Starting phenix.real_space_refine on Sun Aug 24 09:33:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmi_41390/08_2025/8tmi_41390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmi_41390/08_2025/8tmi_41390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tmi_41390/08_2025/8tmi_41390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmi_41390/08_2025/8tmi_41390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tmi_41390/08_2025/8tmi_41390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmi_41390/08_2025/8tmi_41390.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 65 5.16 5 C 11483 2.51 5 N 2889 2.21 5 O 3283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17724 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2804 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "C" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2899 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "E" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2797 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.64, per 1000 atoms: 0.21 Number of scatterers: 17724 At special positions: 0 Unit cell: (122.82, 133.5, 160.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 4 11.99 O 3283 8.00 N 2889 7.00 C 11483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 499.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4124 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 18 sheets defined 49.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.538A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.805A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.016A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'A' and resid 46 through 51 removed outlier: 4.434A pdb=" N VAL A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 51' Processing helix chain 'A' and resid 52 through 55 removed outlier: 3.616A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.710A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.123A pdb=" N LEU A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.592A pdb=" N LYS A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 239 Proline residue: A 227 - end of helix removed outlier: 3.807A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 283 removed outlier: 3.788A pdb=" N VAL A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 313 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 326 through 345 Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.550A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.570A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 239 Proline residue: B 227 - end of helix removed outlier: 3.526A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 312 removed outlier: 3.547A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 328 through 347 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 49 through 55 removed outlier: 4.488A pdb=" N PHE C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.616A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 165 through 201 removed outlier: 3.618A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 239 Proline residue: C 227 - end of helix removed outlier: 3.531A pdb=" N VAL C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 282 removed outlier: 3.722A pdb=" N TYR C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 312 Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.124A pdb=" N ARG C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 323' Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.603A pdb=" N PHE C 345 " --> pdb=" O MET C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Proline residue: D 52 - end of helix removed outlier: 4.291A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.551A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 159 through 164 removed outlier: 4.507A pdb=" N LYS D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 202 removed outlier: 3.950A pdb=" N PHE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 229 removed outlier: 4.330A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix Processing helix chain 'D' and resid 231 through 238 Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 247 through 311 removed outlier: 4.320A pdb=" N VAL D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 326 through 349 Processing helix chain 'E' and resid 46 through 54 removed outlier: 3.655A pdb=" N LEU E 51 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.787A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.781A pdb=" N TYR E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 238 removed outlier: 3.509A pdb=" N VAL E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Proline residue: E 227 - end of helix removed outlier: 3.640A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 235 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 312 removed outlier: 3.715A pdb=" N GLY E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix removed outlier: 3.577A pdb=" N TYR E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 348 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.276A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR H 102 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN H 111 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.276A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.542A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.542A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.405A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.611A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 57 through 60 removed outlier: 5.053A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS F 96 " --> pdb=" O TRP F 116 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP F 116 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG F 98 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 57 through 60 removed outlier: 5.053A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 44 removed outlier: 4.129A pdb=" N GLU A 121 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A 116 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 44 removed outlier: 3.894A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 123 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.736A pdb=" N ASN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 31 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 44 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 29 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN C 140 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 64 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 128 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 127 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 40 through 43 removed outlier: 3.805A pdb=" N PHE D 42 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 127 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 110 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.274A pdb=" N ASP D 116 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 119 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 39 through 44 removed outlier: 3.666A pdb=" N VAL E 31 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN E 140 " --> pdb=" O ILE E 64 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3036 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5582 1.34 - 1.46: 3712 1.46 - 1.58: 8715 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 18126 Sorted by residual: bond pdb=" C SER G 31 " pdb=" N SER G 32 " ideal model delta sigma weight residual 1.334 1.308 0.026 1.79e-02 3.12e+03 2.07e+00 bond pdb=" CB PHE D 306 " pdb=" CG PHE D 306 " ideal model delta sigma weight residual 1.502 1.471 0.031 2.30e-02 1.89e+03 1.84e+00 bond pdb=" CB VAL E 199 " pdb=" CG1 VAL E 199 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.41e+00 bond pdb=" CG1 ILE A 337 " pdb=" CD1 ILE A 337 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.39e+00 bond pdb=" CA SER C 282 " pdb=" C SER C 282 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.41e-02 5.03e+03 1.16e+00 ... (remaining 18121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 23988 1.68 - 3.37: 484 3.37 - 5.05: 89 5.05 - 6.73: 20 6.73 - 8.42: 3 Bond angle restraints: 24584 Sorted by residual: angle pdb=" N VAL D 231 " pdb=" CA VAL D 231 " pdb=" C VAL D 231 " ideal model delta sigma weight residual 111.48 107.69 3.79 9.40e-01 1.13e+00 1.62e+01 angle pdb=" N GLU D 198 " pdb=" CA GLU D 198 " pdb=" CB GLU D 198 " ideal model delta sigma weight residual 110.16 115.60 -5.44 1.48e+00 4.57e-01 1.35e+01 angle pdb=" N VAL A 146 " pdb=" CA VAL A 146 " pdb=" C VAL A 146 " ideal model delta sigma weight residual 112.29 109.06 3.23 9.40e-01 1.13e+00 1.18e+01 angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 121.64 114.92 6.72 2.13e+00 2.20e-01 9.96e+00 angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 122.06 116.22 5.84 1.86e+00 2.89e-01 9.86e+00 ... (remaining 24579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9692 17.97 - 35.95: 942 35.95 - 53.92: 170 53.92 - 71.90: 33 71.90 - 89.87: 22 Dihedral angle restraints: 10859 sinusoidal: 4464 harmonic: 6395 Sorted by residual: dihedral pdb=" CA LYS B 348 " pdb=" C LYS B 348 " pdb=" N LYS B 349 " pdb=" CA LYS B 349 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP D 180 " pdb=" C ASP D 180 " pdb=" N TYR D 181 " pdb=" CA TYR D 181 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU D 228 " pdb=" C LEU D 228 " pdb=" N ARG D 229 " pdb=" CA ARG D 229 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 10856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1908 0.038 - 0.076: 623 0.076 - 0.114: 213 0.114 - 0.152: 37 0.152 - 0.190: 2 Chirality restraints: 2783 Sorted by residual: chirality pdb=" CB VAL E 146 " pdb=" CA VAL E 146 " pdb=" CG1 VAL E 146 " pdb=" CG2 VAL E 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA VAL B 248 " pdb=" N VAL B 248 " pdb=" C VAL B 248 " pdb=" CB VAL B 248 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB VAL C 239 " pdb=" CA VAL C 239 " pdb=" CG1 VAL C 239 " pdb=" CG2 VAL C 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 2780 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 327 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO D 328 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 306 " -0.006 2.00e-02 2.50e+03 1.63e-02 4.64e+00 pdb=" CG PHE C 306 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 306 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 306 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE C 306 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 306 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 306 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 171 " 0.022 2.00e-02 2.50e+03 1.46e-02 4.24e+00 pdb=" CG TYR B 171 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 171 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 171 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 171 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 171 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 171 " 0.001 2.00e-02 2.50e+03 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 377 2.69 - 3.25: 17480 3.25 - 3.80: 27918 3.80 - 4.35: 36172 4.35 - 4.90: 61109 Nonbonded interactions: 143056 Sorted by model distance: nonbonded pdb=" OD1 ASN C 288 " pdb=" OG1 THR D 287 " model vdw 2.142 3.040 nonbonded pdb=" O GLU B 204 " pdb=" OG1 THR B 207 " model vdw 2.168 3.040 nonbonded pdb=" O GLN G 7 " pdb=" NE2 GLN G 101 " model vdw 2.190 3.120 nonbonded pdb=" OD2 ASP B 145 " pdb=" NH2 ARG B 151 " model vdw 2.213 3.120 nonbonded pdb=" OG SER L 15 " pdb=" OD2 ASP L 18 " model vdw 2.221 3.040 ... (remaining 143051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 350) selection = (chain 'B' and resid 18 through 350) selection = (chain 'C' and resid 18 through 350) selection = (chain 'D' and resid 18 through 350) selection = (chain 'E' and resid 18 through 350) } ncs_group { reference = (chain 'F' and resid 1 through 122) selection = chain 'H' } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } 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=0.49 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: 3.260 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.980 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 0.046 18130 Z= 0.171 Angle : 0.608 8.416 24592 Z= 0.327 Chirality : 0.043 0.190 2783 Planarity : 0.004 0.054 3076 Dihedral : 14.917 89.873 6723 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 2143 helix: 2.02 (0.16), residues: 948 sheet: 1.18 (0.24), residues: 473 loop : -1.18 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 202 TYR 0.034 0.002 TYR B 171 PHE 0.033 0.001 PHE C 306 TRP 0.011 0.001 TRP D 350 HIS 0.017 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00391 (18126) covalent geometry : angle 0.60827 (24584) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.74775 ( 8) hydrogen bonds : bond 0.16556 ( 1045) hydrogen bonds : angle 6.45924 ( 3036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.482 Fit side-chains REVERT: L 25 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7483 (ttm-80) REVERT: G 6 THR cc_start: 0.8396 (p) cc_final: 0.8174 (p) REVERT: F 1 GLU cc_start: 0.6654 (tp30) cc_final: 0.6431 (tp30) REVERT: A 146 VAL cc_start: 0.9340 (m) cc_final: 0.9086 (m) REVERT: A 152 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 222 ARG cc_start: 0.8256 (ttp80) cc_final: 0.8030 (ttt-90) REVERT: C 90 ILE cc_start: 0.5021 (mt) cc_final: 0.4700 (tt) REVERT: D 105 TYR cc_start: 0.6704 (p90) cc_final: 0.6359 (p90) REVERT: D 125 GLU cc_start: 0.6607 (mp0) cc_final: 0.6389 (mp0) REVERT: D 307 ILE cc_start: 0.8357 (mm) cc_final: 0.8143 (mm) REVERT: E 133 LYS cc_start: 0.7446 (mmtp) cc_final: 0.7034 (mmtt) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.1296 time to fit residues: 79.0554 Evaluate side-chains 367 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.0040 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN L 4 GLN G 80 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.200092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.156066 restraints weight = 21376.392| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.86 r_work: 0.3244 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18130 Z= 0.157 Angle : 0.599 7.082 24592 Z= 0.322 Chirality : 0.044 0.190 2783 Planarity : 0.005 0.051 3076 Dihedral : 4.554 24.613 2396 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.21 % Allowed : 8.40 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.18), residues: 2143 helix: 2.04 (0.16), residues: 961 sheet: 1.27 (0.24), residues: 454 loop : -1.16 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 5 TYR 0.020 0.001 TYR B 236 PHE 0.028 0.001 PHE C 306 TRP 0.015 0.001 TRP C 325 HIS 0.006 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00346 (18126) covalent geometry : angle 0.59914 (24584) SS BOND : bond 0.00429 ( 4) SS BOND : angle 0.62566 ( 8) hydrogen bonds : bond 0.05880 ( 1045) hydrogen bonds : angle 4.89807 ( 3036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 394 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7113 (tp30) cc_final: 0.6731 (tp30) REVERT: F 87 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7502 (mtt180) REVERT: A 22 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7161 (pttp) REVERT: A 152 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 191 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8385 (mm-30) REVERT: A 237 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7140 (mtp85) REVERT: C 32 MET cc_start: 0.7704 (mmm) cc_final: 0.7306 (mmm) REVERT: C 39 PHE cc_start: 0.7888 (p90) cc_final: 0.7534 (p90) REVERT: C 98 LYS cc_start: 0.6848 (tmtt) cc_final: 0.6480 (tptp) REVERT: C 189 ASP cc_start: 0.8862 (t70) cc_final: 0.8454 (t0) REVERT: D 105 TYR cc_start: 0.7030 (p90) cc_final: 0.6629 (p90) REVERT: D 112 MET cc_start: 0.6906 (mtt) cc_final: 0.6627 (mtt) REVERT: D 125 GLU cc_start: 0.6898 (mp0) cc_final: 0.6577 (mp0) REVERT: D 255 TYR cc_start: 0.5779 (t80) cc_final: 0.4970 (t80) REVERT: D 311 TYR cc_start: 0.7434 (m-10) cc_final: 0.7050 (m-10) REVERT: D 345 PHE cc_start: 0.7532 (m-80) cc_final: 0.7152 (m-80) REVERT: E 133 LYS cc_start: 0.7651 (mmtp) cc_final: 0.7155 (mmtt) REVERT: E 200 LEU cc_start: 0.7880 (tp) cc_final: 0.7675 (tp) REVERT: E 229 ARG cc_start: 0.8918 (mtp180) cc_final: 0.8535 (mtp180) outliers start: 24 outliers final: 18 residues processed: 400 average time/residue: 0.1107 time to fit residues: 68.8119 Evaluate side-chains 381 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 362 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 104 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 165 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN G 7 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS A 314 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN E 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.201569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.157405 restraints weight = 21573.417| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.91 r_work: 0.3224 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18130 Z= 0.188 Angle : 0.600 7.078 24592 Z= 0.323 Chirality : 0.044 0.205 2783 Planarity : 0.005 0.053 3076 Dihedral : 4.584 24.481 2396 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 12.17 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.18), residues: 2143 helix: 1.99 (0.16), residues: 964 sheet: 1.19 (0.24), residues: 455 loop : -1.27 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 67 TYR 0.021 0.001 TYR F 103 PHE 0.018 0.001 PHE C 306 TRP 0.012 0.001 TRP A 226 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00438 (18126) covalent geometry : angle 0.59951 (24584) SS BOND : bond 0.00421 ( 4) SS BOND : angle 0.69045 ( 8) hydrogen bonds : bond 0.05903 ( 1045) hydrogen bonds : angle 4.72413 ( 3036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 369 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7517 (ttm-80) REVERT: F 1 GLU cc_start: 0.7119 (tp30) cc_final: 0.6734 (tp30) REVERT: F 87 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7478 (mtt180) REVERT: A 22 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7300 (pttp) REVERT: A 152 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7105 (mt-10) REVERT: A 237 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7182 (mtp85) REVERT: C 32 MET cc_start: 0.7725 (mmm) cc_final: 0.7288 (mmm) REVERT: C 39 PHE cc_start: 0.7876 (p90) cc_final: 0.7326 (p90) REVERT: C 98 LYS cc_start: 0.6939 (tmtt) cc_final: 0.6499 (tptp) REVERT: C 193 ASP cc_start: 0.7472 (m-30) cc_final: 0.7214 (m-30) REVERT: C 256 ASP cc_start: 0.7689 (m-30) cc_final: 0.7476 (m-30) REVERT: D 105 TYR cc_start: 0.7062 (p90) cc_final: 0.6635 (p90) REVERT: D 112 MET cc_start: 0.6848 (mtt) cc_final: 0.6499 (mtt) REVERT: D 125 GLU cc_start: 0.6795 (mp0) cc_final: 0.6373 (mp0) REVERT: D 255 TYR cc_start: 0.5985 (t80) cc_final: 0.5407 (t80) REVERT: D 300 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7854 (mp) REVERT: D 311 TYR cc_start: 0.7424 (m-10) cc_final: 0.6976 (m-10) REVERT: E 35 SER cc_start: 0.7479 (t) cc_final: 0.7009 (t) REVERT: E 133 LYS cc_start: 0.7736 (mmtp) cc_final: 0.7165 (mmtt) REVERT: E 201 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7134 (tm-30) REVERT: E 229 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8504 (mtp180) outliers start: 43 outliers final: 34 residues processed: 390 average time/residue: 0.1197 time to fit residues: 70.2604 Evaluate side-chains 396 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 360 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 177 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN G 7 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 213 GLN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.201220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.158574 restraints weight = 21499.801| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.73 r_work: 0.3239 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18130 Z= 0.160 Angle : 0.572 7.894 24592 Z= 0.307 Chirality : 0.043 0.212 2783 Planarity : 0.004 0.054 3076 Dihedral : 4.508 24.619 2396 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.82 % Allowed : 13.68 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 2143 helix: 2.07 (0.16), residues: 962 sheet: 1.15 (0.24), residues: 453 loop : -1.23 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 5 TYR 0.019 0.001 TYR F 103 PHE 0.017 0.001 PHE C 306 TRP 0.010 0.001 TRP A 226 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00361 (18126) covalent geometry : angle 0.57155 (24584) SS BOND : bond 0.00402 ( 4) SS BOND : angle 0.62126 ( 8) hydrogen bonds : bond 0.05583 ( 1045) hydrogen bonds : angle 4.53631 ( 3036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 366 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7026 (tp30) cc_final: 0.6629 (tp30) REVERT: F 87 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7497 (mtt180) REVERT: A 22 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7206 (pttp) REVERT: A 152 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 237 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7159 (mtp85) REVERT: A 334 MET cc_start: 0.4923 (mmt) cc_final: 0.2474 (tmm) REVERT: B 201 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6487 (tm-30) REVERT: C 32 MET cc_start: 0.7705 (mmm) cc_final: 0.7354 (mmm) REVERT: C 39 PHE cc_start: 0.7914 (p90) cc_final: 0.7563 (p90) REVERT: C 98 LYS cc_start: 0.7099 (tmtt) cc_final: 0.6877 (tmtt) REVERT: C 189 ASP cc_start: 0.8828 (t70) cc_final: 0.8387 (t0) REVERT: C 256 ASP cc_start: 0.7681 (m-30) cc_final: 0.7471 (m-30) REVERT: D 105 TYR cc_start: 0.7005 (p90) cc_final: 0.6643 (p90) REVERT: D 255 TYR cc_start: 0.6115 (t80) cc_final: 0.5718 (t80) REVERT: E 35 SER cc_start: 0.7747 (t) cc_final: 0.7286 (t) REVERT: E 54 ARG cc_start: 0.6099 (ptt-90) cc_final: 0.5704 (ptt-90) REVERT: E 133 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7415 (mmtt) REVERT: E 229 ARG cc_start: 0.8951 (mtp180) cc_final: 0.8494 (mtp180) outliers start: 56 outliers final: 40 residues processed: 393 average time/residue: 0.1143 time to fit residues: 68.7713 Evaluate side-chains 393 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 108 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN G 101 GLN F 77 ASN A 314 ASN C 83 HIS ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.196381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.150662 restraints weight = 21571.311| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.93 r_work: 0.3236 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18130 Z= 0.141 Angle : 0.558 8.151 24592 Z= 0.300 Chirality : 0.043 0.235 2783 Planarity : 0.004 0.052 3076 Dihedral : 4.407 24.612 2396 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.56 % Allowed : 15.64 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2143 helix: 2.15 (0.16), residues: 962 sheet: 1.16 (0.24), residues: 453 loop : -1.22 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 5 TYR 0.017 0.001 TYR F 103 PHE 0.014 0.001 PHE B 301 TRP 0.010 0.001 TRP A 226 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00309 (18126) covalent geometry : angle 0.55766 (24584) SS BOND : bond 0.00788 ( 4) SS BOND : angle 0.65801 ( 8) hydrogen bonds : bond 0.05332 ( 1045) hydrogen bonds : angle 4.42067 ( 3036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 376 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: F 1 GLU cc_start: 0.7029 (tp30) cc_final: 0.6549 (tp30) REVERT: F 87 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7533 (mtt180) REVERT: A 22 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7110 (pttp) REVERT: A 152 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 237 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7155 (mtp85) REVERT: A 246 GLU cc_start: 0.7658 (mp0) cc_final: 0.7304 (mp0) REVERT: A 334 MET cc_start: 0.5001 (mmt) cc_final: 0.2409 (tmm) REVERT: B 201 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6568 (tm-30) REVERT: C 24 ARG cc_start: 0.8279 (mmt90) cc_final: 0.7997 (mmt90) REVERT: C 32 MET cc_start: 0.7752 (mmm) cc_final: 0.7378 (mmm) REVERT: C 39 PHE cc_start: 0.8034 (p90) cc_final: 0.7751 (p90) REVERT: C 98 LYS cc_start: 0.7034 (tmtt) cc_final: 0.6553 (tptp) REVERT: C 139 PHE cc_start: 0.7273 (m-80) cc_final: 0.7066 (m-80) REVERT: C 189 ASP cc_start: 0.8810 (t70) cc_final: 0.8352 (t0) REVERT: C 193 ASP cc_start: 0.7452 (m-30) cc_final: 0.7186 (m-30) REVERT: C 313 MET cc_start: 0.5130 (OUTLIER) cc_final: 0.4886 (tpp) REVERT: D 105 TYR cc_start: 0.7018 (p90) cc_final: 0.6619 (p90) REVERT: D 178 VAL cc_start: 0.7022 (t) cc_final: 0.6739 (m) REVERT: D 255 TYR cc_start: 0.5988 (t80) cc_final: 0.5577 (t80) REVERT: D 311 TYR cc_start: 0.7475 (m-10) cc_final: 0.6971 (m-10) REVERT: E 35 SER cc_start: 0.7719 (t) cc_final: 0.7239 (t) REVERT: E 133 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7537 (mmtt) REVERT: E 229 ARG cc_start: 0.8971 (mtp180) cc_final: 0.8494 (mtp180) outliers start: 51 outliers final: 40 residues processed: 401 average time/residue: 0.1283 time to fit residues: 78.6983 Evaluate side-chains 399 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 357 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 188 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 201 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN F 77 ASN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN A 314 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.194812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.148745 restraints weight = 21593.311| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.97 r_work: 0.3208 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18130 Z= 0.169 Angle : 0.581 7.179 24592 Z= 0.313 Chirality : 0.043 0.242 2783 Planarity : 0.004 0.054 3076 Dihedral : 4.458 24.411 2396 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.71 % Allowed : 16.09 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.18), residues: 2143 helix: 2.09 (0.16), residues: 961 sheet: 1.13 (0.24), residues: 450 loop : -1.26 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 5 TYR 0.020 0.001 TYR F 103 PHE 0.027 0.001 PHE C 306 TRP 0.009 0.001 TRP C 325 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00390 (18126) covalent geometry : angle 0.58080 (24584) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.66477 ( 8) hydrogen bonds : bond 0.05549 ( 1045) hydrogen bonds : angle 4.41420 ( 3036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7758 (ttm-80) REVERT: F 1 GLU cc_start: 0.7050 (tp30) cc_final: 0.6576 (tp30) REVERT: F 87 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7551 (mtt180) REVERT: A 22 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7215 (pttp) REVERT: A 152 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 232 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8777 (mm) REVERT: A 237 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7158 (mtp85) REVERT: B 201 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6653 (tm-30) REVERT: C 24 ARG cc_start: 0.8322 (mmt90) cc_final: 0.8019 (mmt90) REVERT: C 32 MET cc_start: 0.7657 (mmm) cc_final: 0.7350 (mmm) REVERT: C 39 PHE cc_start: 0.8019 (p90) cc_final: 0.7760 (p90) REVERT: C 139 PHE cc_start: 0.7092 (m-80) cc_final: 0.6803 (m-80) REVERT: C 189 ASP cc_start: 0.8880 (t70) cc_final: 0.8425 (t0) REVERT: C 193 ASP cc_start: 0.7555 (m-30) cc_final: 0.7290 (m-30) REVERT: D 32 MET cc_start: 0.5492 (mtt) cc_final: 0.5084 (mmp) REVERT: D 105 TYR cc_start: 0.7045 (p90) cc_final: 0.6647 (p90) REVERT: D 255 TYR cc_start: 0.6187 (t80) cc_final: 0.5697 (t80) REVERT: E 24 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6938 (mtm-85) REVERT: E 35 SER cc_start: 0.7763 (t) cc_final: 0.7269 (t) REVERT: E 133 LYS cc_start: 0.7854 (mmtp) cc_final: 0.7505 (mmtt) REVERT: E 163 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8242 (mmtp) REVERT: E 229 ARG cc_start: 0.8998 (mtp180) cc_final: 0.8512 (mtp180) REVERT: E 341 MET cc_start: 0.7773 (tpp) cc_final: 0.7388 (tpt) outliers start: 54 outliers final: 43 residues processed: 390 average time/residue: 0.1206 time to fit residues: 70.8546 Evaluate side-chains 409 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 76 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 169 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN D 74 GLN E 126 GLN E 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.196932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.150857 restraints weight = 21686.085| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.07 r_work: 0.3273 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18130 Z= 0.139 Angle : 0.559 7.419 24592 Z= 0.301 Chirality : 0.043 0.257 2783 Planarity : 0.004 0.061 3076 Dihedral : 4.354 24.474 2396 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.77 % Allowed : 16.69 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.18), residues: 2143 helix: 2.13 (0.16), residues: 963 sheet: 1.15 (0.24), residues: 453 loop : -1.25 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 5 TYR 0.017 0.001 TYR F 103 PHE 0.018 0.001 PHE C 306 TRP 0.008 0.001 TRP C 325 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00305 (18126) covalent geometry : angle 0.55878 (24584) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.57641 ( 8) hydrogen bonds : bond 0.05207 ( 1045) hydrogen bonds : angle 4.30981 ( 3036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 376 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7126 (tp30) cc_final: 0.6643 (tp30) REVERT: F 87 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7576 (mtt180) REVERT: A 22 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7090 (pttp) REVERT: A 152 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7138 (mt-10) REVERT: A 232 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8808 (mm) REVERT: A 237 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7080 (mtp85) REVERT: B 189 ASP cc_start: 0.8206 (t0) cc_final: 0.8003 (t0) REVERT: B 201 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6710 (tm-30) REVERT: C 24 ARG cc_start: 0.8306 (mmt90) cc_final: 0.8007 (mmt90) REVERT: C 32 MET cc_start: 0.7788 (mmm) cc_final: 0.7466 (mmm) REVERT: C 39 PHE cc_start: 0.7998 (p90) cc_final: 0.7727 (p90) REVERT: C 98 LYS cc_start: 0.7297 (tmtt) cc_final: 0.6819 (tptp) REVERT: C 139 PHE cc_start: 0.7232 (m-80) cc_final: 0.6899 (m-80) REVERT: C 189 ASP cc_start: 0.8869 (t70) cc_final: 0.8400 (t0) REVERT: C 193 ASP cc_start: 0.7579 (m-30) cc_final: 0.7287 (m-30) REVERT: D 32 MET cc_start: 0.5398 (mtt) cc_final: 0.4610 (mmp) REVERT: D 105 TYR cc_start: 0.7145 (p90) cc_final: 0.6733 (p90) REVERT: D 178 VAL cc_start: 0.6996 (t) cc_final: 0.6761 (m) REVERT: D 255 TYR cc_start: 0.6278 (t80) cc_final: 0.5741 (t80) REVERT: E 24 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: E 35 SER cc_start: 0.7847 (t) cc_final: 0.7364 (t) REVERT: E 133 LYS cc_start: 0.7784 (mmtp) cc_final: 0.7471 (mmtt) REVERT: E 163 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8262 (mmtp) REVERT: E 229 ARG cc_start: 0.8968 (mtp180) cc_final: 0.8490 (mtp180) outliers start: 55 outliers final: 44 residues processed: 400 average time/residue: 0.1218 time to fit residues: 74.0682 Evaluate side-chains 410 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 364 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 183 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 0.0980 chunk 179 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 193 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 GLN G 101 GLN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.199602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.154914 restraints weight = 21437.070| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.85 r_work: 0.3229 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18130 Z= 0.153 Angle : 0.578 8.199 24592 Z= 0.311 Chirality : 0.043 0.281 2783 Planarity : 0.004 0.075 3076 Dihedral : 4.364 24.388 2396 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.71 % Allowed : 17.14 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.18), residues: 2143 helix: 2.13 (0.16), residues: 962 sheet: 1.11 (0.24), residues: 465 loop : -1.27 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 5 TYR 0.019 0.001 TYR C 279 PHE 0.015 0.001 PHE B 301 TRP 0.007 0.001 TRP C 325 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00347 (18126) covalent geometry : angle 0.57778 (24584) SS BOND : bond 0.00393 ( 4) SS BOND : angle 0.49843 ( 8) hydrogen bonds : bond 0.05275 ( 1045) hydrogen bonds : angle 4.30801 ( 3036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7653 (tpp-160) REVERT: G 25 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7480 (mtp85) REVERT: F 1 GLU cc_start: 0.7151 (tp30) cc_final: 0.6578 (tp30) REVERT: F 87 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7567 (mtt180) REVERT: A 22 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7176 (pttp) REVERT: A 152 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7096 (mt-10) REVERT: A 232 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 237 ARG cc_start: 0.7525 (mtp85) cc_final: 0.7042 (mtt-85) REVERT: A 334 MET cc_start: 0.4825 (mmt) cc_final: 0.2424 (tmm) REVERT: B 201 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6720 (tm-30) REVERT: C 24 ARG cc_start: 0.8384 (mmt90) cc_final: 0.8032 (mmt90) REVERT: C 32 MET cc_start: 0.7840 (mmm) cc_final: 0.7494 (mmm) REVERT: C 39 PHE cc_start: 0.8109 (p90) cc_final: 0.7741 (p90) REVERT: C 98 LYS cc_start: 0.7309 (tmtt) cc_final: 0.6796 (tptp) REVERT: C 125 GLU cc_start: 0.7076 (tt0) cc_final: 0.6746 (mp0) REVERT: C 139 PHE cc_start: 0.7166 (m-80) cc_final: 0.6779 (m-80) REVERT: C 189 ASP cc_start: 0.8844 (t70) cc_final: 0.8398 (t0) REVERT: C 193 ASP cc_start: 0.7495 (m-30) cc_final: 0.7245 (m-30) REVERT: D 32 MET cc_start: 0.5304 (mtt) cc_final: 0.4410 (mmp) REVERT: D 105 TYR cc_start: 0.7171 (p90) cc_final: 0.6774 (p90) REVERT: D 178 VAL cc_start: 0.6935 (t) cc_final: 0.6714 (m) REVERT: D 255 TYR cc_start: 0.6219 (t80) cc_final: 0.5681 (t80) REVERT: E 24 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6938 (mtm-85) REVERT: E 35 SER cc_start: 0.7774 (t) cc_final: 0.7282 (t) REVERT: E 202 ARG cc_start: 0.6267 (mpp80) cc_final: 0.6010 (mpp-170) REVERT: E 229 ARG cc_start: 0.8991 (mtp180) cc_final: 0.8506 (mtp180) outliers start: 54 outliers final: 47 residues processed: 385 average time/residue: 0.1095 time to fit residues: 64.4193 Evaluate side-chains 403 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 354 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 164 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 209 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 GLN G 101 GLN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.195176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.149137 restraints weight = 21569.355| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.04 r_work: 0.3213 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18130 Z= 0.188 Angle : 0.604 8.070 24592 Z= 0.326 Chirality : 0.044 0.294 2783 Planarity : 0.005 0.064 3076 Dihedral : 4.473 24.328 2396 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 2.51 % Allowed : 17.50 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.18), residues: 2143 helix: 2.02 (0.16), residues: 963 sheet: 1.11 (0.24), residues: 456 loop : -1.36 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 5 TYR 0.022 0.002 TYR F 103 PHE 0.015 0.001 PHE B 301 TRP 0.008 0.001 TRP C 325 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00441 (18126) covalent geometry : angle 0.60421 (24584) SS BOND : bond 0.00427 ( 4) SS BOND : angle 0.68624 ( 8) hydrogen bonds : bond 0.05610 ( 1045) hydrogen bonds : angle 4.37305 ( 3036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 365 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7477 (tpp-160) REVERT: F 1 GLU cc_start: 0.7175 (tp30) cc_final: 0.6626 (tp30) REVERT: F 87 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7599 (mtt180) REVERT: A 22 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7220 (pttp) REVERT: A 152 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 232 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8823 (mm) REVERT: A 237 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7135 (mtp85) REVERT: A 334 MET cc_start: 0.4899 (mmt) cc_final: 0.2438 (tmm) REVERT: B 189 ASP cc_start: 0.8221 (t0) cc_final: 0.7999 (t0) REVERT: B 201 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6803 (tm-30) REVERT: C 24 ARG cc_start: 0.8294 (mmt90) cc_final: 0.7669 (mmt90) REVERT: C 32 MET cc_start: 0.7701 (mmm) cc_final: 0.7390 (mmm) REVERT: C 39 PHE cc_start: 0.8042 (p90) cc_final: 0.7728 (p90) REVERT: C 98 LYS cc_start: 0.7357 (tmtt) cc_final: 0.7009 (tmtt) REVERT: C 125 GLU cc_start: 0.7206 (tt0) cc_final: 0.6870 (mp0) REVERT: C 139 PHE cc_start: 0.7262 (m-80) cc_final: 0.6927 (m-80) REVERT: C 189 ASP cc_start: 0.8972 (t70) cc_final: 0.8497 (t0) REVERT: C 193 ASP cc_start: 0.7633 (m-30) cc_final: 0.7322 (m-30) REVERT: D 32 MET cc_start: 0.5482 (mtt) cc_final: 0.4856 (mmp) REVERT: D 255 TYR cc_start: 0.6296 (t80) cc_final: 0.5881 (t80) REVERT: E 24 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6969 (mtm-85) REVERT: E 35 SER cc_start: 0.7879 (t) cc_final: 0.7381 (t) REVERT: E 229 ARG cc_start: 0.9004 (mtp180) cc_final: 0.8672 (mtp180) REVERT: E 341 MET cc_start: 0.7790 (tpp) cc_final: 0.7388 (tpt) outliers start: 50 outliers final: 47 residues processed: 389 average time/residue: 0.1260 time to fit residues: 74.3104 Evaluate side-chains 412 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 51 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 0.3980 chunk 153 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.196238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.149884 restraints weight = 21450.468| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.18 r_work: 0.3198 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18130 Z= 0.160 Angle : 0.591 11.775 24592 Z= 0.317 Chirality : 0.044 0.299 2783 Planarity : 0.004 0.057 3076 Dihedral : 4.444 24.390 2396 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 2.46 % Allowed : 17.80 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2143 helix: 2.10 (0.16), residues: 957 sheet: 1.08 (0.24), residues: 463 loop : -1.32 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 5 TYR 0.020 0.001 TYR F 103 PHE 0.052 0.001 PHE C 306 TRP 0.008 0.001 TRP C 325 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00366 (18126) covalent geometry : angle 0.59056 (24584) SS BOND : bond 0.00419 ( 4) SS BOND : angle 0.56717 ( 8) hydrogen bonds : bond 0.05451 ( 1045) hydrogen bonds : angle 4.33761 ( 3036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7461 (tpp-160) REVERT: F 1 GLU cc_start: 0.7168 (tp30) cc_final: 0.6585 (tp30) REVERT: F 87 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7555 (mtt180) REVERT: A 22 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7243 (pttp) REVERT: A 152 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7169 (mt-10) REVERT: A 232 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8758 (mm) REVERT: A 237 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7046 (mtt-85) REVERT: A 334 MET cc_start: 0.4780 (mmt) cc_final: 0.2356 (tmm) REVERT: B 189 ASP cc_start: 0.8189 (t0) cc_final: 0.7971 (t0) REVERT: C 24 ARG cc_start: 0.8396 (mmt90) cc_final: 0.7685 (mmt90) REVERT: C 32 MET cc_start: 0.7826 (mmm) cc_final: 0.7444 (mmm) REVERT: C 39 PHE cc_start: 0.8086 (p90) cc_final: 0.7710 (p90) REVERT: C 98 LYS cc_start: 0.7375 (tmtt) cc_final: 0.7022 (tmtt) REVERT: C 125 GLU cc_start: 0.7149 (tt0) cc_final: 0.6771 (mp0) REVERT: C 139 PHE cc_start: 0.7296 (m-80) cc_final: 0.6945 (m-80) REVERT: C 189 ASP cc_start: 0.8921 (t70) cc_final: 0.8458 (t0) REVERT: C 193 ASP cc_start: 0.7632 (m-30) cc_final: 0.7313 (m-30) REVERT: D 32 MET cc_start: 0.5396 (mtt) cc_final: 0.4749 (mmp) REVERT: D 255 TYR cc_start: 0.6188 (t80) cc_final: 0.5787 (t80) REVERT: E 24 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6950 (mtm-85) REVERT: E 35 SER cc_start: 0.7859 (t) cc_final: 0.7333 (t) REVERT: E 229 ARG cc_start: 0.9004 (mtp180) cc_final: 0.8671 (mtp180) REVERT: E 341 MET cc_start: 0.7733 (tpp) cc_final: 0.7401 (tpt) outliers start: 49 outliers final: 46 residues processed: 388 average time/residue: 0.1288 time to fit residues: 76.0514 Evaluate side-chains 408 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 360 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 198 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.195466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.148889 restraints weight = 21712.527| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.27 r_work: 0.3214 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18130 Z= 0.175 Angle : 0.766 59.200 24592 Z= 0.434 Chirality : 0.043 0.279 2783 Planarity : 0.004 0.055 3076 Dihedral : 4.442 24.396 2396 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 2.56 % Allowed : 17.65 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.18), residues: 2143 helix: 2.10 (0.16), residues: 957 sheet: 1.08 (0.24), residues: 463 loop : -1.32 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 5 TYR 0.020 0.001 TYR F 103 PHE 0.038 0.001 PHE C 306 TRP 0.007 0.001 TRP A 226 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00397 (18126) covalent geometry : angle 0.76637 (24584) SS BOND : bond 0.00429 ( 4) SS BOND : angle 0.53278 ( 8) hydrogen bonds : bond 0.05470 ( 1045) hydrogen bonds : angle 4.33820 ( 3036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4479.33 seconds wall clock time: 77 minutes 18.62 seconds (4638.62 seconds total)