Starting phenix.real_space_refine on Mon Jul 28 21:52:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7raz_24390/07_2025/7raz_24390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7raz_24390/07_2025/7raz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2025/7raz_24390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2025/7raz_24390.map" model { file = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2025/7raz_24390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7raz_24390/07_2025/7raz_24390.cif" } resolution = 3.4 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= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 18 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: 18 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: 18 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: 18 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: 18 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: 18 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: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.29, per 1000 atoms: 0.60 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: 2.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.06 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: 3.02 Time building geometry restraints manager: 3.24 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: 6148 26.06 - 52.11: 220 52.11 - 78.17: 22 78.17 - 104.23: 11 104.23 - 130.28: 4 Dihedral angle restraints: 6405 sinusoidal: 2618 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 6402 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: 0.02 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: 0.490 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.780 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 13.679 130.284 3969 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 (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: 1.13 (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 TRP 0.002 0.001 TRP E 240 PHE 0.030 0.002 PHE B 127 TYR 0.007 0.001 TYR F 135 ARG 0.003 0.000 ARG F 238 Details of bonding type rmsd hydrogen bonds : bond 0.09035 ( 611) hydrogen bonds : angle 4.34058 ( 1782) covalent geometry : bond 0.00430 (10612) covalent geometry : angle 0.87051 (14322) *********************** 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 : 1.119 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: 0.8276 (tmm) cc_final: 0.7996 (tmm) REVERT: B 181 GLU cc_start: 0.8686 (tp30) cc_final: 0.8162 (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: 0.2157 time to fit residues: 44.2255 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 : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.3980 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3253 r_free = 0.3253 target = 0.055628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043622 restraints weight = 51839.069| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 4.06 r_work: 0.2617 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10612 Z= 0.162 Angle : 0.615 9.734 14322 Z= 0.304 Chirality : 0.044 0.184 1666 Planarity : 0.003 0.022 1827 Dihedral : 11.707 142.716 1610 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.18 % Allowed : 8.68 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1316 helix: 1.66 (0.21), residues: 560 sheet: 0.60 (0.30), residues: 273 loop : -0.53 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 251 PHE 0.025 0.001 PHE G 151 TYR 0.012 0.001 TYR A 194 ARG 0.002 0.000 ARG E 256 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 611) hydrogen bonds : angle 4.07445 ( 1782) covalent geometry : bond 0.00361 (10612) covalent geometry : angle 0.61541 (14322) *********************** 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 140 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.9419 (mm-40) cc_final: 0.9025 (mm-40) REVERT: A 227 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8834 (tm-30) REVERT: A 273 MET cc_start: 0.8996 (tmm) cc_final: 0.8581 (tmm) REVERT: B 112 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8629 (tp-100) REVERT: B 181 GLU cc_start: 0.8919 (tp30) cc_final: 0.8390 (tp30) REVERT: C 149 GLN cc_start: 0.9392 (mm-40) cc_final: 0.9100 (mm-40) REVERT: C 187 GLU cc_start: 0.8761 (tp30) cc_final: 0.8474 (tp30) REVERT: D 227 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8685 (tm-30) REVERT: F 149 GLN cc_start: 0.9347 (mm-40) cc_final: 0.9036 (mm-40) REVERT: G 273 MET cc_start: 0.8967 (tmm) cc_final: 0.8612 (tmm) outliers start: 13 outliers final: 8 residues processed: 132 average time/residue: 0.2603 time to fit residues: 49.9173 Evaluate side-chains 121 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 123 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 0.0470 chunk 94 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 overall best weight: 3.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3242 r_free = 0.3242 target = 0.055219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.042944 restraints weight = 52396.817| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.23 r_work: 0.2598 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10612 Z= 0.175 Angle : 0.616 9.778 14322 Z= 0.300 Chirality : 0.044 0.177 1666 Planarity : 0.003 0.023 1827 Dihedral : 10.830 147.557 1610 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.18 % Allowed : 12.48 % 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 (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: 0.89 (0.22), residues: 1316 helix: 1.62 (0.21), residues: 560 sheet: 0.56 (0.29), residues: 273 loop : -0.56 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 251 PHE 0.018 0.001 PHE G 151 TYR 0.009 0.001 TYR G 135 ARG 0.002 0.000 ARG F 238 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 611) hydrogen bonds : angle 3.97085 ( 1782) covalent geometry : bond 0.00390 (10612) covalent geometry : angle 0.61607 (14322) *********************** 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 135 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.422 Fit side-chains REVERT: A 134 GLU cc_start: 0.8520 (pt0) cc_final: 0.8182 (pm20) REVERT: A 149 GLN cc_start: 0.9405 (mm-40) cc_final: 0.9006 (mm-40) REVERT: A 227 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 273 MET cc_start: 0.8988 (tmm) cc_final: 0.8248 (tmm) REVERT: B 112 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8608 (tp-100) REVERT: B 181 GLU cc_start: 0.8972 (tp30) cc_final: 0.8415 (tp30) REVERT: C 149 GLN cc_start: 0.9383 (mm-40) cc_final: 0.9082 (mm-40) REVERT: C 155 MET cc_start: 0.9043 (ptm) cc_final: 0.8344 (tmm) REVERT: D 227 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8642 (tm-30) REVERT: E 157 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9125 (p) REVERT: F 149 GLN cc_start: 0.9385 (mm-40) cc_final: 0.9071 (mm-40) REVERT: F 187 GLU cc_start: 0.8482 (tp30) cc_final: 0.8275 (tp30) REVERT: G 273 MET cc_start: 0.9006 (tmm) cc_final: 0.8487 (tmm) outliers start: 13 outliers final: 9 residues processed: 127 average time/residue: 0.2567 time to fit residues: 49.0541 Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F 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 171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 9.9990 chunk 41 optimal weight: 0.0370 chunk 13 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 123 optimal weight: 0.0020 chunk 67 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** G 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 = 0.3261 r_free = 0.3261 target = 0.056143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.043847 restraints weight = 51396.163| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.22 r_work: 0.2648 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10612 Z= 0.097 Angle : 0.606 10.455 14322 Z= 0.290 Chirality : 0.044 0.170 1666 Planarity : 0.003 0.023 1827 Dihedral : 10.150 151.655 1610 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.36 % Allowed : 14.92 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1316 helix: 1.70 (0.22), residues: 560 sheet: 0.59 (0.30), residues: 273 loop : -0.61 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 251 PHE 0.016 0.001 PHE G 151 TYR 0.007 0.001 TYR A 135 ARG 0.002 0.000 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 611) hydrogen bonds : angle 3.81772 ( 1782) covalent geometry : bond 0.00203 (10612) covalent geometry : angle 0.60561 (14322) *********************** 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 138 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.136 Fit side-chains REVERT: A 149 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9065 (mm-40) REVERT: A 227 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 273 MET cc_start: 0.8979 (tmm) cc_final: 0.8482 (tmm) REVERT: B 112 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8608 (tp-100) REVERT: B 181 GLU cc_start: 0.8942 (tp30) cc_final: 0.8365 (tp30) REVERT: C 149 GLN cc_start: 0.9474 (mm-40) cc_final: 0.9165 (mm-40) REVERT: C 273 MET cc_start: 0.9026 (tmm) cc_final: 0.8709 (tmm) REVERT: D 169 LYS cc_start: 0.9693 (mtpp) cc_final: 0.9352 (ttmt) REVERT: D 227 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8591 (tm-30) REVERT: E 157 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9129 (p) REVERT: E 161 LYS cc_start: 0.8977 (mmpt) cc_final: 0.8772 (mmpt) REVERT: F 149 GLN cc_start: 0.9369 (mm-40) cc_final: 0.9059 (mm-40) REVERT: G 155 MET cc_start: 0.8731 (ptm) cc_final: 0.8471 (tmm) REVERT: G 273 MET cc_start: 0.8957 (tmm) cc_final: 0.8539 (tmm) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.2120 time to fit residues: 39.2597 Evaluate side-chains 126 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU 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 81 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.042958 restraints weight = 52139.167| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 4.13 r_work: 0.2580 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10612 Z= 0.259 Angle : 0.670 9.767 14322 Z= 0.327 Chirality : 0.044 0.155 1666 Planarity : 0.003 0.022 1827 Dihedral : 9.778 156.873 1610 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.99 % Allowed : 15.82 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1316 helix: 1.59 (0.21), residues: 560 sheet: 0.55 (0.30), residues: 273 loop : -0.59 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 251 PHE 0.016 0.001 PHE D 151 TYR 0.010 0.001 TYR A 194 ARG 0.004 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 611) hydrogen bonds : angle 3.96723 ( 1782) covalent geometry : bond 0.00568 (10612) covalent geometry : angle 0.67024 (14322) *********************** 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 140 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.116 Fit side-chains REVERT: A 149 GLN cc_start: 0.9416 (mm-40) cc_final: 0.8993 (mm-40) REVERT: A 227 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8666 (tm-30) REVERT: A 273 MET cc_start: 0.9008 (tmm) cc_final: 0.8360 (tmm) REVERT: B 112 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8641 (tp-100) REVERT: B 273 MET cc_start: 0.9016 (tmm) cc_final: 0.8487 (tmm) REVERT: C 149 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9059 (mm-40) REVERT: D 227 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8512 (tm-30) REVERT: E 157 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9042 (p) REVERT: F 126 MET cc_start: 0.9323 (ppp) cc_final: 0.9064 (ppp) REVERT: F 127 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8840 (m-80) REVERT: F 149 GLN cc_start: 0.9395 (mm-40) cc_final: 0.8978 (mm-40) REVERT: G 273 MET cc_start: 0.8997 (tmm) cc_final: 0.8604 (tmm) outliers start: 22 outliers final: 10 residues processed: 130 average time/residue: 0.2085 time to fit residues: 39.6353 Evaluate side-chains 126 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 127 PHE 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 157 THR Chi-restraints excluded: chain F 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 87 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 123 optimal weight: 0.0770 chunk 129 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3253 r_free = 0.3253 target = 0.055684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043539 restraints weight = 52304.432| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 4.11 r_work: 0.2625 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10612 Z= 0.111 Angle : 0.641 12.155 14322 Z= 0.306 Chirality : 0.044 0.166 1666 Planarity : 0.003 0.022 1827 Dihedral : 9.365 158.760 1610 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.72 % Allowed : 17.09 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1316 helix: 1.62 (0.21), residues: 560 sheet: 0.52 (0.29), residues: 273 loop : -0.63 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 251 PHE 0.018 0.001 PHE G 151 TYR 0.009 0.001 TYR B 135 ARG 0.004 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 611) hydrogen bonds : angle 3.88681 ( 1782) covalent geometry : bond 0.00245 (10612) covalent geometry : angle 0.64113 (14322) *********************** 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 137 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.190 Fit side-chains REVERT: A 149 GLN cc_start: 0.9519 (mm-40) cc_final: 0.9079 (mm-40) REVERT: A 227 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 273 MET cc_start: 0.8951 (tmm) cc_final: 0.8353 (tmm) REVERT: B 112 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8575 (tp-100) REVERT: C 149 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9120 (mm-40) REVERT: C 155 MET cc_start: 0.8619 (ptm) cc_final: 0.8344 (tmm) REVERT: C 227 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8584 (tm-30) REVERT: C 273 MET cc_start: 0.9022 (tmm) cc_final: 0.8589 (tmm) REVERT: D 155 MET cc_start: 0.8857 (ptm) cc_final: 0.8496 (tmm) REVERT: D 169 LYS cc_start: 0.9711 (mtpp) cc_final: 0.9378 (mtmt) REVERT: D 227 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8549 (tm-30) REVERT: E 157 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9226 (p) REVERT: E 161 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8872 (mmpt) REVERT: F 126 MET cc_start: 0.9280 (ppp) cc_final: 0.9053 (ppp) REVERT: F 127 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8809 (m-80) REVERT: F 149 GLN cc_start: 0.9426 (mm-40) cc_final: 0.9013 (mm-40) REVERT: G 155 MET cc_start: 0.8778 (ptm) cc_final: 0.8519 (tmm) REVERT: G 273 MET cc_start: 0.8986 (tmm) cc_final: 0.8717 (tmm) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.2213 time to fit residues: 39.6085 Evaluate side-chains 129 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 E residue 112 GLN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 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 58 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3241 r_free = 0.3241 target = 0.055068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.042896 restraints weight = 53062.414| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 4.20 r_work: 0.2589 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10612 Z= 0.186 Angle : 0.666 12.289 14322 Z= 0.317 Chirality : 0.044 0.154 1666 Planarity : 0.003 0.027 1827 Dihedral : 9.151 159.956 1610 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.26 % Allowed : 17.54 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1316 helix: 1.64 (0.21), residues: 560 sheet: 0.47 (0.29), residues: 273 loop : -0.60 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 251 PHE 0.027 0.001 PHE D 151 TYR 0.008 0.001 TYR A 194 ARG 0.007 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 611) hydrogen bonds : angle 3.94755 ( 1782) covalent geometry : bond 0.00413 (10612) covalent geometry : angle 0.66627 (14322) *********************** 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 142 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.150 Fit side-chains REVERT: A 149 GLN cc_start: 0.9453 (mm-40) cc_final: 0.9034 (mm-40) REVERT: A 227 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8746 (tm-30) REVERT: A 273 MET cc_start: 0.9020 (tmm) cc_final: 0.8380 (tmm) REVERT: B 112 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8554 (tp-100) REVERT: B 273 MET cc_start: 0.8972 (tmm) cc_final: 0.8767 (tmm) REVERT: C 149 GLN cc_start: 0.9442 (mm-40) cc_final: 0.9087 (mm-40) REVERT: C 155 MET cc_start: 0.8798 (ptm) cc_final: 0.8335 (tmm) REVERT: C 273 MET cc_start: 0.9058 (tmm) cc_final: 0.8615 (tmm) REVERT: D 155 MET cc_start: 0.8911 (ptm) cc_final: 0.8534 (tmm) REVERT: D 227 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8544 (tm-30) REVERT: E 157 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9230 (p) REVERT: E 161 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8819 (mmpt) REVERT: E 273 MET cc_start: 0.9062 (tpp) cc_final: 0.8776 (tpp) REVERT: F 126 MET cc_start: 0.9330 (ppp) cc_final: 0.9107 (ppp) REVERT: F 127 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: F 149 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8972 (mm-40) REVERT: G 155 MET cc_start: 0.8897 (ptm) cc_final: 0.8401 (tmm) REVERT: G 273 MET cc_start: 0.9022 (tmm) cc_final: 0.8707 (tmm) outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 0.2160 time to fit residues: 41.2905 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 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 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 9 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3242 r_free = 0.3242 target = 0.055251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043132 restraints weight = 52301.143| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.11 r_work: 0.2612 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10612 Z= 0.133 Angle : 0.675 12.734 14322 Z= 0.317 Chirality : 0.044 0.161 1666 Planarity : 0.003 0.023 1827 Dihedral : 8.896 160.023 1610 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.99 % Allowed : 18.35 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1316 helix: 1.68 (0.22), residues: 560 sheet: 0.47 (0.29), residues: 273 loop : -0.66 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 251 PHE 0.025 0.001 PHE D 151 TYR 0.007 0.001 TYR F 135 ARG 0.008 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 611) hydrogen bonds : angle 3.91077 ( 1782) covalent geometry : bond 0.00300 (10612) covalent geometry : angle 0.67497 (14322) *********************** 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 144 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.726 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: 0.9247 (tm-30) cc_final: 0.8766 (tm-30) REVERT: A 273 MET cc_start: 0.8968 (tmm) cc_final: 0.8345 (tmm) REVERT: B 112 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8614 (tp-100) REVERT: B 273 MET cc_start: 0.8976 (tmm) cc_final: 0.8765 (tmm) REVERT: C 149 GLN cc_start: 0.9493 (mm-40) cc_final: 0.9143 (mm-40) REVERT: C 155 MET cc_start: 0.8828 (ptm) cc_final: 0.8420 (tmm) REVERT: C 227 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8624 (tm-30) REVERT: C 273 MET cc_start: 0.9028 (tmm) cc_final: 0.8643 (tmm) REVERT: D 169 LYS cc_start: 0.9700 (mtpp) cc_final: 0.9301 (mtmt) REVERT: D 227 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8540 (tm-30) REVERT: E 157 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9231 (p) REVERT: E 161 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8852 (mmpt) REVERT: F 126 MET cc_start: 0.9336 (ppp) cc_final: 0.9136 (ppp) REVERT: F 127 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: F 149 GLN cc_start: 0.9417 (mm-40) cc_final: 0.9002 (mm-40) REVERT: G 155 MET cc_start: 0.8890 (ptm) cc_final: 0.8428 (tmm) REVERT: G 227 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8993 (tm-30) REVERT: G 273 MET cc_start: 0.9021 (tmm) cc_final: 0.8717 (tmm) outliers start: 22 outliers final: 18 residues processed: 131 average time/residue: 0.2137 time to fit residues: 42.1806 Evaluate side-chains 136 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 MET 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 175 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 127 PHE 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 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 92 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 38 optimal weight: 50.0000 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 50.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3240 r_free = 0.3240 target = 0.055211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042972 restraints weight = 52816.482| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.16 r_work: 0.2611 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1861 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= 0.132 Angle : 0.682 12.858 14322 Z= 0.318 Chirality : 0.044 0.171 1666 Planarity : 0.003 0.027 1827 Dihedral : 8.683 159.300 1610 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 18.35 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1316 helix: 1.72 (0.22), residues: 560 sheet: 0.47 (0.29), residues: 273 loop : -0.65 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 251 PHE 0.022 0.001 PHE D 151 TYR 0.005 0.001 TYR A 194 ARG 0.006 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 611) hydrogen bonds : angle 3.93955 ( 1782) covalent geometry : bond 0.00300 (10612) covalent geometry : angle 0.68166 (14322) *********************** 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 145 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.398 Fit side-chains REVERT: A 149 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9076 (mm-40) REVERT: A 227 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 273 MET cc_start: 0.8961 (tmm) cc_final: 0.8330 (tmm) REVERT: B 112 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8555 (tp-100) REVERT: B 273 MET cc_start: 0.8980 (tmm) cc_final: 0.8762 (tmm) REVERT: C 149 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9123 (mm-40) REVERT: C 155 MET cc_start: 0.8844 (ptm) cc_final: 0.8435 (tmm) REVERT: C 227 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8562 (tm-30) REVERT: C 273 MET cc_start: 0.9036 (tmm) cc_final: 0.8649 (tmm) REVERT: D 169 LYS cc_start: 0.9698 (mtpp) cc_final: 0.9356 (mtmt) REVERT: D 227 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8528 (tm-30) REVERT: E 157 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9209 (p) REVERT: E 161 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8839 (mmpt) REVERT: F 127 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8875 (m-80) REVERT: F 149 GLN cc_start: 0.9414 (mm-40) cc_final: 0.8999 (mm-40) REVERT: G 155 MET cc_start: 0.8930 (ptm) cc_final: 0.8371 (tmm) REVERT: G 273 MET cc_start: 0.9016 (tmm) cc_final: 0.8686 (tmm) outliers start: 25 outliers final: 21 residues processed: 132 average time/residue: 0.2676 time to fit residues: 50.9733 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 : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 239 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 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 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 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 Chi-restraints excluded: chain G residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 91 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 110 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3235 r_free = 0.3235 target = 0.055032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042797 restraints weight = 52315.544| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.14 r_work: 0.2613 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 10612 Z= 0.191 Angle : 0.939 59.199 14322 Z= 0.509 Chirality : 0.044 0.166 1666 Planarity : 0.003 0.024 1827 Dihedral : 8.681 159.289 1610 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.05 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 18.54 % Favored : 79.20 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1316 helix: 1.72 (0.22), residues: 560 sheet: 0.47 (0.29), residues: 273 loop : -0.66 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 251 PHE 0.021 0.001 PHE D 151 TYR 0.005 0.001 TYR A 194 ARG 0.007 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 611) hydrogen bonds : angle 3.93094 ( 1782) covalent geometry : bond 0.00408 (10612) covalent geometry : angle 0.93936 (14322) ********************** 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 142 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.140 Fit side-chains REVERT: A 149 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9062 (mm-40) REVERT: A 227 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8739 (tm-30) REVERT: A 273 MET cc_start: 0.8934 (tmm) cc_final: 0.8293 (tmm) REVERT: B 112 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8536 (tp-100) REVERT: C 149 GLN cc_start: 0.9464 (mm-40) cc_final: 0.9096 (mm-40) REVERT: C 155 MET cc_start: 0.8919 (ptm) cc_final: 0.8383 (tmm) REVERT: C 227 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8532 (tm-30) REVERT: D 169 LYS cc_start: 0.9685 (mtpp) cc_final: 0.9342 (mtmt) REVERT: D 227 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8492 (tm-30) REVERT: E 157 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9153 (p) REVERT: E 161 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8760 (mmpt) REVERT: F 127 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8836 (m-80) REVERT: F 149 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8968 (mm-40) REVERT: G 155 MET cc_start: 0.9007 (ptm) cc_final: 0.8385 (tmm) REVERT: G 273 MET cc_start: 0.8970 (tmm) cc_final: 0.8639 (tmm) outliers start: 25 outliers final: 20 residues processed: 128 average time/residue: 0.1925 time to fit residues: 36.8481 Evaluate side-chains 139 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 239 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 175 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 127 PHE 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 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 Chi-restraints excluded: chain G residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 50.0000 chunk 132 optimal weight: 0.0970 chunk 93 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 50.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3234 r_free = 0.3234 target = 0.055233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.043362 restraints weight = 52014.732| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.05 r_work: 0.2616 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 10612 Z= 0.191 Angle : 0.939 59.199 14322 Z= 0.509 Chirality : 0.044 0.166 1666 Planarity : 0.003 0.024 1827 Dihedral : 8.681 159.289 1610 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.05 % Favored : 97.87 % Rotamer: Outliers : 1.99 % Allowed : 18.72 % Favored : 79.29 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1316 helix: 1.72 (0.22), residues: 560 sheet: 0.47 (0.29), residues: 273 loop : -0.66 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 251 PHE 0.021 0.001 PHE D 151 TYR 0.005 0.001 TYR A 194 ARG 0.007 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 611) hydrogen bonds : angle 3.93094 ( 1782) covalent geometry : bond 0.00408 (10612) covalent geometry : angle 0.93936 (14322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4977.57 seconds wall clock time: 90 minutes 8.95 seconds (5408.95 seconds total)