695 (mp) REVERT: Y 97 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8169 (p) REVERT: Z 10 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7549 (mptt) REVERT: Z 86 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7435 (ttm-80) REVERT: Z 173 LEU cc_start: 0.4589 (OUTLIER) cc_final: 0.4120 (tm) REVERT: Z 183 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8440 (tptm) REVERT: Z 230 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7761 (mppt) outliers start: 60 outliers final: 25 residues processed: 342 average time/residue: 1.4416 time to fit residues: 539.6159 Evaluate side-chains 326 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 C residue 8 VAL Chi-restraints excluded: chain D residue 17 LEU 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 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 41 MET Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 113 THR 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 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 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 149 MET Chi-restraints excluded: chain Y residue 152 VAL 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 230 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 170 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 157 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 61 HIS I 179 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Z 239 GLN Z 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095292 restraints weight = 16697.715| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.35 r_work: 0.3022 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.7226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 15750 Z= 0.187 Angle : 0.666 10.591 21384 Z= 0.352 Chirality : 0.046 0.281 2565 Planarity : 0.005 0.064 2610 Dihedral : 4.867 41.213 2191 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.93 % Favored : 95.77 % Rotamer: Outliers : 4.23 % Allowed : 21.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2010 helix: 2.05 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.58 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 26 HIS 0.006 0.002 HIS Z 61 PHE 0.012 0.002 PHE D 211 TYR 0.019 0.002 TYR C 9 ARG 0.010 0.001 ARG Z 164 Details of bonding type rmsd hydrogen bonds : bond 0.05317 ( 1030) hydrogen bonds : angle 4.03374 ( 3084) SS BOND : bond 0.01906 ( 3) SS BOND : angle 5.30017 ( 6) covalent geometry : bond 0.00433 (15747) covalent geometry : angle 0.65984 (21378) *********************** 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 361 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 293 time to evaluate : 1.791 Fit side-chains REVERT: A 41 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8053 (ptt) REVERT: B 9 ASN cc_start: 0.8032 (m-40) cc_final: 0.7715 (m-40) REVERT: B 29 ASP cc_start: 0.7808 (m-30) cc_final: 0.7598 (m-30) REVERT: B 39 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 40 GLU cc_start: 0.8024 (tp30) cc_final: 0.7619 (mm-30) REVERT: B 42 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7976 (mttm) REVERT: C 41 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8136 (ptt) REVERT: D 92 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8260 (ttmt) REVERT: E 11 ASP cc_start: 0.7952 (m-30) cc_final: 0.7570 (m-30) REVERT: E 152 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8800 (mtt) REVERT: E 157 TYR cc_start: 0.8160 (m-80) cc_final: 0.7903 (m-80) REVERT: E 169 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7070 (pp) REVERT: E 249 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8220 (tptt) REVERT: F 7 LYS cc_start: 0.8122 (tttm) cc_final: 0.7823 (tttm) REVERT: F 44 ASN cc_start: 0.7807 (m-40) cc_final: 0.7539 (m-40) REVERT: G 19 ARG cc_start: 0.8013 (mpt90) cc_final: 0.7221 (mmm160) REVERT: H 137 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7439 (ttt180) REVERT: I 31 MET cc_start: 0.8479 (mtt) cc_final: 0.8083 (mtt) REVERT: I 237 GLN cc_start: 0.8366 (mt0) cc_final: 0.7959 (mt0) REVERT: I 241 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: I 303 MET cc_start: 0.8688 (mtt) cc_final: 0.8356 (mtt) REVERT: J 39 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7536 (mm-30) REVERT: J 40 GLU cc_start: 0.7976 (tp30) cc_final: 0.7744 (mm-30) REVERT: J 68 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8454 (mt-10) REVERT: Z 10 LYS cc_start: 0.7841 (ttmt) cc_final: 0.7545 (tptt) REVERT: Z 86 ARG cc_start: 0.7969 (ttt-90) cc_final: 0.7521 (ttm-80) REVERT: Z 173 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.4326 (tm) REVERT: Z 230 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7925 (mppt) REVERT: Z 250 ILE cc_start: 0.8789 (mm) cc_final: 0.8562 (mm) outliers start: 68 outliers final: 35 residues processed: 336 average time/residue: 1.3407 time to fit residues: 492.9841 Evaluate side-chains 328 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 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 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 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 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR 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 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 9 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 136 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Z 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092822 restraints weight = 16828.262| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.35 r_work: 0.2987 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 15750 Z= 0.247 Angle : 0.751 12.024 21384 Z= 0.397 Chirality : 0.050 0.296 2565 Planarity : 0.006 0.067 2610 Dihedral : 5.231 59.445 2191 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.03 % Favored : 95.67 % Rotamer: Outliers : 4.79 % Allowed : 20.46 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 2010 helix: 1.80 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 26 HIS 0.008 0.002 HIS Y 28 PHE 0.015 0.002 PHE E 65 TYR 0.034 0.003 TYR C 9 ARG 0.014 0.001 ARG I 164 Details of bonding type rmsd hydrogen bonds : bond 0.05941 ( 1030) hydrogen bonds : angle 4.21765 ( 3084) SS BOND : bond 0.02386 ( 3) SS BOND : angle 5.95426 ( 6) covalent geometry : bond 0.00588 (15747) covalent geometry : angle 0.74435 (21378) *********************** 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 367 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 290 time to evaluate : 1.765 Fit side-chains REVERT: A 41 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8098 (ptt) REVERT: B 9 ASN cc_start: 0.8053 (m-40) cc_final: 0.7760 (m-40) REVERT: B 29 ASP cc_start: 0.7844 (m-30) cc_final: 0.7614 (m-30) REVERT: B 39 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7311 (mm-30) REVERT: B 40 GLU cc_start: 0.8079 (tp30) cc_final: 0.7776 (mm-30) REVERT: C 41 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8155 (ptt) REVERT: D 92 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8305 (ttmt) REVERT: E 11 ASP cc_start: 0.7940 (m-30) cc_final: 0.7570 (m-30) REVERT: E 152 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8811 (mtt) REVERT: E 251 THR cc_start: 0.8932 (m) cc_final: 0.8608 (t) REVERT: F 7 LYS cc_start: 0.8227 (tttm) cc_final: 0.7964 (tttm) REVERT: F 44 ASN cc_start: 0.7814 (m-40) cc_final: 0.7608 (m-40) REVERT: G 12 ASN cc_start: 0.8342 (m-40) cc_final: 0.7390 (p0) REVERT: G 19 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7248 (mmm160) REVERT: H 137 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.7421 (ttt180) REVERT: H 176 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8497 (mmm) REVERT: I 31 MET cc_start: 0.8584 (mtt) cc_final: 0.8243 (mtt) REVERT: I 164 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7050 (mpt-90) REVERT: I 178 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7931 (mp) REVERT: I 241 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: I 303 MET cc_start: 0.8699 (mtt) cc_final: 0.8364 (mtt) REVERT: J 39 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7536 (mm-30) REVERT: Z 10 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7535 (tptt) REVERT: Z 142 ILE cc_start: 0.8834 (pp) cc_final: 0.8591 (mt) REVERT: Z 173 LEU cc_start: 0.4726 (OUTLIER) cc_final: 0.4171 (tm) REVERT: Z 223 ASP cc_start: 0.7707 (m-30) cc_final: 0.7363 (m-30) REVERT: Z 230 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8014 (mppt) REVERT: Z 241 GLN cc_start: 0.7851 (tt0) cc_final: 0.7317 (mt0) outliers start: 77 outliers final: 44 residues processed: 342 average time/residue: 1.4584 time to fit residues: 546.6425 Evaluate side-chains 342 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 17 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 86 TRP 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 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET 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 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 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 152 VAL Chi-restraints excluded: chain H residue 176 MET 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 212 VAL Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 17 THR 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 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 207 GLU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 130 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 212 VAL Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 0.0030 chunk 115 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- 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 237 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096084 restraints weight = 16830.574| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.36 r_work: 0.3040 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 15750 Z= 0.153 Angle : 0.626 10.562 21384 Z= 0.329 Chirality : 0.043 0.271 2565 Planarity : 0.005 0.062 2610 Dihedral : 4.882 43.823 2191 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.73 % Favored : 96.07 % Rotamer: Outliers : 3.36 % Allowed : 22.01 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2010 helix: 2.12 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.64 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 26 HIS 0.004 0.001 HIS Y 28 PHE 0.010 0.001 PHE Y 211 TYR 0.012 0.001 TYR B 14 ARG 0.010 0.001 ARG Z 164 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 1030) hydrogen bonds : angle 3.96937 ( 3084) SS BOND : bond 0.02398 ( 3) SS BOND : angle 5.22035 ( 6) covalent geometry : bond 0.00344 (15747) covalent geometry : angle 0.62019 (21378) *********************** 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 343 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 289 time to evaluate : 1.745 Fit side-chains REVERT: A 41 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8130 (ptt) REVERT: B 9 ASN cc_start: 0.7995 (m-40) cc_final: 0.7672 (m-40) REVERT: B 29 ASP cc_start: 0.7817 (m-30) cc_final: 0.7614 (m-30) REVERT: B 39 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 40 GLU cc_start: 0.8036 (tp30) cc_final: 0.7735 (mm-30) REVERT: B 42 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7950 (mttm) REVERT: B 84 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8106 (ptpt) REVERT: D 92 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8271 (ttmt) REVERT: E 11 ASP cc_start: 0.7959 (m-30) cc_final: 0.7656 (m-30) REVERT: E 249 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8205 (tptt) REVERT: F 7 LYS cc_start: 0.8160 (tttm) cc_final: 0.7885 (tttm) REVERT: G 19 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7215 (mmm160) REVERT: H 137 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.7332 (ttt180) REVERT: H 176 MET cc_start: 0.8660 (tpp) cc_final: 0.8392 (mmm) REVERT: I 31 MET cc_start: 0.8541 (mtt) cc_final: 0.8174 (mtt) REVERT: I 84 GLU cc_start: 0.8471 (tt0) cc_final: 0.8208 (tt0) REVERT: I 164 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7050 (mpt-90) REVERT: I 241 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6986 (mp10) REVERT: J 39 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7382 (mm-30) REVERT: J 40 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7666 (mm-30) REVERT: J 65 ASN cc_start: 0.7888 (t0) cc_final: 0.7677 (t0) REVERT: Z 10 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7507 (tptt) REVERT: Z 173 LEU cc_start: 0.4730 (OUTLIER) cc_final: 0.4186 (tm) REVERT: Z 223 ASP cc_start: 0.7636 (m-30) cc_final: 0.7351 (m-30) REVERT: Z 230 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7964 (mppt) REVERT: Z 241 GLN cc_start: 0.7985 (tt0) cc_final: 0.7387 (mt0) REVERT: Z 250 ILE cc_start: 0.8795 (mm) cc_final: 0.8591 (mt) outliers start: 54 outliers final: 34 residues processed: 325 average time/residue: 1.4574 time to fit residues: 519.7336 Evaluate side-chains 326 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 286 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 28 LYS 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 132 LYS Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 208 THR 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 152 VAL Chi-restraints excluded: chain H residue 178 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 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 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 130 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 137 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 171 optimal weight: 0.0010 chunk 34 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN D 125 HIS E 179 GLN I 237 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 = 0.3618 r_free = 0.3618 target = 0.131517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100044 restraints weight = 16914.923| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.35 r_work: 0.3097 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.7375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15750 Z= 0.125 Angle : 0.572 9.670 21384 Z= 0.299 Chirality : 0.041 0.217 2565 Planarity : 0.005 0.053 2610 Dihedral : 4.594 28.408 2191 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 2.05 % Allowed : 23.32 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.19), residues: 2010 helix: 2.32 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.55 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 26 HIS 0.003 0.001 HIS Z 298 PHE 0.008 0.001 PHE Y 211 TYR 0.012 0.001 TYR J 14 ARG 0.011 0.001 ARG Z 164 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 1030) hydrogen bonds : angle 3.77459 ( 3084) SS BOND : bond 0.02213 ( 3) SS BOND : angle 4.13280 ( 6) covalent geometry : bond 0.00265 (15747) covalent geometry : angle 0.56807 (21378) *********************** 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 331 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 298 time to evaluate : 1.647 Fit side-chains REVERT: A 41 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8093 (ptt) REVERT: B 9 ASN cc_start: 0.7991 (m-40) cc_final: 0.7693 (m-40) REVERT: B 39 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7321 (mm-30) REVERT: B 40 GLU cc_start: 0.7956 (tp30) cc_final: 0.7667 (mm-30) REVERT: D 92 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8168 (ttmt) REVERT: E 11 ASP cc_start: 0.7923 (m-30) cc_final: 0.7647 (m-30) REVERT: E 249 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8176 (tptt) REVERT: G 19 ARG cc_start: 0.7947 (mpt90) cc_final: 0.7052 (mmm160) REVERT: H 137 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7321 (ttt180) REVERT: H 176 MET cc_start: 0.8594 (tpp) cc_final: 0.8351 (mmm) REVERT: I 31 MET cc_start: 0.8445 (mtt) cc_final: 0.8163 (mtt) REVERT: I 164 ARG cc_start: 0.7540 (mtm110) cc_final: 0.6971 (mpt-90) REVERT: I 237 GLN cc_start: 0.8307 (mt0) cc_final: 0.8088 (mt0) REVERT: J 39 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7380 (mm-30) REVERT: J 40 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7669 (mm-30) REVERT: J 68 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8281 (mt-10) REVERT: Z 10 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7592 (tptt) REVERT: Z 173 LEU cc_start: 0.4767 (OUTLIER) cc_final: 0.4184 (tm) REVERT: Z 183 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8299 (tttm) REVERT: Z 233 GLN cc_start: 0.8248 (tt0) cc_final: 0.8036 (tt0) REVERT: Z 241 GLN cc_start: 0.7873 (tt0) cc_final: 0.7371 (mt0) REVERT: Z 250 ILE cc_start: 0.8714 (mm) cc_final: 0.8482 (mt) outliers start: 33 outliers final: 20 residues processed: 324 average time/residue: 1.4070 time to fit residues: 496.7749 Evaluate side-chains 311 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET 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 E residue 117 TRP Chi-restraints excluded: chain E residue 208 THR 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 H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain I residue 22 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 Z residue 19 SER Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095494 restraints weight = 16886.510| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.37 r_work: 0.3028 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.7433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 15750 Z= 0.180 Angle : 0.672 12.401 21384 Z= 0.352 Chirality : 0.045 0.273 2565 Planarity : 0.005 0.090 2610 Dihedral : 4.871 35.749 2191 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.08 % Favored : 95.62 % Rotamer: Outliers : 2.30 % Allowed : 23.20 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2010 helix: 2.12 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 26 HIS 0.006 0.001 HIS Z 61 PHE 0.011 0.002 PHE E 65 TYR 0.019 0.002 TYR B 14 ARG 0.013 0.001 ARG Z 164 Details of bonding type rmsd hydrogen bonds : bond 0.05069 ( 1030) hydrogen bonds : angle 3.97692 ( 3084) SS BOND : bond 0.02615 ( 3) SS BOND : angle 5.78049 ( 6) covalent geometry : bond 0.00417 (15747) covalent geometry : angle 0.66501 (21378) ********************** 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 321 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 1.966 Fit side-chains REVERT: A 41 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8076 (ptt) REVERT: B 9 ASN cc_start: 0.8016 (m-40) cc_final: 0.7705 (m-40) REVERT: B 39 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 40 GLU cc_start: 0.8023 (tp30) cc_final: 0.7731 (mm-30) REVERT: B 42 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7996 (mttm) REVERT: D 92 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8274 (tttt) REVERT: E 11 ASP cc_start: 0.7971 (m-30) cc_final: 0.7662 (m-30) REVERT: E 249 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8155 (tptt) REVERT: G 19 ARG cc_start: 0.8014 (mpt90) cc_final: 0.7189 (mmm160) REVERT: H 137 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7383 (ttt180) REVERT: H 176 MET cc_start: 0.8667 (tpp) cc_final: 0.8411 (mmm) REVERT: I 31 MET cc_start: 0.8565 (mtt) cc_final: 0.8187 (mtt) REVERT: I 164 ARG cc_start: 0.7551 (mtm110) cc_final: 0.6971 (mpt-90) REVERT: I 237 GLN cc_start: 0.8303 (mt0) cc_final: 0.8097 (mt0) REVERT: J 39 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7365 (mm-30) REVERT: Z 173 LEU cc_start: 0.4752 (OUTLIER) cc_final: 0.4125 (tm) REVERT: Z 223 ASP cc_start: 0.7647 (m-30) cc_final: 0.7350 (m-30) REVERT: Z 241 GLN cc_start: 0.7906 (tt0) cc_final: 0.7421 (mt0) outliers start: 37 outliers final: 27 residues processed: 312 average time/residue: 1.5211 time to fit residues: 516.5032 Evaluate side-chains 310 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 2.585 ------------------------------------------------------------------------------- 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 28 LYS 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 E residue 117 TRP Chi-restraints excluded: chain E residue 208 THR 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 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR 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 J residue 86 TRP 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 130 SER Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 76 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** E 238 GLN I 179 GLN I 238 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.095646 restraints weight = 16702.773| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.33 r_work: 0.3030 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 15750 Z= 0.175 Angle : 0.668 12.518 21384 Z= 0.349 Chirality : 0.045 0.271 2565 Planarity : 0.005 0.084 2610 Dihedral : 4.921 40.132 2191 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.83 % Favored : 95.92 % Rotamer: Outliers : 2.61 % Allowed : 22.76 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2010 helix: 2.07 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 26 HIS 0.005 0.001 HIS Y 28 PHE 0.011 0.002 PHE D 211 TYR 0.019 0.002 TYR B 14 ARG 0.013 0.001 ARG Z 164 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 1030) hydrogen bonds : angle 4.00517 ( 3084) SS BOND : bond 0.02601 ( 3) SS BOND : angle 5.73467 ( 6) covalent geometry : bond 0.00405 (15747) covalent geometry : angle 0.66086 (21378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16993.24 seconds wall clock time: 296 minutes 5.43 seconds (17765.43 seconds total)