Starting phenix.real_space_refine on Mon May 19 17:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmi_41390/05_2025/8tmi_41390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmi_41390/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmi_41390/05_2025/8tmi_41390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmi_41390/05_2025/8tmi_41390.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmi_41390/05_2025/8tmi_41390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmi_41390/05_2025/8tmi_41390.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.88, per 1000 atoms: 0.61 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: 4.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.85 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: 5.98 Time building geometry restraints manager: 5.32 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 41.270 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.890 ------------------------------------------------------------------------------- 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 : 11.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (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 TRP 0.011 0.001 TRP D 350 HIS 0.017 0.001 HIS C 212 PHE 0.033 0.001 PHE C 306 TYR 0.034 0.002 TYR B 171 ARG 0.010 0.001 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.16556 ( 1045) hydrogen bonds : angle 6.45924 ( 3036) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.74775 ( 8) covalent geometry : bond 0.00391 (18126) covalent geometry : angle 0.60827 (24584) *********************** 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 : 1.852 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: 0.2821 time to fit residues: 171.7697 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 : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.0870 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4079 r_free = 0.4079 target = 0.199360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.155177 restraints weight = 21460.707| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.88 r_work: 0.3237 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 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 = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18130 Z= 0.166 Angle : 0.608 7.234 24592 Z= 0.328 Chirality : 0.044 0.190 2783 Planarity : 0.005 0.051 3076 Dihedral : 4.569 24.612 2396 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.21 % Allowed : 8.65 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2143 helix: 2.02 (0.16), residues: 962 sheet: 1.25 (0.24), residues: 456 loop : -1.20 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 325 HIS 0.006 0.001 HIS C 212 PHE 0.027 0.001 PHE C 306 TYR 0.020 0.001 TYR B 171 ARG 0.007 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.05988 ( 1045) hydrogen bonds : angle 4.94743 ( 3036) SS BOND : bond 0.00451 ( 4) SS BOND : angle 0.60119 ( 8) covalent geometry : bond 0.00371 (18126) covalent geometry : angle 0.60845 (24584) *********************** 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 416 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 392 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7120 (tp30) cc_final: 0.6738 (tp30) REVERT: F 87 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7491 (mtt180) REVERT: A 152 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 191 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8385 (mm-30) REVERT: A 198 GLU cc_start: 0.7232 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 237 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7121 (mtp85) REVERT: B 289 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 32 MET cc_start: 0.7652 (mmm) cc_final: 0.7293 (mmm) REVERT: C 39 PHE cc_start: 0.7874 (p90) cc_final: 0.7534 (p90) REVERT: C 98 LYS cc_start: 0.6895 (tmtt) cc_final: 0.6533 (tptp) REVERT: C 189 ASP cc_start: 0.8864 (t70) cc_final: 0.8379 (t0) REVERT: D 105 TYR cc_start: 0.7038 (p90) cc_final: 0.6634 (p90) REVERT: D 112 MET cc_start: 0.6866 (mtt) cc_final: 0.6574 (mtt) REVERT: D 125 GLU cc_start: 0.6889 (mp0) cc_final: 0.6571 (mp0) REVERT: D 255 TYR cc_start: 0.5787 (t80) cc_final: 0.4986 (t80) REVERT: D 311 TYR cc_start: 0.7436 (m-10) cc_final: 0.7052 (m-10) REVERT: E 133 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7160 (mmtt) REVERT: E 200 LEU cc_start: 0.7904 (tp) cc_final: 0.7700 (tp) REVERT: E 229 ARG cc_start: 0.8917 (mtp180) cc_final: 0.8523 (mtp180) REVERT: E 341 MET cc_start: 0.7641 (tpp) cc_final: 0.7326 (tpt) outliers start: 24 outliers final: 18 residues processed: 398 average time/residue: 0.2832 time to fit residues: 172.2754 Evaluate side-chains 375 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 357 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 305 THR 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 E residue 104 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.202633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.159936 restraints weight = 21306.050| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.49 r_work: 0.3255 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 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 = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18130 Z= 0.163 Angle : 0.581 7.051 24592 Z= 0.313 Chirality : 0.043 0.201 2783 Planarity : 0.004 0.051 3076 Dihedral : 4.525 24.550 2396 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.01 % Allowed : 12.42 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2143 helix: 2.05 (0.16), residues: 963 sheet: 1.20 (0.24), residues: 453 loop : -1.22 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 226 HIS 0.004 0.001 HIS A 257 PHE 0.018 0.001 PHE C 306 TYR 0.020 0.001 TYR B 236 ARG 0.007 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05727 ( 1045) hydrogen bonds : angle 4.68939 ( 3036) SS BOND : bond 0.00404 ( 4) SS BOND : angle 0.61048 ( 8) covalent geometry : bond 0.00370 (18126) covalent geometry : angle 0.58089 (24584) *********************** 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 407 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 367 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7494 (ttm-80) REVERT: F 1 GLU cc_start: 0.7014 (tp30) cc_final: 0.6622 (tp30) REVERT: F 87 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7471 (mtt180) REVERT: A 152 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 198 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6746 (mm-30) REVERT: A 237 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7133 (mtp85) REVERT: A 246 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: B 289 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7908 (mm-30) REVERT: C 32 MET cc_start: 0.7720 (mmm) cc_final: 0.7313 (mmm) REVERT: C 39 PHE cc_start: 0.7882 (p90) cc_final: 0.7366 (p90) REVERT: C 98 LYS cc_start: 0.6909 (tmtt) cc_final: 0.6466 (tptp) REVERT: C 193 ASP cc_start: 0.7397 (m-30) cc_final: 0.7140 (m-30) REVERT: C 256 ASP cc_start: 0.7609 (m-30) cc_final: 0.7396 (m-30) REVERT: D 105 TYR cc_start: 0.7036 (p90) cc_final: 0.6620 (p90) REVERT: D 112 MET cc_start: 0.6756 (mtt) cc_final: 0.6416 (mtt) REVERT: D 125 GLU cc_start: 0.6765 (mp0) cc_final: 0.6341 (mp0) REVERT: D 255 TYR cc_start: 0.5974 (t80) cc_final: 0.5323 (t80) REVERT: E 35 SER cc_start: 0.7498 (t) cc_final: 0.7037 (t) REVERT: E 133 LYS cc_start: 0.7696 (mmtp) cc_final: 0.7150 (mmtt) REVERT: E 229 ARG cc_start: 0.8934 (mtp180) cc_final: 0.8499 (mtp180) outliers start: 40 outliers final: 29 residues processed: 387 average time/residue: 0.2790 time to fit residues: 164.8748 Evaluate side-chains 390 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 360 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 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 136 VAL Chi-restraints excluded: chain A residue 246 GLU 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 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 C residue 78 GLU 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 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 46 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 33 optimal weight: 0.0670 chunk 192 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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 285 ASN A 314 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.193477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.146857 restraints weight = 21598.279| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.26 r_work: 0.3185 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18130 Z= 0.198 Angle : 0.602 7.536 24592 Z= 0.324 Chirality : 0.044 0.217 2783 Planarity : 0.005 0.054 3076 Dihedral : 4.612 24.475 2396 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.66 % Allowed : 14.18 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2143 helix: 1.97 (0.16), residues: 964 sheet: 1.09 (0.24), residues: 452 loop : -1.28 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 226 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.002 PHE C 306 TYR 0.022 0.002 TYR F 103 ARG 0.010 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05917 ( 1045) hydrogen bonds : angle 4.62523 ( 3036) SS BOND : bond 0.00434 ( 4) SS BOND : angle 0.72419 ( 8) covalent geometry : bond 0.00464 (18126) covalent geometry : angle 0.60246 (24584) *********************** 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 429 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 376 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: F 1 GLU cc_start: 0.7101 (tp30) cc_final: 0.6709 (tp30) REVERT: F 87 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7519 (mtt180) REVERT: A 152 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 198 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6853 (mm-30) REVERT: A 237 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7270 (mtp85) REVERT: B 201 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6580 (tm-30) REVERT: C 32 MET cc_start: 0.7785 (mmm) cc_final: 0.7445 (mmm) REVERT: C 39 PHE cc_start: 0.7857 (p90) cc_final: 0.7395 (p90) REVERT: C 189 ASP cc_start: 0.8957 (t70) cc_final: 0.8520 (t0) REVERT: D 105 TYR cc_start: 0.7058 (p90) cc_final: 0.6640 (p90) REVERT: D 255 TYR cc_start: 0.6093 (t80) cc_final: 0.5553 (t80) REVERT: E 35 SER cc_start: 0.7823 (t) cc_final: 0.7340 (t) REVERT: E 54 ARG cc_start: 0.6133 (ptt-90) cc_final: 0.5930 (ptt-90) REVERT: E 133 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7586 (mmtt) REVERT: E 229 ARG cc_start: 0.8994 (mtp180) cc_final: 0.8529 (mtp180) REVERT: E 291 MET cc_start: 0.7972 (ttm) cc_final: 0.7644 (mtp) REVERT: E 341 MET cc_start: 0.7793 (tpp) cc_final: 0.7396 (tpt) outliers start: 53 outliers final: 37 residues processed: 403 average time/residue: 0.2954 time to fit residues: 178.6649 Evaluate side-chains 399 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 362 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 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 A residue 134 ASN 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 18 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 160 ILE 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 213 GLN Chi-restraints excluded: chain C residue 277 ASP 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 142 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 116 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 211 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 205 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 83 HIS ** 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 = 0.4026 r_free = 0.4026 target = 0.194669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.149587 restraints weight = 21817.196| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.89 r_work: 0.3219 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18130 Z= 0.159 Angle : 0.576 8.164 24592 Z= 0.309 Chirality : 0.043 0.230 2783 Planarity : 0.004 0.053 3076 Dihedral : 4.517 24.644 2396 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.56 % Allowed : 15.23 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2143 helix: 2.07 (0.16), residues: 962 sheet: 1.09 (0.24), residues: 450 loop : -1.27 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 226 HIS 0.004 0.001 HIS D 257 PHE 0.014 0.001 PHE B 301 TYR 0.019 0.001 TYR F 103 ARG 0.010 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05594 ( 1045) hydrogen bonds : angle 4.49910 ( 3036) SS BOND : bond 0.00502 ( 4) SS BOND : angle 0.77341 ( 8) covalent geometry : bond 0.00360 (18126) covalent geometry : angle 0.57596 (24584) *********************** 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 423 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 372 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7045 (tp30) cc_final: 0.6590 (tp30) REVERT: F 87 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7504 (mtt180) REVERT: A 152 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7154 (mt-10) REVERT: A 198 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6719 (mm-30) REVERT: A 237 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7157 (mtp85) REVERT: A 334 MET cc_start: 0.4721 (mmt) cc_final: 0.2344 (tmm) REVERT: B 201 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6591 (tm-30) REVERT: B 289 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 24 ARG cc_start: 0.8259 (mmt90) cc_final: 0.7974 (mmt90) REVERT: C 32 MET cc_start: 0.7710 (mmm) cc_final: 0.7362 (mmm) REVERT: C 39 PHE cc_start: 0.7965 (p90) cc_final: 0.7609 (p90) REVERT: C 98 LYS cc_start: 0.7212 (tmtt) cc_final: 0.6776 (tptp) REVERT: C 189 ASP cc_start: 0.8926 (t70) cc_final: 0.8493 (t0) REVERT: D 105 TYR cc_start: 0.7011 (p90) cc_final: 0.6629 (p90) REVERT: D 255 TYR cc_start: 0.6169 (t80) cc_final: 0.5696 (t80) REVERT: E 35 SER cc_start: 0.7774 (t) cc_final: 0.7301 (t) REVERT: E 133 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7558 (mmtt) REVERT: E 229 ARG cc_start: 0.8971 (mtp180) cc_final: 0.8482 (mtp180) outliers start: 51 outliers final: 41 residues processed: 398 average time/residue: 0.2813 time to fit residues: 169.3073 Evaluate side-chains 396 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 355 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 A residue 134 ASN Chi-restraints excluded: chain A residue 180 ASP 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 160 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 224 THR 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 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 248 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 182 optimal weight: 0.0050 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 134 optimal weight: 0.0670 chunk 87 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 overall best weight: 0.8136 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN ** A 68 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.193856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.148510 restraints weight = 21620.847| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.94 r_work: 0.3196 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 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 = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18130 Z= 0.180 Angle : 0.591 8.494 24592 Z= 0.318 Chirality : 0.044 0.248 2783 Planarity : 0.005 0.060 3076 Dihedral : 4.548 24.668 2396 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.97 % Allowed : 15.64 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2143 helix: 2.04 (0.16), residues: 962 sheet: 1.02 (0.24), residues: 456 loop : -1.31 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 226 HIS 0.005 0.001 HIS H 35 PHE 0.028 0.001 PHE C 306 TYR 0.021 0.001 TYR F 103 ARG 0.013 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05721 ( 1045) hydrogen bonds : angle 4.48298 ( 3036) SS BOND : bond 0.00401 ( 4) SS BOND : angle 0.64189 ( 8) covalent geometry : bond 0.00419 (18126) covalent geometry : angle 0.59081 (24584) *********************** 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 420 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7725 (ttm-80) REVERT: F 1 GLU cc_start: 0.7066 (tp30) cc_final: 0.6557 (tp30) REVERT: F 87 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7493 (mtt180) REVERT: A 152 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 198 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6775 (mm-30) REVERT: A 232 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8775 (mm) REVERT: A 237 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7188 (mtp85) REVERT: A 291 MET cc_start: 0.8426 (mmt) cc_final: 0.8226 (mmt) REVERT: A 334 MET cc_start: 0.4941 (mmt) cc_final: 0.2486 (tmm) REVERT: B 201 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6586 (tm-30) REVERT: B 289 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7966 (mm-30) REVERT: C 24 ARG cc_start: 0.8337 (mmt90) cc_final: 0.8026 (mmt90) REVERT: C 32 MET cc_start: 0.7681 (mmm) cc_final: 0.7352 (mmm) REVERT: C 39 PHE cc_start: 0.8047 (p90) cc_final: 0.7757 (p90) REVERT: C 98 LYS cc_start: 0.7215 (tmtt) cc_final: 0.6707 (tptp) REVERT: C 189 ASP cc_start: 0.8946 (t70) cc_final: 0.8507 (t0) REVERT: D 105 TYR cc_start: 0.7082 (p90) cc_final: 0.6658 (p90) REVERT: D 189 ASP cc_start: 0.5813 (m-30) cc_final: 0.5247 (m-30) REVERT: D 255 TYR cc_start: 0.6185 (t80) cc_final: 0.5743 (t80) REVERT: E 35 SER cc_start: 0.7820 (t) cc_final: 0.7322 (t) REVERT: E 133 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7514 (mmtt) REVERT: E 163 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8260 (mmtp) REVERT: E 229 ARG cc_start: 0.8993 (mtp180) cc_final: 0.8647 (mtp180) REVERT: E 341 MET cc_start: 0.7777 (tpp) cc_final: 0.7385 (tpt) outliers start: 59 outliers final: 46 residues processed: 390 average time/residue: 0.2924 time to fit residues: 170.3754 Evaluate side-chains 404 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 357 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 134 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 LEU 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 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 192 ILE Chi-restraints excluded: chain B residue 224 THR 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 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 3 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 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** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 212 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.193183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.147602 restraints weight = 21608.738| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.98 r_work: 0.3201 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 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 = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18130 Z= 0.191 Angle : 0.603 8.848 24592 Z= 0.324 Chirality : 0.044 0.274 2783 Planarity : 0.005 0.071 3076 Dihedral : 4.583 24.705 2396 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.92 % Allowed : 16.44 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2143 helix: 1.99 (0.16), residues: 962 sheet: 0.95 (0.24), residues: 456 loop : -1.34 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 226 HIS 0.005 0.001 HIS H 35 PHE 0.019 0.001 PHE C 306 TYR 0.022 0.002 TYR F 103 ARG 0.016 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05810 ( 1045) hydrogen bonds : angle 4.48812 ( 3036) SS BOND : bond 0.00423 ( 4) SS BOND : angle 0.67013 ( 8) covalent geometry : bond 0.00448 (18126) covalent geometry : angle 0.60290 (24584) *********************** 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: 58 poor density : 373 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: F 1 GLU cc_start: 0.7066 (tp30) cc_final: 0.6590 (tp30) REVERT: F 87 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7580 (mtt180) REVERT: A 33 ASN cc_start: 0.8533 (t0) cc_final: 0.8085 (t0) REVERT: A 152 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 232 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8761 (mm) REVERT: A 237 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7192 (mtp85) REVERT: A 334 MET cc_start: 0.4949 (mmt) cc_final: 0.2489 (ttp) REVERT: B 201 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6598 (tm-30) REVERT: B 289 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7933 (mm-30) REVERT: C 32 MET cc_start: 0.7582 (mmm) cc_final: 0.7217 (mmm) REVERT: C 39 PHE cc_start: 0.8010 (p90) cc_final: 0.7741 (p90) REVERT: C 98 LYS cc_start: 0.7315 (tmtt) cc_final: 0.6825 (tptp) REVERT: C 189 ASP cc_start: 0.8910 (t70) cc_final: 0.8452 (t0) REVERT: D 255 TYR cc_start: 0.6178 (t80) cc_final: 0.5688 (t80) REVERT: E 35 SER cc_start: 0.7906 (t) cc_final: 0.7372 (t) REVERT: E 133 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7508 (mmtt) REVERT: E 163 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8293 (mmtp) REVERT: E 229 ARG cc_start: 0.8986 (mtp180) cc_final: 0.8644 (mtp180) outliers start: 58 outliers final: 44 residues processed: 404 average time/residue: 0.2925 time to fit residues: 176.8621 Evaluate side-chains 408 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 134 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 LEU 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 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 224 THR Chi-restraints excluded: chain B residue 232 LEU 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 277 ASP 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 198 GLU 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 207 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 185 optimal weight: 0.0670 chunk 131 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** L 4 GLN G 101 GLN ** A 68 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.199442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.155011 restraints weight = 21405.492| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.70 r_work: 0.3233 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 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 = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18130 Z= 0.146 Angle : 0.571 9.392 24592 Z= 0.307 Chirality : 0.043 0.275 2783 Planarity : 0.004 0.053 3076 Dihedral : 4.457 24.782 2396 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 2.51 % Allowed : 17.19 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2143 helix: 2.15 (0.16), residues: 956 sheet: 0.94 (0.24), residues: 463 loop : -1.29 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 226 HIS 0.003 0.001 HIS D 257 PHE 0.015 0.001 PHE B 301 TYR 0.018 0.001 TYR D 171 ARG 0.011 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05409 ( 1045) hydrogen bonds : angle 4.38678 ( 3036) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.54394 ( 8) covalent geometry : bond 0.00327 (18126) covalent geometry : angle 0.57122 (24584) *********************** 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 413 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 363 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7117 (tp30) cc_final: 0.6584 (tp30) REVERT: F 87 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7543 (mtt180) REVERT: A 33 ASN cc_start: 0.8581 (t0) cc_final: 0.8140 (t0) REVERT: A 152 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7236 (mt-10) REVERT: A 237 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7125 (mtp85) REVERT: A 246 GLU cc_start: 0.7703 (mp0) cc_final: 0.7375 (mp0) REVERT: A 334 MET cc_start: 0.4987 (mmt) cc_final: 0.2488 (ttp) REVERT: B 201 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6616 (tm-30) REVERT: B 289 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 24 ARG cc_start: 0.8365 (mmt90) cc_final: 0.7983 (mmt90) REVERT: C 32 MET cc_start: 0.7789 (mmm) cc_final: 0.7423 (mmm) REVERT: C 39 PHE cc_start: 0.8132 (p90) cc_final: 0.7750 (p90) REVERT: C 98 LYS cc_start: 0.7274 (tmtt) cc_final: 0.6777 (tptp) REVERT: C 125 GLU cc_start: 0.7185 (tt0) cc_final: 0.6801 (mp0) REVERT: C 189 ASP cc_start: 0.8923 (t70) cc_final: 0.8448 (t0) REVERT: D 105 TYR cc_start: 0.7178 (p90) cc_final: 0.6768 (p90) REVERT: D 178 VAL cc_start: 0.7027 (t) cc_final: 0.6794 (m) REVERT: D 255 TYR cc_start: 0.6236 (t80) cc_final: 0.5895 (t80) REVERT: E 35 SER cc_start: 0.7994 (t) cc_final: 0.7457 (t) REVERT: E 163 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8299 (mmtp) REVERT: E 229 ARG cc_start: 0.8971 (mtp180) cc_final: 0.8639 (mtp180) REVERT: E 341 MET cc_start: 0.7779 (tpp) cc_final: 0.7394 (tpt) outliers start: 50 outliers final: 43 residues processed: 386 average time/residue: 0.2826 time to fit residues: 165.0285 Evaluate side-chains 402 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 H residue 106 SER 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 A residue 134 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 1 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 224 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain C residue 213 GLN 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 198 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 180 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 202 optimal weight: 0.0000 chunk 179 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 68 HIS ** 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** ** D 74 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.195303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.147983 restraints weight = 21661.985| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.35 r_work: 0.3198 rms_B_bonded: 4.07 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: 0.7785 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18130 Z= 0.150 Angle : 0.579 9.881 24592 Z= 0.310 Chirality : 0.043 0.290 2783 Planarity : 0.004 0.054 3076 Dihedral : 4.434 24.657 2396 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 2.61 % Allowed : 17.75 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2143 helix: 2.13 (0.16), residues: 956 sheet: 0.96 (0.24), residues: 462 loop : -1.28 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 226 HIS 0.003 0.001 HIS B 120 PHE 0.017 0.001 PHE D 42 TYR 0.019 0.001 TYR F 103 ARG 0.010 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 1045) hydrogen bonds : angle 4.36091 ( 3036) SS BOND : bond 0.00370 ( 4) SS BOND : angle 0.57853 ( 8) covalent geometry : bond 0.00339 (18126) covalent geometry : angle 0.57949 (24584) *********************** 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 404 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 352 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7665 (tpp-160) REVERT: F 1 GLU cc_start: 0.7169 (tp30) cc_final: 0.6596 (tp30) REVERT: F 87 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7549 (mtt180) REVERT: A 33 ASN cc_start: 0.8569 (t0) cc_final: 0.8158 (t0) REVERT: A 152 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7266 (mt-10) REVERT: A 237 ARG cc_start: 0.7636 (mtp85) cc_final: 0.7103 (mtp85) REVERT: A 334 MET cc_start: 0.5030 (mmt) cc_final: 0.2439 (ttp) REVERT: B 189 ASP cc_start: 0.8207 (t0) cc_final: 0.7997 (t0) REVERT: B 201 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6682 (tm-30) REVERT: B 289 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7974 (mm-30) REVERT: C 24 ARG cc_start: 0.8417 (mmt90) cc_final: 0.7766 (mmt90) REVERT: C 32 MET cc_start: 0.7911 (mmm) cc_final: 0.7502 (mmm) REVERT: C 39 PHE cc_start: 0.8146 (p90) cc_final: 0.7736 (p90) REVERT: C 98 LYS cc_start: 0.7319 (tmtt) cc_final: 0.6826 (tptp) REVERT: C 125 GLU cc_start: 0.7150 (tt0) cc_final: 0.6768 (mp0) REVERT: C 189 ASP cc_start: 0.8952 (t70) cc_final: 0.8539 (t0) REVERT: C 313 MET cc_start: 0.5387 (OUTLIER) cc_final: 0.3955 (tpt) REVERT: D 189 ASP cc_start: 0.5669 (m-30) cc_final: 0.4779 (m-30) REVERT: D 255 TYR cc_start: 0.6208 (t80) cc_final: 0.5813 (t80) REVERT: D 302 MET cc_start: 0.8154 (mmm) cc_final: 0.7879 (mmm) REVERT: E 35 SER cc_start: 0.7975 (t) cc_final: 0.7435 (t) REVERT: E 163 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8316 (mmtp) REVERT: E 229 ARG cc_start: 0.8997 (mtp180) cc_final: 0.8669 (mtp180) outliers start: 52 outliers final: 45 residues processed: 377 average time/residue: 0.2794 time to fit residues: 159.9713 Evaluate side-chains 394 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 348 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 H residue 106 SER 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 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 A residue 134 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 1 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 224 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 314 ASN 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 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 198 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 104 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN B 314 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.191780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.144780 restraints weight = 21660.238| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.33 r_work: 0.3160 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18130 Z= 0.242 Angle : 0.650 10.235 24592 Z= 0.348 Chirality : 0.046 0.310 2783 Planarity : 0.005 0.057 3076 Dihedral : 4.652 24.587 2396 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 2.41 % Allowed : 17.75 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2143 helix: 1.93 (0.16), residues: 954 sheet: 0.90 (0.24), residues: 456 loop : -1.43 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 325 HIS 0.007 0.001 HIS H 35 PHE 0.035 0.002 PHE C 306 TYR 0.025 0.002 TYR F 103 ARG 0.011 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.06062 ( 1045) hydrogen bonds : angle 4.51689 ( 3036) SS BOND : bond 0.00511 ( 4) SS BOND : angle 0.61578 ( 8) covalent geometry : bond 0.00580 (18126) covalent geometry : angle 0.65048 (24584) ********************** 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 404 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 356 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 25 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.7445 (tpp-160) REVERT: G 5 MET cc_start: 0.8743 (mtp) cc_final: 0.8402 (mtp) REVERT: F 1 GLU cc_start: 0.7195 (tp30) cc_final: 0.6660 (tp30) REVERT: F 51 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9039 (tp) REVERT: F 87 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7640 (mtt180) REVERT: A 33 ASN cc_start: 0.8599 (t0) cc_final: 0.8334 (t0) REVERT: A 152 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7294 (mt-10) REVERT: A 237 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7224 (mtp85) REVERT: B 5 ARG cc_start: 0.6841 (ttp-170) cc_final: 0.6546 (ttp80) REVERT: B 201 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6763 (tm-30) REVERT: B 289 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 313 MET cc_start: 0.5912 (ptm) cc_final: 0.5698 (ptt) REVERT: C 24 ARG cc_start: 0.8384 (mmt90) cc_final: 0.7752 (mmt90) REVERT: C 32 MET cc_start: 0.7858 (mmm) cc_final: 0.7443 (mmm) REVERT: C 39 PHE cc_start: 0.8160 (p90) cc_final: 0.7733 (p90) REVERT: C 75 ARG cc_start: 0.8121 (tpt90) cc_final: 0.7873 (mmm160) REVERT: C 98 LYS cc_start: 0.7370 (tmtt) cc_final: 0.6943 (tmtt) REVERT: C 189 ASP cc_start: 0.8954 (t70) cc_final: 0.8545 (t0) REVERT: D 189 ASP cc_start: 0.5805 (m-30) cc_final: 0.5208 (m-30) REVERT: E 35 SER cc_start: 0.8029 (t) cc_final: 0.7511 (t) REVERT: E 133 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7500 (mmtt) REVERT: E 163 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8325 (mmtp) REVERT: E 229 ARG cc_start: 0.9008 (mtp180) cc_final: 0.8659 (mtp180) REVERT: E 291 MET cc_start: 0.7776 (mtm) cc_final: 0.7504 (mtp) REVERT: E 341 MET cc_start: 0.7788 (tpp) cc_final: 0.7462 (tpt) outliers start: 48 outliers final: 39 residues processed: 382 average time/residue: 0.2923 time to fit residues: 168.3147 Evaluate side-chains 391 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 351 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 H residue 106 SER 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 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 51 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 280 LEU 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 224 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 213 GLN 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 198 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 7 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 92 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 86 optimal weight: 0.4980 chunk 201 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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** L 4 GLN L 90 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 140 GLN B 314 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN D 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.195634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.150315 restraints weight = 21717.268| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.95 r_work: 0.3228 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 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 = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18130 Z= 0.144 Angle : 0.589 11.521 24592 Z= 0.314 Chirality : 0.043 0.299 2783 Planarity : 0.004 0.054 3076 Dihedral : 4.486 24.772 2396 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 2.06 % Allowed : 18.40 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2143 helix: 2.04 (0.16), residues: 962 sheet: 0.91 (0.24), residues: 462 loop : -1.28 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 226 HIS 0.003 0.001 HIS A 68 PHE 0.038 0.001 PHE C 306 TYR 0.017 0.001 TYR F 103 ARG 0.009 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 1045) hydrogen bonds : angle 4.36842 ( 3036) SS BOND : bond 0.00435 ( 4) SS BOND : angle 0.57480 ( 8) covalent geometry : bond 0.00317 (18126) covalent geometry : angle 0.58903 (24584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10013.86 seconds wall clock time: 173 minutes 45.46 seconds (10425.46 seconds total)