Starting phenix.real_space_refine on Thu Jul 2 22:51:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.cif" model { file = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2026/7raz_24390.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 28 5.16 5 C 6699 2.51 5 N 1799 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "B" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "C" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "D" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "E" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "F" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "G" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.61, per 1000 atoms: 0.25 Number of scatterers: 10472 At special positions: 0 Unit cell: (98.44, 97.37, 116.63, 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 28 16.00 P 7 15.00 O 1939 8.00 N 1799 7.00 C 6699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 490.3 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 42.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 94 through 128 removed outlier: 4.956A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.852A pdb=" N VAL A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 94 through 128 removed outlier: 4.723A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.878A pdb=" N VAL B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 92 through 128 removed outlier: 4.118A pdb=" N VAL C 96 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.884A pdb=" N VAL C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 92 through 128 removed outlier: 4.073A pdb=" N VAL D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.792A pdb=" N VAL D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 94 through 128 removed outlier: 4.973A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.854A pdb=" N VAL E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 92 through 128 removed outlier: 4.174A pdb=" N VAL F 96 " --> pdb=" O GLN F 92 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 197 through 212 removed outlier: 3.876A pdb=" N VAL F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 94 through 128 removed outlier: 4.956A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 Processing helix chain 'G' and resid 197 through 212 removed outlier: 3.882A pdb=" N VAL G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 7.121A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 162 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 175 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL E 145 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG E 156 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D 175 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 175 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.225A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 277 removed outlier: 6.113A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.067A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 5.734A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.038A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.005A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 5.775A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.152A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1782 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: 1.56 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1736 1.31 - 1.43: 2611 1.43 - 1.56: 6195 1.56 - 1.68: 14 1.68 - 1.81: 56 Bond restraints: 10612 Sorted by residual: bond pdb=" C8 PTY C 301 " pdb=" O7 PTY C 301 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C8 PTY B 301 " pdb=" O7 PTY B 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C8 PTY D 301 " pdb=" O7 PTY D 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C8 PTY F 301 " pdb=" O7 PTY F 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C8 PTY A 301 " pdb=" O7 PTY A 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 10607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 14127 3.37 - 6.74: 174 6.74 - 10.11: 8 10.11 - 13.48: 6 13.48 - 16.85: 7 Bond angle restraints: 14322 Sorted by residual: angle pdb=" O11 PTY D 301 " pdb=" P1 PTY D 301 " pdb=" O14 PTY D 301 " ideal model delta sigma weight residual 92.90 109.75 -16.85 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O11 PTY F 301 " pdb=" P1 PTY F 301 " pdb=" O14 PTY F 301 " ideal model delta sigma weight residual 92.90 109.71 -16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O11 PTY E 301 " pdb=" P1 PTY E 301 " pdb=" O14 PTY E 301 " ideal model delta sigma weight residual 92.90 109.61 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O11 PTY C 301 " pdb=" P1 PTY C 301 " pdb=" O14 PTY C 301 " ideal model delta sigma weight residual 92.90 109.52 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O11 PTY G 301 " pdb=" P1 PTY G 301 " pdb=" O14 PTY G 301 " ideal model delta sigma weight residual 92.90 109.35 -16.45 3.00e+00 1.11e-01 3.01e+01 ... (remaining 14317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.06: 6144 26.06 - 52.11: 213 52.11 - 78.17: 19 78.17 - 104.23: 11 104.23 - 130.28: 4 Dihedral angle restraints: 6391 sinusoidal: 2604 harmonic: 3787 Sorted by residual: dihedral pdb=" CA MET A 126 " pdb=" C MET A 126 " pdb=" N PHE A 127 " pdb=" CA PHE A 127 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C3 PTY C 301 " pdb=" O11 PTY C 301 " pdb=" P1 PTY C 301 " pdb=" O12 PTY C 301 " ideal model delta sinusoidal sigma weight residual -59.77 70.51 -130.28 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CA MET D 126 " pdb=" C MET D 126 " pdb=" N PHE D 127 " pdb=" CA PHE D 127 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1066 0.035 - 0.071: 395 0.071 - 0.106: 158 0.106 - 0.142: 43 0.142 - 0.177: 4 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA MET A 126 " pdb=" N MET A 126 " pdb=" C MET A 126 " pdb=" CB MET A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA ILE E 176 " pdb=" N ILE E 176 " pdb=" C ILE E 176 " pdb=" CB ILE E 176 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1663 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " 0.012 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE B 127 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 127 " 0.011 2.00e-02 2.50e+03 1.29e-02 2.92e+00 pdb=" CG PHE C 127 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 127 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 127 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 127 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 127 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 127 " 0.011 2.00e-02 2.50e+03 1.26e-02 2.78e+00 pdb=" CG PHE G 127 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE G 127 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 127 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE G 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 127 " 0.001 2.00e-02 2.50e+03 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1018 2.74 - 3.28: 11144 3.28 - 3.82: 17876 3.82 - 4.36: 19872 4.36 - 4.90: 34337 Nonbonded interactions: 84247 Sorted by model distance: nonbonded pdb=" O VAL A 192 " pdb=" OG SER A 232 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR F 194 " pdb=" O GLY F 229 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN B 276 " pdb=" OD1 ASP C 274 " model vdw 2.214 3.120 nonbonded pdb=" OE2 GLU F 227 " pdb=" ND2 ASN F 234 " model vdw 2.247 3.120 nonbonded pdb=" OE2 GLU B 227 " pdb=" ND2 ASN B 234 " model vdw 2.251 3.120 ... (remaining 84242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.290 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 0.069 10612 Z= 0.203 Angle : 0.871 16.852 14322 Z= 0.378 Chirality : 0.044 0.177 1666 Planarity : 0.003 0.022 1827 Dihedral : 13.501 130.284 3955 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.23), residues: 1316 helix: 2.05 (0.23), residues: 546 sheet: 0.55 (0.31), residues: 259 loop : -0.56 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 238 TYR 0.007 0.001 TYR F 135 PHE 0.030 0.002 PHE B 127 TRP 0.002 0.001 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (10612) covalent geometry : angle 0.87051 / 0.38 (14322) hydrogen bonds : bond 0.09035 / 6.25 ( 611) hydrogen bonds : angle 4.34058 / 3.15 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.414 Fit side-chains REVERT: A 149 GLN cc_start: 0.9336 (mm-40) cc_final: 0.8944 (mm-40) REVERT: A 227 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 273 MET cc_start: 0.8277 (tmm) cc_final: 0.7996 (tmm) REVERT: B 181 GLU cc_start: 0.8686 (tp30) cc_final: 0.8161 (tp30) REVERT: C 149 GLN cc_start: 0.9300 (mm-40) cc_final: 0.9009 (mm-40) REVERT: C 155 MET cc_start: 0.8507 (ptm) cc_final: 0.8176 (tmm) REVERT: C 227 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8007 (tm-30) REVERT: D 151 PHE cc_start: 0.8274 (p90) cc_final: 0.8061 (p90) REVERT: D 227 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8473 (tm-30) REVERT: F 149 GLN cc_start: 0.9309 (mm-40) cc_final: 0.9011 (mm-40) REVERT: G 227 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8583 (tm-30) REVERT: G 273 MET cc_start: 0.8361 (tmm) cc_final: 0.7890 (tmm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0888 time to fit residues: 18.6300 Evaluate side-chains 117 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 112 GLN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043862 restraints weight = 51904.360| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.11 r_work: 0.2618 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10612 Z= 0.159 Angle : 0.615 9.882 14322 Z= 0.304 Chirality : 0.044 0.186 1666 Planarity : 0.003 0.022 1827 Dihedral : 11.435 143.026 1596 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.18 % Allowed : 8.41 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1316 helix: 1.63 (0.21), residues: 560 sheet: 0.60 (0.29), residues: 273 loop : -0.54 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 256 TYR 0.014 0.001 TYR A 194 PHE 0.026 0.001 PHE G 151 TRP 0.001 0.000 TRP E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10612) covalent geometry : angle 0.61461 / 0.30 (14322) hydrogen bonds : bond 0.03851 / 2.59 ( 611) hydrogen bonds : angle 4.06210 / 2.96 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.9422 (mm-40) cc_final: 0.9028 (mm-40) REVERT: A 227 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8815 (tm-30) REVERT: A 273 MET cc_start: 0.8993 (tmm) cc_final: 0.8573 (tmm) REVERT: B 181 GLU cc_start: 0.8916 (tp30) cc_final: 0.8385 (tp30) REVERT: C 149 GLN cc_start: 0.9392 (mm-40) cc_final: 0.9103 (mm-40) REVERT: D 155 MET cc_start: 0.8723 (ptm) cc_final: 0.8464 (tmm) REVERT: D 227 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8660 (tm-30) REVERT: F 149 GLN cc_start: 0.9350 (mm-40) cc_final: 0.9039 (mm-40) REVERT: G 273 MET cc_start: 0.8960 (tmm) cc_final: 0.8600 (tmm) outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 0.0820 time to fit residues: 15.7743 Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 122 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 112 optimal weight: 0.0970 chunk 44 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043451 restraints weight = 52258.973| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.16 r_work: 0.2625 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10612 Z= 0.130 Angle : 0.610 9.772 14322 Z= 0.293 Chirality : 0.044 0.178 1666 Planarity : 0.003 0.024 1827 Dihedral : 10.649 146.404 1596 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.81 % Allowed : 12.84 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1316 helix: 1.64 (0.21), residues: 560 sheet: 0.58 (0.30), residues: 273 loop : -0.58 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 131 TYR 0.009 0.001 TYR G 135 PHE 0.020 0.001 PHE G 151 TRP 0.001 0.000 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10612) covalent geometry : angle 0.61020 / 0.29 (14322) hydrogen bonds : bond 0.03531 / 2.38 ( 611) hydrogen bonds : angle 3.92309 / 2.86 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8422 (pt0) cc_final: 0.8193 (pm20) REVERT: A 149 GLN cc_start: 0.9462 (mm-40) cc_final: 0.9052 (mm-40) REVERT: A 227 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 273 MET cc_start: 0.8976 (tmm) cc_final: 0.8221 (tmm) REVERT: B 112 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8696 (tp-100) REVERT: B 181 GLU cc_start: 0.8912 (tp30) cc_final: 0.8363 (tp30) REVERT: C 149 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9147 (mm-40) REVERT: C 155 MET cc_start: 0.8914 (ptm) cc_final: 0.8369 (tmm) REVERT: D 227 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8677 (tm-30) REVERT: E 157 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9175 (p) REVERT: E 161 LYS cc_start: 0.9036 (mmpt) cc_final: 0.8829 (mmpt) REVERT: F 149 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9055 (mm-40) REVERT: G 273 MET cc_start: 0.9021 (tmm) cc_final: 0.8458 (tmm) outliers start: 9 outliers final: 5 residues processed: 127 average time/residue: 0.0890 time to fit residues: 16.8884 Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 59 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 127 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN E 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.043986 restraints weight = 52152.425| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.25 r_work: 0.2658 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10612 Z= 0.096 Angle : 0.605 10.369 14322 Z= 0.288 Chirality : 0.044 0.173 1666 Planarity : 0.003 0.023 1827 Dihedral : 9.972 150.028 1596 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.54 % Allowed : 15.28 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1316 helix: 1.67 (0.22), residues: 560 sheet: 0.63 (0.30), residues: 273 loop : -0.61 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 256 TYR 0.005 0.001 TYR G 250 PHE 0.018 0.001 PHE D 151 TRP 0.001 0.000 TRP E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (10612) covalent geometry : angle 0.60481 / 0.29 (14322) hydrogen bonds : bond 0.03339 / 2.26 ( 611) hydrogen bonds : angle 3.80688 / 2.78 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.397 Fit side-chains REVERT: A 149 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9067 (mm-40) REVERT: A 227 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8820 (tm-30) REVERT: A 273 MET cc_start: 0.8958 (tmm) cc_final: 0.8403 (tmm) REVERT: B 112 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8602 (tp-100) REVERT: B 181 GLU cc_start: 0.8916 (tp30) cc_final: 0.8329 (tp30) REVERT: C 149 GLN cc_start: 0.9488 (mm-40) cc_final: 0.9179 (mm-40) REVERT: C 273 MET cc_start: 0.9029 (tmm) cc_final: 0.8734 (tmm) REVERT: D 227 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8586 (tm-30) REVERT: E 157 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9123 (p) REVERT: E 161 LYS cc_start: 0.8977 (mmpt) cc_final: 0.8769 (mmpt) REVERT: E 273 MET cc_start: 0.8951 (tpp) cc_final: 0.8441 (tpp) REVERT: F 149 GLN cc_start: 0.9357 (mm-40) cc_final: 0.9011 (mm-40) REVERT: G 273 MET cc_start: 0.8939 (tmm) cc_final: 0.8582 (tmm) outliers start: 17 outliers final: 9 residues processed: 131 average time/residue: 0.0870 time to fit residues: 16.7033 Evaluate side-chains 129 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.055818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043656 restraints weight = 52333.581| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 4.16 r_work: 0.2630 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10612 Z= 0.143 Angle : 0.634 10.262 14322 Z= 0.300 Chirality : 0.044 0.160 1666 Planarity : 0.003 0.023 1827 Dihedral : 9.589 152.390 1596 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.54 % Allowed : 16.73 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.22), residues: 1316 helix: 1.65 (0.22), residues: 560 sheet: 0.65 (0.30), residues: 273 loop : -0.66 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 128 TYR 0.006 0.001 TYR A 135 PHE 0.017 0.001 PHE G 151 TRP 0.002 0.000 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10612) covalent geometry : angle 0.63359 / 0.30 (14322) hydrogen bonds : bond 0.03283 / 2.22 ( 611) hydrogen bonds : angle 3.80776 / 2.78 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.410 Fit side-chains REVERT: A 149 GLN cc_start: 0.9449 (mm-40) cc_final: 0.9015 (mm-40) REVERT: A 227 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8732 (tm-30) REVERT: A 273 MET cc_start: 0.8945 (tmm) cc_final: 0.8326 (tmm) REVERT: B 112 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8602 (tp-100) REVERT: B 181 GLU cc_start: 0.8980 (tp30) cc_final: 0.8376 (tp30) REVERT: C 149 GLN cc_start: 0.9427 (mm-40) cc_final: 0.9091 (mm-40) REVERT: C 187 GLU cc_start: 0.8651 (tp30) cc_final: 0.8416 (tp30) REVERT: D 227 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8548 (tm-30) REVERT: E 157 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9025 (p) REVERT: E 161 LYS cc_start: 0.8931 (mmpt) cc_final: 0.8711 (mmpt) REVERT: E 273 MET cc_start: 0.8983 (tpp) cc_final: 0.8760 (tpp) REVERT: F 149 GLN cc_start: 0.9393 (mm-40) cc_final: 0.9005 (mm-40) REVERT: G 227 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8869 (tm-30) REVERT: G 273 MET cc_start: 0.8934 (tmm) cc_final: 0.8502 (tmm) outliers start: 17 outliers final: 8 residues processed: 127 average time/residue: 0.0885 time to fit residues: 16.6950 Evaluate side-chains 124 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 0 optimal weight: 100.0000 chunk 129 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 83 optimal weight: 0.2980 chunk 23 optimal weight: 0.0050 chunk 85 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 0.0370 overall best weight: 1.5874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043272 restraints weight = 52886.596| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.15 r_work: 0.2645 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10612 Z= 0.112 Angle : 0.633 12.106 14322 Z= 0.298 Chirality : 0.044 0.164 1666 Planarity : 0.003 0.024 1827 Dihedral : 9.075 153.821 1596 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.63 % Allowed : 17.00 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1316 helix: 1.65 (0.22), residues: 560 sheet: 0.65 (0.30), residues: 273 loop : -0.67 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.008 0.001 TYR G 135 PHE 0.024 0.001 PHE D 151 TRP 0.001 0.000 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (10612) covalent geometry : angle 0.63301 / 0.30 (14322) hydrogen bonds : bond 0.03287 / 2.23 ( 611) hydrogen bonds : angle 3.80270 / 2.80 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.368 Fit side-chains REVERT: A 149 GLN cc_start: 0.9495 (mm-40) cc_final: 0.9069 (mm-40) REVERT: A 227 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8820 (tm-30) REVERT: A 273 MET cc_start: 0.8923 (tmm) cc_final: 0.8316 (tmm) REVERT: B 112 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8629 (tp-100) REVERT: B 181 GLU cc_start: 0.8957 (tp30) cc_final: 0.8334 (tp30) REVERT: C 149 GLN cc_start: 0.9487 (mm-40) cc_final: 0.9128 (mm-40) REVERT: C 155 MET cc_start: 0.8859 (ptm) cc_final: 0.8328 (tmm) REVERT: C 187 GLU cc_start: 0.8615 (tp30) cc_final: 0.8380 (tp30) REVERT: D 227 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8577 (tm-30) REVERT: E 157 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9201 (p) REVERT: E 161 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8794 (mmpt) REVERT: F 149 GLN cc_start: 0.9423 (mm-40) cc_final: 0.8999 (mm-40) REVERT: G 273 MET cc_start: 0.8947 (tmm) cc_final: 0.8555 (tmm) outliers start: 18 outliers final: 12 residues processed: 129 average time/residue: 0.0938 time to fit residues: 17.5973 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 0.0370 chunk 83 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.043957 restraints weight = 52276.189| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.21 r_work: 0.2653 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10612 Z= 0.100 Angle : 0.659 12.272 14322 Z= 0.306 Chirality : 0.044 0.156 1666 Planarity : 0.003 0.024 1827 Dihedral : 8.713 153.238 1596 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.26 % Allowed : 17.36 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1316 helix: 1.71 (0.22), residues: 560 sheet: 0.67 (0.30), residues: 273 loop : -0.69 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 128 TYR 0.010 0.001 TYR A 135 PHE 0.021 0.001 PHE D 151 TRP 0.002 0.000 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10612) covalent geometry : angle 0.65873 / 0.31 (14322) hydrogen bonds : bond 0.03212 / 2.19 ( 611) hydrogen bonds : angle 3.80179 / 2.80 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.406 Fit side-chains REVERT: A 149 GLN cc_start: 0.9512 (mm-40) cc_final: 0.9070 (mm-40) REVERT: A 227 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8827 (tm-30) REVERT: A 273 MET cc_start: 0.8885 (tmm) cc_final: 0.8251 (tmm) REVERT: B 112 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8575 (tp-100) REVERT: B 181 GLU cc_start: 0.8952 (tp30) cc_final: 0.8320 (tp30) REVERT: C 149 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9111 (mm-40) REVERT: C 187 GLU cc_start: 0.8587 (tp30) cc_final: 0.8331 (tp30) REVERT: C 227 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8610 (tm-30) REVERT: D 227 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8657 (tm-30) REVERT: E 157 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9151 (p) REVERT: F 149 GLN cc_start: 0.9421 (mm-40) cc_final: 0.8992 (mm-40) REVERT: G 227 GLU cc_start: 0.9249 (tm-30) cc_final: 0.9006 (tm-30) REVERT: G 273 MET cc_start: 0.8957 (tmm) cc_final: 0.8455 (tmm) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 0.0807 time to fit residues: 15.5606 Evaluate side-chains 132 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 100.0000 chunk 116 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 74 optimal weight: 0.0870 chunk 93 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.054875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042646 restraints weight = 52350.419| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 4.17 r_work: 0.2630 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10612 Z= 0.138 Angle : 0.670 12.755 14322 Z= 0.313 Chirality : 0.044 0.149 1666 Planarity : 0.003 0.023 1827 Dihedral : 8.403 152.561 1596 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.90 % Allowed : 18.08 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1316 helix: 1.71 (0.22), residues: 560 sheet: 0.66 (0.30), residues: 273 loop : -0.70 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 128 TYR 0.008 0.001 TYR F 135 PHE 0.020 0.001 PHE D 151 TRP 0.001 0.000 TRP C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10612) covalent geometry : angle 0.67044 / 0.31 (14322) hydrogen bonds : bond 0.03241 / 2.20 ( 611) hydrogen bonds : angle 3.84475 / 2.82 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.395 Fit side-chains REVERT: A 149 GLN cc_start: 0.9464 (mm-40) cc_final: 0.9040 (mm-40) REVERT: A 227 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8808 (tm-30) REVERT: A 273 MET cc_start: 0.8891 (tmm) cc_final: 0.8254 (tmm) REVERT: B 112 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8555 (tp-100) REVERT: B 181 GLU cc_start: 0.8981 (tp30) cc_final: 0.8338 (tp30) REVERT: C 149 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9101 (mm-40) REVERT: C 155 MET cc_start: 0.8952 (ptm) cc_final: 0.8431 (tmm) REVERT: C 187 GLU cc_start: 0.8551 (tp30) cc_final: 0.8350 (tp30) REVERT: D 227 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8531 (tm-30) REVERT: E 157 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9125 (p) REVERT: F 127 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: F 149 GLN cc_start: 0.9427 (mm-40) cc_final: 0.9014 (mm-40) REVERT: G 273 MET cc_start: 0.8954 (tmm) cc_final: 0.8506 (tmm) outliers start: 21 outliers final: 15 residues processed: 124 average time/residue: 0.0812 time to fit residues: 14.9897 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 100.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.040725 restraints weight = 53056.830| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 4.23 r_work: 0.2559 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10612 Z= 0.265 Angle : 0.739 12.397 14322 Z= 0.355 Chirality : 0.045 0.179 1666 Planarity : 0.003 0.029 1827 Dihedral : 8.268 153.368 1596 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.08 % Allowed : 18.63 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1316 helix: 1.55 (0.22), residues: 560 sheet: 0.46 (0.29), residues: 273 loop : -0.58 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 128 TYR 0.013 0.001 TYR A 194 PHE 0.022 0.002 PHE D 151 TRP 0.004 0.001 TRP C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.26 (10612) covalent geometry : angle 0.73860 / 0.36 (14322) hydrogen bonds : bond 0.03583 / 2.43 ( 611) hydrogen bonds : angle 4.07611 / 2.98 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.420 Fit side-chains REVERT: A 149 GLN cc_start: 0.9428 (mm-40) cc_final: 0.9020 (mm-40) REVERT: A 227 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8784 (tm-30) REVERT: A 273 MET cc_start: 0.8951 (tmm) cc_final: 0.8285 (tmm) REVERT: B 112 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8546 (tp-100) REVERT: C 149 GLN cc_start: 0.9397 (mm-40) cc_final: 0.9041 (mm-40) REVERT: C 155 MET cc_start: 0.9129 (ptm) cc_final: 0.8325 (tmm) REVERT: C 227 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8619 (tm-30) REVERT: D 227 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8612 (tm-30) REVERT: E 157 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9160 (p) REVERT: F 127 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8903 (m-80) REVERT: F 149 GLN cc_start: 0.9392 (mm-40) cc_final: 0.8983 (mm-40) REVERT: G 227 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8922 (tm-30) REVERT: G 273 MET cc_start: 0.8992 (tmm) cc_final: 0.8572 (tmm) outliers start: 23 outliers final: 13 residues processed: 132 average time/residue: 0.0874 time to fit residues: 17.1156 Evaluate side-chains 126 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042205 restraints weight = 51825.372| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 4.12 r_work: 0.2609 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10612 Z= 0.117 Angle : 0.713 13.367 14322 Z= 0.333 Chirality : 0.044 0.145 1666 Planarity : 0.003 0.032 1827 Dihedral : 8.027 151.228 1596 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.72 % Allowed : 19.26 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1316 helix: 1.69 (0.22), residues: 553 sheet: 0.47 (0.29), residues: 273 loop : -0.46 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 128 TYR 0.006 0.001 TYR A 194 PHE 0.021 0.001 PHE D 151 TRP 0.002 0.000 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10612) covalent geometry : angle 0.71339 / 0.33 (14322) hydrogen bonds : bond 0.03468 / 2.35 ( 611) hydrogen bonds : angle 3.96279 / 2.90 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.376 Fit side-chains REVERT: A 149 GLN cc_start: 0.9499 (mm-40) cc_final: 0.9110 (mm-40) REVERT: A 227 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8711 (tm-30) REVERT: A 273 MET cc_start: 0.8898 (tmm) cc_final: 0.8256 (tmm) REVERT: B 112 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8512 (tp-100) REVERT: C 149 GLN cc_start: 0.9424 (mm-40) cc_final: 0.9082 (mm-40) REVERT: C 155 MET cc_start: 0.9007 (ptm) cc_final: 0.8449 (tmm) REVERT: C 227 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 155 MET cc_start: 0.8913 (ptm) cc_final: 0.8430 (tmm) REVERT: D 227 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8541 (tm-30) REVERT: E 157 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9186 (p) REVERT: F 127 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8855 (m-80) REVERT: F 149 GLN cc_start: 0.9409 (mm-40) cc_final: 0.9023 (mm-40) REVERT: G 227 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8915 (tm-30) REVERT: G 273 MET cc_start: 0.8950 (tmm) cc_final: 0.8632 (tmm) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.0752 time to fit residues: 14.8943 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 63 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042930 restraints weight = 52334.855| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.10 r_work: 0.2616 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10612 Z= 0.134 Angle : 0.705 13.148 14322 Z= 0.330 Chirality : 0.044 0.211 1666 Planarity : 0.003 0.029 1827 Dihedral : 7.807 148.690 1596 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.27 % Allowed : 20.16 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.23), residues: 1316 helix: 1.74 (0.22), residues: 553 sheet: 0.46 (0.29), residues: 273 loop : -0.47 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 128 TYR 0.007 0.001 TYR A 135 PHE 0.020 0.001 PHE D 151 TRP 0.002 0.000 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10612) covalent geometry : angle 0.70455 / 0.33 (14322) hydrogen bonds : bond 0.03417 / 2.32 ( 611) hydrogen bonds : angle 3.94674 / 2.88 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2108.63 seconds wall clock time: 36 minutes 57.52 seconds (2217.52 seconds total)