Starting phenix.real_space_refine on Wed Mar 4 11:40:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vym_21464/03_2026/6vym_21464.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vym_21464/03_2026/6vym_21464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vym_21464/03_2026/6vym_21464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vym_21464/03_2026/6vym_21464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vym_21464/03_2026/6vym_21464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vym_21464/03_2026/6vym_21464.map" } resolution = 3.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8715 2.51 5 N 2373 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "B" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "C" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "D" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "E" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Time building chain proxies: 3.00, per 1000 atoms: 0.22 Number of scatterers: 13573 At special positions: 0 Unit cell: (100, 99, 111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2443 8.00 N 2373 7.00 C 8715 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: 0.88 Conformation dependent library (CDL) restraints added in 553.0 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 53.5% alpha, 18.2% 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 28 through 60 Processing helix chain 'A' and resid 64 through 90 removed outlier: 3.643A pdb=" N PHE A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 127 removed outlier: 4.037A pdb=" N VAL A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 60 Processing helix chain 'B' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 60 Processing helix chain 'C' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 264 removed outlier: 3.652A pdb=" N LEU C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 60 Processing helix chain 'D' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 60 Processing helix chain 'E' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.585A pdb=" N ILE E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 264 removed outlier: 3.652A pdb=" N LEU E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 60 Processing helix chain 'F' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE F 68 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.037A pdb=" N VAL F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.585A pdb=" N ILE F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU F 254 " --> pdb=" O TYR F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 60 Processing helix chain 'G' and resid 64 through 90 removed outlier: 3.643A pdb=" N PHE G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 127 removed outlier: 4.035A pdb=" N VAL G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 123 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 125 " --> pdb=" O GLY G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 removed outlier: 3.585A pdb=" N ILE G 170 " --> pdb=" O PRO G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU G 254 " --> pdb=" O TYR G 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 5.133A pdb=" N VAL A 145 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 164 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL G 145 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG G 156 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL F 145 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG F 156 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 164 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE E 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL E 145 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG E 156 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL D 145 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG D 156 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 164 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL C 145 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG C 156 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 164 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL B 145 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG B 156 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 164 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 3.634A 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: 7.286A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 276 removed outlier: 6.809A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 7.284A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 7.285A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 7.285A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 7.285A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 7.284A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 7.284A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2667 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4055 1.34 - 1.45: 1891 1.45 - 1.57: 7718 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 13748 Sorted by residual: bond pdb=" C ILE F 39 " pdb=" N VAL F 40 " ideal model delta sigma weight residual 1.335 1.426 -0.091 1.09e-02 8.42e+03 6.95e+01 bond pdb=" C VAL F 40 " pdb=" N GLY F 41 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.19e-02 7.06e+03 1.83e+01 bond pdb=" C PHE E 268 " pdb=" N PRO E 269 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.20e-02 6.94e+03 2.62e+00 bond pdb=" C PHE D 268 " pdb=" N PRO D 269 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.20e-02 6.94e+03 2.57e+00 bond pdb=" C PHE B 268 " pdb=" N PRO B 269 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.20e-02 6.94e+03 2.46e+00 ... (remaining 13743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 18127 2.34 - 4.68: 469 4.68 - 7.02: 25 7.02 - 9.36: 13 9.36 - 11.71: 7 Bond angle restraints: 18641 Sorted by residual: angle pdb=" O ILE F 39 " pdb=" C ILE F 39 " pdb=" N VAL F 40 " ideal model delta sigma weight residual 121.87 126.84 -4.97 9.70e-01 1.06e+00 2.63e+01 angle pdb=" CA ILE F 39 " pdb=" C ILE F 39 " pdb=" N VAL F 40 " ideal model delta sigma weight residual 117.15 112.24 4.91 1.14e+00 7.69e-01 1.86e+01 angle pdb=" N GLY F 41 " pdb=" CA GLY F 41 " pdb=" C GLY F 41 " ideal model delta sigma weight residual 113.86 108.62 5.24 1.50e+00 4.44e-01 1.22e+01 angle pdb=" N ILE F 39 " pdb=" CA ILE F 39 " pdb=" C ILE F 39 " ideal model delta sigma weight residual 110.62 114.07 -3.45 1.02e+00 9.61e-01 1.14e+01 angle pdb=" C VAL F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta sigma weight residual 120.34 124.58 -4.24 1.26e+00 6.30e-01 1.13e+01 ... (remaining 18636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.53: 6650 11.53 - 23.07: 1060 23.07 - 34.60: 396 34.60 - 46.13: 126 46.13 - 57.66: 28 Dihedral angle restraints: 8260 sinusoidal: 3171 harmonic: 5089 Sorted by residual: dihedral pdb=" CA PHE D 127 " pdb=" C PHE D 127 " pdb=" N ARG D 128 " pdb=" CA ARG D 128 " ideal model delta harmonic sigma weight residual 180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PHE A 127 " pdb=" C PHE A 127 " pdb=" N ARG A 128 " pdb=" CA ARG A 128 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE C 127 " pdb=" C PHE C 127 " pdb=" N ARG C 128 " pdb=" CA ARG C 128 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2011 0.086 - 0.171: 243 0.171 - 0.257: 17 0.257 - 0.343: 4 0.343 - 0.428: 7 Chirality restraints: 2282 Sorted by residual: chirality pdb=" CB ILE D 176 " pdb=" CA ILE D 176 " pdb=" CG1 ILE D 176 " pdb=" CG2 ILE D 176 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE E 176 " pdb=" CA ILE E 176 " pdb=" CG1 ILE E 176 " pdb=" CG2 ILE E 176 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CB ILE B 176 " pdb=" CA ILE B 176 " pdb=" CG1 ILE B 176 " pdb=" CG2 ILE B 176 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 2279 not shown) Planarity restraints: 2366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 40 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C VAL F 40 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL F 40 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY F 41 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO C 271 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 270 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO E 271 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 271 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 271 " 0.027 5.00e-02 4.00e+02 ... (remaining 2363 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4546 2.85 - 3.36: 13032 3.36 - 3.88: 22379 3.88 - 4.39: 24500 4.39 - 4.90: 43346 Nonbonded interactions: 107803 Sorted by model distance: nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.339 3.040 nonbonded pdb=" O SER G 179 " pdb=" OG SER G 179 " model vdw 2.339 3.040 nonbonded pdb=" O SER E 179 " pdb=" OG SER E 179 " model vdw 2.339 3.040 nonbonded pdb=" O SER B 179 " pdb=" OG SER B 179 " model vdw 2.339 3.040 nonbonded pdb=" O SER C 179 " pdb=" OG SER C 179 " model vdw 2.339 3.040 ... (remaining 107798 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 group one per residue 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.006 0.091 13748 Z= 0.299 Angle : 0.876 11.706 18641 Z= 0.484 Chirality : 0.059 0.428 2282 Planarity : 0.006 0.047 2366 Dihedral : 14.085 57.663 4984 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % 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: -4.56 (0.15), residues: 1764 helix: -2.56 (0.12), residues: 896 sheet: -3.05 (0.31), residues: 189 loop : -3.48 (0.18), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.008 0.001 TYR B 194 PHE 0.010 0.003 PHE B 130 TRP 0.005 0.002 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00641 (13748) covalent geometry : angle 0.87580 (18641) hydrogen bonds : bond 0.15862 ( 911) hydrogen bonds : angle 8.22214 ( 2667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 138 LEU cc_start: 0.8682 (mp) cc_final: 0.8465 (mp) REVERT: A 157 THR cc_start: 0.9412 (t) cc_final: 0.9146 (m) REVERT: A 161 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8934 (mtmm) REVERT: A 200 GLN cc_start: 0.8726 (tt0) cc_final: 0.8518 (tt0) REVERT: A 202 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8758 (mtpp) REVERT: A 273 MET cc_start: 0.8136 (ttm) cc_final: 0.7624 (ttm) REVERT: B 47 MET cc_start: 0.4077 (ttt) cc_final: 0.3650 (mtt) REVERT: B 111 LEU cc_start: 0.8787 (mp) cc_final: 0.8572 (mp) REVERT: B 157 THR cc_start: 0.9256 (t) cc_final: 0.8932 (m) REVERT: B 273 MET cc_start: 0.8068 (ttm) cc_final: 0.7540 (ttm) REVERT: C 47 MET cc_start: 0.4280 (ttt) cc_final: 0.3934 (mtt) REVERT: C 126 MET cc_start: 0.7484 (ttt) cc_final: 0.7194 (ttt) REVERT: C 151 PHE cc_start: 0.8789 (m-80) cc_final: 0.8583 (m-80) REVERT: C 200 GLN cc_start: 0.8681 (tt0) cc_final: 0.8372 (tt0) REVERT: C 273 MET cc_start: 0.8253 (ttm) cc_final: 0.8014 (ttm) REVERT: D 47 MET cc_start: 0.3559 (ttt) cc_final: 0.3088 (mtt) REVERT: D 157 THR cc_start: 0.8945 (t) cc_final: 0.8728 (m) REVERT: D 186 ASN cc_start: 0.8780 (m-40) cc_final: 0.8569 (m-40) REVERT: D 190 ILE cc_start: 0.9565 (mp) cc_final: 0.9331 (mt) REVERT: D 200 GLN cc_start: 0.8741 (tt0) cc_final: 0.8527 (tt0) REVERT: D 203 GLN cc_start: 0.8316 (tp40) cc_final: 0.8094 (tp40) REVERT: D 270 TYR cc_start: 0.9008 (m-80) cc_final: 0.8436 (m-80) REVERT: D 273 MET cc_start: 0.7905 (ttm) cc_final: 0.7662 (ttm) REVERT: E 47 MET cc_start: 0.3441 (ttt) cc_final: 0.3193 (ttt) REVERT: E 138 LEU cc_start: 0.8503 (mp) cc_final: 0.8239 (mp) REVERT: E 159 ASP cc_start: 0.8389 (p0) cc_final: 0.8126 (p0) REVERT: E 161 LYS cc_start: 0.9122 (mtmt) cc_final: 0.8842 (mtmm) REVERT: E 277 PHE cc_start: 0.7593 (m-10) cc_final: 0.7117 (m-10) REVERT: F 47 MET cc_start: 0.4310 (ttt) cc_final: 0.3874 (mtt) REVERT: F 115 LEU cc_start: 0.9121 (tt) cc_final: 0.8822 (tp) REVERT: F 190 ILE cc_start: 0.9619 (mp) cc_final: 0.9373 (mt) REVERT: F 200 GLN cc_start: 0.8926 (tt0) cc_final: 0.8671 (tt0) REVERT: F 272 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8507 (mm-40) REVERT: G 273 MET cc_start: 0.7991 (ttm) cc_final: 0.7313 (ttm) REVERT: G 274 ASP cc_start: 0.8146 (t0) cc_final: 0.7458 (t70) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1080 time to fit residues: 65.7017 Evaluate side-chains 281 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 167 ASN B 167 ASN C 167 ASN D 167 ASN E 167 ASN F 167 ASN G 112 GLN G 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.164714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113499 restraints weight = 19168.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117562 restraints weight = 9800.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120219 restraints weight = 6538.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121537 restraints weight = 5148.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122089 restraints weight = 4534.125| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13748 Z= 0.146 Angle : 0.588 8.624 18641 Z= 0.310 Chirality : 0.046 0.293 2282 Planarity : 0.004 0.035 2366 Dihedral : 5.349 23.517 1939 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.98 % Allowed : 16.09 % Favored : 80.93 % 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: -2.55 (0.17), residues: 1764 helix: -0.51 (0.16), residues: 903 sheet: -2.38 (0.34), residues: 154 loop : -3.12 (0.18), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.008 0.001 TYR G 135 PHE 0.015 0.001 PHE E 178 TRP 0.006 0.001 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00318 (13748) covalent geometry : angle 0.58774 (18641) hydrogen bonds : bond 0.04214 ( 911) hydrogen bonds : angle 5.20403 ( 2667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 316 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8754 (mtmm) REVERT: A 210 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8747 (mm-40) REVERT: A 273 MET cc_start: 0.8339 (ttm) cc_final: 0.7377 (ttm) REVERT: B 47 MET cc_start: 0.3626 (ttt) cc_final: 0.3316 (mtt) REVERT: B 111 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 273 MET cc_start: 0.8260 (ttm) cc_final: 0.7517 (ttm) REVERT: C 47 MET cc_start: 0.4190 (ttt) cc_final: 0.3911 (mtt) REVERT: C 126 MET cc_start: 0.7719 (ttt) cc_final: 0.7399 (ttt) REVERT: C 127 PHE cc_start: 0.6994 (t80) cc_final: 0.6597 (t80) REVERT: C 138 LEU cc_start: 0.8954 (mp) cc_final: 0.8670 (mp) REVERT: C 157 THR cc_start: 0.9430 (t) cc_final: 0.9142 (m) REVERT: C 272 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8850 (mm-40) REVERT: C 273 MET cc_start: 0.8150 (ttm) cc_final: 0.7750 (ttm) REVERT: C 274 ASP cc_start: 0.7992 (t0) cc_final: 0.7534 (t70) REVERT: D 47 MET cc_start: 0.3126 (ttt) cc_final: 0.2728 (mtt) REVERT: D 127 PHE cc_start: 0.7126 (t80) cc_final: 0.6761 (t80) REVERT: D 151 PHE cc_start: 0.8881 (m-80) cc_final: 0.8584 (m-80) REVERT: D 203 GLN cc_start: 0.8677 (tp40) cc_final: 0.8326 (tp40) REVERT: D 270 TYR cc_start: 0.9090 (m-80) cc_final: 0.8626 (m-80) REVERT: D 272 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8901 (mm-40) REVERT: D 273 MET cc_start: 0.7633 (ttm) cc_final: 0.7182 (ttm) REVERT: D 278 LYS cc_start: 0.8193 (mttp) cc_final: 0.7845 (mttp) REVERT: E 161 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8755 (mtmm) REVERT: E 181 GLU cc_start: 0.8794 (tp30) cc_final: 0.8562 (tp30) REVERT: E 273 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7555 (mtm) REVERT: F 47 MET cc_start: 0.4098 (ttt) cc_final: 0.3716 (mtt) REVERT: F 115 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8665 (tt) REVERT: F 134 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7294 (mt-10) REVERT: F 157 THR cc_start: 0.9274 (t) cc_final: 0.9008 (m) REVERT: F 210 GLN cc_start: 0.9020 (tp40) cc_final: 0.8763 (mm110) REVERT: F 272 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8575 (mm-40) REVERT: F 273 MET cc_start: 0.8055 (ttm) cc_final: 0.7851 (ttm) REVERT: G 157 THR cc_start: 0.9342 (t) cc_final: 0.9040 (m) REVERT: G 274 ASP cc_start: 0.8031 (t0) cc_final: 0.7604 (t70) outliers start: 43 outliers final: 15 residues processed: 344 average time/residue: 0.0934 time to fit residues: 50.0167 Evaluate side-chains 282 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 84 optimal weight: 0.1980 chunk 138 optimal weight: 0.0070 chunk 152 optimal weight: 30.0000 chunk 108 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107745 restraints weight = 19107.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111672 restraints weight = 9641.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114221 restraints weight = 6363.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115779 restraints weight = 4980.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116503 restraints weight = 4337.446| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13748 Z= 0.155 Angle : 0.582 9.214 18641 Z= 0.305 Chirality : 0.045 0.372 2282 Planarity : 0.003 0.033 2366 Dihedral : 5.117 22.946 1939 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.91 % Allowed : 17.06 % Favored : 80.03 % 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: -1.65 (0.19), residues: 1764 helix: 0.41 (0.17), residues: 896 sheet: -1.89 (0.29), residues: 238 loop : -3.02 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.008 0.001 TYR G 135 PHE 0.015 0.001 PHE D 277 TRP 0.003 0.000 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00339 (13748) covalent geometry : angle 0.58237 (18641) hydrogen bonds : bond 0.04026 ( 911) hydrogen bonds : angle 4.76033 ( 2667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.491 Fit side-chains REVERT: A 210 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8335 (mm-40) REVERT: A 273 MET cc_start: 0.8236 (ttm) cc_final: 0.7359 (ttm) REVERT: B 47 MET cc_start: 0.3735 (ttt) cc_final: 0.3449 (mtt) REVERT: B 273 MET cc_start: 0.8270 (ttm) cc_final: 0.7539 (ttm) REVERT: C 47 MET cc_start: 0.4238 (ttt) cc_final: 0.3945 (mtt) REVERT: C 115 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8795 (tt) REVERT: C 126 MET cc_start: 0.7579 (ttt) cc_final: 0.7248 (ttt) REVERT: C 127 PHE cc_start: 0.6963 (t80) cc_final: 0.6547 (t80) REVERT: C 138 LEU cc_start: 0.9001 (mp) cc_final: 0.8721 (mp) REVERT: C 157 THR cc_start: 0.9482 (t) cc_final: 0.9133 (m) REVERT: C 272 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8806 (mm-40) REVERT: C 273 MET cc_start: 0.8112 (ttm) cc_final: 0.7742 (ttm) REVERT: D 47 MET cc_start: 0.3257 (ttt) cc_final: 0.2798 (mtt) REVERT: D 127 PHE cc_start: 0.7069 (t80) cc_final: 0.6709 (t80) REVERT: D 151 PHE cc_start: 0.8830 (m-80) cc_final: 0.8620 (m-80) REVERT: D 187 GLU cc_start: 0.7566 (tp30) cc_final: 0.7341 (tp30) REVERT: D 203 GLN cc_start: 0.8571 (tp40) cc_final: 0.8230 (tp40) REVERT: D 270 TYR cc_start: 0.9114 (m-80) cc_final: 0.8667 (m-80) REVERT: D 273 MET cc_start: 0.7562 (ttm) cc_final: 0.7178 (ttm) REVERT: E 181 GLU cc_start: 0.8669 (tp30) cc_final: 0.8434 (tp30) REVERT: E 273 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7729 (mtm) REVERT: F 47 MET cc_start: 0.4343 (ttt) cc_final: 0.3924 (mtt) REVERT: F 115 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8806 (tt) REVERT: F 134 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7454 (mt-10) REVERT: F 149 GLN cc_start: 0.8433 (mt0) cc_final: 0.8180 (mm-40) REVERT: F 157 THR cc_start: 0.9371 (t) cc_final: 0.9117 (m) REVERT: F 212 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7885 (tm-30) REVERT: F 272 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8484 (mm-40) REVERT: G 115 LEU cc_start: 0.9255 (tp) cc_final: 0.8962 (tt) REVERT: G 157 THR cc_start: 0.9405 (t) cc_final: 0.9117 (m) REVERT: G 274 ASP cc_start: 0.8067 (t0) cc_final: 0.7685 (t70) outliers start: 42 outliers final: 23 residues processed: 304 average time/residue: 0.0903 time to fit residues: 43.1144 Evaluate side-chains 270 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.106569 restraints weight = 19087.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110471 restraints weight = 9646.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112956 restraints weight = 6373.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114211 restraints weight = 4994.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115427 restraints weight = 4394.429| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13748 Z= 0.161 Angle : 0.575 8.606 18641 Z= 0.300 Chirality : 0.045 0.397 2282 Planarity : 0.003 0.034 2366 Dihedral : 4.976 21.638 1939 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.19 % Allowed : 18.59 % Favored : 78.22 % 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: -1.23 (0.19), residues: 1764 helix: 0.80 (0.17), residues: 896 sheet: -1.63 (0.30), residues: 238 loop : -2.93 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 256 TYR 0.008 0.001 TYR D 135 PHE 0.022 0.001 PHE D 277 TRP 0.004 0.001 TRP D 240 Details of bonding type rmsd covalent geometry : bond 0.00363 (13748) covalent geometry : angle 0.57506 (18641) hydrogen bonds : bond 0.03954 ( 911) hydrogen bonds : angle 4.53005 ( 2667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 0.498 Fit side-chains REVERT: A 112 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 212 GLU cc_start: 0.8568 (tp30) cc_final: 0.8100 (tm-30) REVERT: A 273 MET cc_start: 0.8159 (ttm) cc_final: 0.7176 (ttm) REVERT: B 47 MET cc_start: 0.3644 (ttt) cc_final: 0.3392 (mtt) REVERT: B 115 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8969 (tt) REVERT: B 212 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 273 MET cc_start: 0.8259 (ttm) cc_final: 0.7468 (ttm) REVERT: C 47 MET cc_start: 0.4144 (ttt) cc_final: 0.3874 (mtt) REVERT: C 115 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8799 (tp) REVERT: C 126 MET cc_start: 0.7755 (ttt) cc_final: 0.7450 (ttt) REVERT: C 127 PHE cc_start: 0.6940 (t80) cc_final: 0.6503 (t80) REVERT: C 138 LEU cc_start: 0.9032 (mp) cc_final: 0.8618 (mp) REVERT: C 157 THR cc_start: 0.9469 (t) cc_final: 0.9211 (m) REVERT: C 212 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8070 (tp30) REVERT: C 272 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8818 (mm-40) REVERT: C 273 MET cc_start: 0.8043 (ttm) cc_final: 0.7638 (ttm) REVERT: C 274 ASP cc_start: 0.7998 (t0) cc_final: 0.7604 (t0) REVERT: D 47 MET cc_start: 0.3224 (ttt) cc_final: 0.2771 (mtt) REVERT: D 127 PHE cc_start: 0.7155 (t80) cc_final: 0.6773 (t80) REVERT: D 187 GLU cc_start: 0.7653 (tt0) cc_final: 0.7358 (tp30) REVERT: D 203 GLN cc_start: 0.8658 (tp40) cc_final: 0.8329 (tp40) REVERT: D 212 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7856 (tp30) REVERT: D 270 TYR cc_start: 0.9140 (m-80) cc_final: 0.8601 (m-80) REVERT: D 272 GLN cc_start: 0.9295 (mm-40) cc_final: 0.9003 (mm-40) REVERT: D 273 MET cc_start: 0.7597 (ttm) cc_final: 0.7358 (ttm) REVERT: E 134 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7238 (mp0) REVERT: E 181 GLU cc_start: 0.8701 (tp30) cc_final: 0.8461 (tp30) REVERT: E 212 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8019 (tp30) REVERT: F 47 MET cc_start: 0.4366 (ttt) cc_final: 0.3957 (mtt) REVERT: F 115 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8879 (tt) REVERT: F 134 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7448 (mt-10) REVERT: F 149 GLN cc_start: 0.8511 (mt0) cc_final: 0.8235 (mt0) REVERT: F 212 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 272 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8482 (mm-40) REVERT: G 138 LEU cc_start: 0.9020 (mt) cc_final: 0.8790 (mt) REVERT: G 157 THR cc_start: 0.9365 (t) cc_final: 0.9153 (m) REVERT: G 212 GLU cc_start: 0.8526 (tp30) cc_final: 0.8221 (tm-30) REVERT: G 274 ASP cc_start: 0.8007 (t0) cc_final: 0.7587 (t70) outliers start: 46 outliers final: 25 residues processed: 291 average time/residue: 0.0849 time to fit residues: 39.5761 Evaluate side-chains 267 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 152 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104350 restraints weight = 19451.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108325 restraints weight = 9933.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110903 restraints weight = 6587.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112494 restraints weight = 5168.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113079 restraints weight = 4507.422| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13748 Z= 0.171 Angle : 0.583 13.165 18641 Z= 0.301 Chirality : 0.045 0.392 2282 Planarity : 0.003 0.034 2366 Dihedral : 4.927 21.790 1939 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.33 % Allowed : 19.83 % Favored : 76.84 % 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: -0.98 (0.19), residues: 1764 helix: 1.03 (0.17), residues: 896 sheet: -1.50 (0.32), residues: 224 loop : -2.83 (0.19), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 256 TYR 0.007 0.001 TYR D 135 PHE 0.017 0.001 PHE D 277 TRP 0.004 0.001 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00384 (13748) covalent geometry : angle 0.58266 (18641) hydrogen bonds : bond 0.03927 ( 911) hydrogen bonds : angle 4.47073 ( 2667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.485 Fit side-chains REVERT: A 112 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 212 GLU cc_start: 0.8606 (tp30) cc_final: 0.8212 (tm-30) REVERT: A 273 MET cc_start: 0.8186 (ttm) cc_final: 0.7219 (ttm) REVERT: B 47 MET cc_start: 0.3617 (ttt) cc_final: 0.3351 (mtt) REVERT: B 212 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 273 MET cc_start: 0.8257 (ttm) cc_final: 0.7457 (ttm) REVERT: C 47 MET cc_start: 0.4184 (ttt) cc_final: 0.3947 (mtt) REVERT: C 115 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8833 (tp) REVERT: C 126 MET cc_start: 0.7935 (ttt) cc_final: 0.7601 (ttt) REVERT: C 212 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8132 (tm-30) REVERT: C 272 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8908 (mm-40) REVERT: C 273 MET cc_start: 0.8020 (ttm) cc_final: 0.7622 (ttm) REVERT: D 47 MET cc_start: 0.3240 (ttt) cc_final: 0.2809 (mtt) REVERT: D 112 GLN cc_start: 0.8527 (tt0) cc_final: 0.8149 (tm-30) REVERT: D 127 PHE cc_start: 0.7241 (t80) cc_final: 0.6851 (t80) REVERT: D 187 GLU cc_start: 0.7668 (tt0) cc_final: 0.7395 (tp30) REVERT: D 203 GLN cc_start: 0.8683 (tp40) cc_final: 0.8358 (tp40) REVERT: D 272 GLN cc_start: 0.9293 (mm-40) cc_final: 0.9086 (mm-40) REVERT: E 69 LEU cc_start: 0.8953 (mm) cc_final: 0.8452 (tp) REVERT: E 134 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7321 (mp0) REVERT: E 146 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8407 (mm) REVERT: E 181 GLU cc_start: 0.8713 (tp30) cc_final: 0.8456 (tp30) REVERT: E 212 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7907 (tp30) REVERT: E 267 SER cc_start: 0.8989 (t) cc_final: 0.8647 (p) REVERT: E 273 MET cc_start: 0.8193 (mtm) cc_final: 0.7627 (mtm) REVERT: F 47 MET cc_start: 0.4306 (ttt) cc_final: 0.3907 (mtt) REVERT: F 115 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8911 (tt) REVERT: F 134 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7445 (mt-10) REVERT: F 149 GLN cc_start: 0.8539 (mt0) cc_final: 0.8194 (mt0) REVERT: F 272 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8466 (mm-40) REVERT: G 157 THR cc_start: 0.9348 (t) cc_final: 0.9134 (m) REVERT: G 203 GLN cc_start: 0.8643 (tp40) cc_final: 0.8429 (tp40) REVERT: G 212 GLU cc_start: 0.8597 (tp30) cc_final: 0.8371 (tm-30) outliers start: 48 outliers final: 26 residues processed: 292 average time/residue: 0.0853 time to fit residues: 39.9072 Evaluate side-chains 266 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 152 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN E 149 GLN G 149 GLN G 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108536 restraints weight = 19094.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112170 restraints weight = 9982.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114636 restraints weight = 6719.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115878 restraints weight = 5304.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116994 restraints weight = 4672.382| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13748 Z= 0.134 Angle : 0.575 10.640 18641 Z= 0.293 Chirality : 0.044 0.300 2282 Planarity : 0.003 0.033 2366 Dihedral : 4.795 20.186 1939 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.36 % Allowed : 22.12 % Favored : 75.52 % 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: -0.75 (0.19), residues: 1764 helix: 1.19 (0.17), residues: 896 sheet: -1.27 (0.32), residues: 224 loop : -2.74 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 256 TYR 0.008 0.001 TYR B 135 PHE 0.011 0.001 PHE E 178 TRP 0.003 0.000 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00300 (13748) covalent geometry : angle 0.57455 (18641) hydrogen bonds : bond 0.03858 ( 911) hydrogen bonds : angle 4.34817 ( 2667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.472 Fit side-chains REVERT: A 112 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8434 (tm-30) REVERT: A 273 MET cc_start: 0.8111 (ttm) cc_final: 0.7187 (ttm) REVERT: B 47 MET cc_start: 0.3726 (ttt) cc_final: 0.3435 (mtt) REVERT: B 273 MET cc_start: 0.8225 (ttm) cc_final: 0.7482 (ttm) REVERT: C 47 MET cc_start: 0.4235 (ttt) cc_final: 0.3965 (mtt) REVERT: C 115 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8841 (tp) REVERT: C 126 MET cc_start: 0.7793 (ttt) cc_final: 0.7532 (ttt) REVERT: C 127 PHE cc_start: 0.6683 (t80) cc_final: 0.6321 (t80) REVERT: C 272 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8868 (mm-40) REVERT: C 273 MET cc_start: 0.8042 (ttm) cc_final: 0.7681 (ttm) REVERT: D 47 MET cc_start: 0.3404 (ttt) cc_final: 0.2943 (mtt) REVERT: D 112 GLN cc_start: 0.8556 (tt0) cc_final: 0.8253 (tm-30) REVERT: D 127 PHE cc_start: 0.7069 (t80) cc_final: 0.6680 (t80) REVERT: D 151 PHE cc_start: 0.8751 (m-80) cc_final: 0.8521 (m-80) REVERT: D 187 GLU cc_start: 0.7557 (tt0) cc_final: 0.7268 (tp30) REVERT: D 203 GLN cc_start: 0.8606 (tp40) cc_final: 0.8301 (tp40) REVERT: E 69 LEU cc_start: 0.8909 (mm) cc_final: 0.8401 (tp) REVERT: E 105 LEU cc_start: 0.8437 (tt) cc_final: 0.8171 (tt) REVERT: E 134 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7111 (mp0) REVERT: E 181 GLU cc_start: 0.8585 (tp30) cc_final: 0.8317 (tp30) REVERT: E 212 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8040 (tp30) REVERT: E 267 SER cc_start: 0.8800 (t) cc_final: 0.8482 (p) REVERT: F 47 MET cc_start: 0.4232 (ttt) cc_final: 0.3827 (mtt) REVERT: F 112 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8224 (tm-30) REVERT: F 115 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8937 (tt) REVERT: F 149 GLN cc_start: 0.8509 (mt0) cc_final: 0.8118 (mt0) REVERT: F 210 GLN cc_start: 0.8930 (tp40) cc_final: 0.8697 (mm-40) REVERT: F 212 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7864 (tp30) REVERT: F 272 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8477 (mm-40) REVERT: G 112 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8650 (tm-30) REVERT: G 203 GLN cc_start: 0.8571 (tp40) cc_final: 0.8354 (tp40) outliers start: 34 outliers final: 23 residues processed: 297 average time/residue: 0.0820 time to fit residues: 39.1731 Evaluate side-chains 267 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 50 optimal weight: 40.0000 chunk 79 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107598 restraints weight = 19089.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110102 restraints weight = 10026.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113042 restraints weight = 6758.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113521 restraints weight = 5054.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113525 restraints weight = 4994.421| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13748 Z= 0.205 Angle : 0.622 9.030 18641 Z= 0.320 Chirality : 0.048 0.498 2282 Planarity : 0.003 0.033 2366 Dihedral : 4.910 22.204 1939 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.26 % Allowed : 21.84 % Favored : 74.90 % 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: -0.73 (0.19), residues: 1764 helix: 1.20 (0.17), residues: 896 sheet: -1.55 (0.32), residues: 210 loop : -2.58 (0.20), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 238 TYR 0.009 0.001 TYR C 135 PHE 0.012 0.001 PHE E 178 TRP 0.004 0.001 TRP G 240 Details of bonding type rmsd covalent geometry : bond 0.00464 (13748) covalent geometry : angle 0.62236 (18641) hydrogen bonds : bond 0.03959 ( 911) hydrogen bonds : angle 4.48225 ( 2667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 0.530 Fit side-chains REVERT: A 112 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 187 GLU cc_start: 0.7779 (tt0) cc_final: 0.7544 (tt0) REVERT: A 273 MET cc_start: 0.8051 (ttm) cc_final: 0.7136 (ttm) REVERT: B 273 MET cc_start: 0.8290 (ttm) cc_final: 0.7486 (ttm) REVERT: C 47 MET cc_start: 0.3955 (ttt) cc_final: 0.3748 (mtt) REVERT: C 112 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 115 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8837 (tp) REVERT: C 126 MET cc_start: 0.7984 (ttt) cc_final: 0.7698 (ttt) REVERT: C 273 MET cc_start: 0.8025 (ttm) cc_final: 0.7566 (ttm) REVERT: D 47 MET cc_start: 0.2939 (ttt) cc_final: 0.2622 (mtt) REVERT: D 112 GLN cc_start: 0.8515 (tt0) cc_final: 0.8126 (tm-30) REVERT: D 127 PHE cc_start: 0.7324 (t80) cc_final: 0.6910 (t80) REVERT: D 151 PHE cc_start: 0.8983 (m-80) cc_final: 0.8734 (m-80) REVERT: D 187 GLU cc_start: 0.7791 (tt0) cc_final: 0.7523 (tp30) REVERT: D 203 GLN cc_start: 0.8739 (tp40) cc_final: 0.8426 (tp40) REVERT: D 212 GLU cc_start: 0.8739 (tp30) cc_final: 0.7969 (tm-30) REVERT: E 69 LEU cc_start: 0.9065 (mm) cc_final: 0.8661 (tp) REVERT: E 134 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7371 (mp0) REVERT: E 146 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8433 (mm) REVERT: E 181 GLU cc_start: 0.8763 (tp30) cc_final: 0.8497 (tp30) REVERT: E 212 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8367 (tp30) REVERT: E 267 SER cc_start: 0.8964 (t) cc_final: 0.8615 (p) REVERT: F 47 MET cc_start: 0.3848 (ttt) cc_final: 0.3569 (mtt) REVERT: F 112 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8154 (tm-30) REVERT: F 115 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8955 (tt) REVERT: F 149 GLN cc_start: 0.8614 (mt0) cc_final: 0.8214 (mt0) REVERT: F 272 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8485 (mm-40) REVERT: G 112 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8514 (tm-30) REVERT: G 203 GLN cc_start: 0.8673 (tp40) cc_final: 0.8457 (tp40) outliers start: 47 outliers final: 32 residues processed: 286 average time/residue: 0.0870 time to fit residues: 39.9287 Evaluate side-chains 272 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 129 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 ASN E 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110460 restraints weight = 18985.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113195 restraints weight = 10128.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115929 restraints weight = 6620.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116920 restraints weight = 4956.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116652 restraints weight = 4767.107| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13748 Z= 0.136 Angle : 0.598 9.762 18641 Z= 0.299 Chirality : 0.045 0.453 2282 Planarity : 0.003 0.033 2366 Dihedral : 4.761 19.781 1939 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.12 % Allowed : 21.98 % Favored : 74.90 % 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: -0.57 (0.19), residues: 1764 helix: 1.30 (0.17), residues: 896 sheet: -1.09 (0.32), residues: 224 loop : -2.64 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 238 TYR 0.009 0.001 TYR F 135 PHE 0.010 0.001 PHE E 178 TRP 0.004 0.000 TRP C 240 Details of bonding type rmsd covalent geometry : bond 0.00310 (13748) covalent geometry : angle 0.59772 (18641) hydrogen bonds : bond 0.03865 ( 911) hydrogen bonds : angle 4.34569 ( 2667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.495 Fit side-chains REVERT: A 112 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8455 (tm-30) REVERT: A 273 MET cc_start: 0.8018 (ttm) cc_final: 0.7053 (ttm) REVERT: B 112 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 212 GLU cc_start: 0.8688 (tp30) cc_final: 0.8129 (tm-30) REVERT: B 273 MET cc_start: 0.8194 (ttm) cc_final: 0.7365 (ttm) REVERT: C 112 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8202 (tm-30) REVERT: C 115 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8859 (tp) REVERT: C 126 MET cc_start: 0.7876 (ttt) cc_final: 0.7608 (ttt) REVERT: C 149 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: C 212 GLU cc_start: 0.8642 (tp30) cc_final: 0.8197 (tm-30) REVERT: C 273 MET cc_start: 0.8091 (ttm) cc_final: 0.7671 (ttm) REVERT: D 47 MET cc_start: 0.3008 (ttt) cc_final: 0.2670 (mtt) REVERT: D 112 GLN cc_start: 0.8525 (tt0) cc_final: 0.8272 (tm-30) REVERT: D 127 PHE cc_start: 0.7189 (t80) cc_final: 0.6746 (t80) REVERT: D 187 GLU cc_start: 0.7641 (tt0) cc_final: 0.7362 (tp30) REVERT: D 203 GLN cc_start: 0.8668 (tp40) cc_final: 0.8347 (tp40) REVERT: D 212 GLU cc_start: 0.8618 (tp30) cc_final: 0.8048 (tm-30) REVERT: E 69 LEU cc_start: 0.9097 (mm) cc_final: 0.8702 (tp) REVERT: E 146 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8452 (mm) REVERT: E 150 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9127 (tp) REVERT: E 181 GLU cc_start: 0.8659 (tp30) cc_final: 0.8397 (tp30) REVERT: E 212 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8012 (tp30) REVERT: E 267 SER cc_start: 0.8789 (t) cc_final: 0.8459 (p) REVERT: F 47 MET cc_start: 0.3870 (ttt) cc_final: 0.3564 (mtt) REVERT: F 112 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8258 (tm-30) REVERT: F 115 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8949 (tt) REVERT: F 149 GLN cc_start: 0.8577 (mt0) cc_final: 0.8208 (mt0) REVERT: F 212 GLU cc_start: 0.8575 (tp30) cc_final: 0.8112 (tm-30) REVERT: G 112 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8587 (tm-30) REVERT: G 203 GLN cc_start: 0.8630 (tp40) cc_final: 0.8421 (tp40) outliers start: 45 outliers final: 31 residues processed: 292 average time/residue: 0.0834 time to fit residues: 39.5972 Evaluate side-chains 280 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 71 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 135 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114091 restraints weight = 19095.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116902 restraints weight = 10113.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119673 restraints weight = 6611.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121832 restraints weight = 4948.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120994 restraints weight = 4702.204| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13748 Z= 0.119 Angle : 0.600 10.580 18641 Z= 0.297 Chirality : 0.046 0.452 2282 Planarity : 0.003 0.037 2366 Dihedral : 4.654 18.687 1939 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.36 % Allowed : 23.09 % Favored : 74.55 % 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: -0.34 (0.19), residues: 1764 helix: 1.43 (0.16), residues: 903 sheet: -0.85 (0.33), residues: 224 loop : -2.51 (0.21), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 238 TYR 0.010 0.001 TYR F 135 PHE 0.011 0.001 PHE E 178 TRP 0.004 0.000 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00265 (13748) covalent geometry : angle 0.59985 (18641) hydrogen bonds : bond 0.03814 ( 911) hydrogen bonds : angle 4.28660 ( 2667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.508 Fit side-chains REVERT: A 112 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 273 MET cc_start: 0.7959 (ttm) cc_final: 0.7370 (ttm) REVERT: B 112 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8311 (tm-30) REVERT: B 212 GLU cc_start: 0.8694 (tp30) cc_final: 0.8108 (tm-30) REVERT: B 274 ASP cc_start: 0.8080 (t70) cc_final: 0.7294 (m-30) REVERT: C 112 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 126 MET cc_start: 0.7891 (ttt) cc_final: 0.7629 (ttt) REVERT: C 212 GLU cc_start: 0.8798 (tp30) cc_final: 0.8273 (tm-30) REVERT: C 273 MET cc_start: 0.7760 (ttm) cc_final: 0.7111 (ttm) REVERT: D 47 MET cc_start: 0.3018 (ttt) cc_final: 0.2695 (mtt) REVERT: D 187 GLU cc_start: 0.7622 (tt0) cc_final: 0.7323 (tp30) REVERT: D 203 GLN cc_start: 0.8661 (tp40) cc_final: 0.8321 (tp40) REVERT: D 212 GLU cc_start: 0.8661 (tp30) cc_final: 0.8068 (tm-30) REVERT: E 69 LEU cc_start: 0.9103 (mm) cc_final: 0.8740 (tp) REVERT: E 150 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9091 (tp) REVERT: E 157 THR cc_start: 0.9160 (t) cc_final: 0.8855 (m) REVERT: E 181 GLU cc_start: 0.8633 (tp30) cc_final: 0.8430 (tp30) REVERT: E 212 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8107 (tp30) REVERT: E 267 SER cc_start: 0.8702 (t) cc_final: 0.8426 (p) REVERT: F 47 MET cc_start: 0.3836 (ttt) cc_final: 0.3541 (mtt) REVERT: F 112 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8283 (tm-30) REVERT: F 115 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8889 (tt) REVERT: F 149 GLN cc_start: 0.8618 (mt0) cc_final: 0.8216 (mt0) REVERT: F 212 GLU cc_start: 0.8615 (tp30) cc_final: 0.8234 (tm-30) REVERT: F 272 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8606 (mm-40) REVERT: G 112 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 34 outliers final: 27 residues processed: 299 average time/residue: 0.0835 time to fit residues: 40.2918 Evaluate side-chains 281 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 142 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.161272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110736 restraints weight = 19091.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113386 restraints weight = 10074.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115964 restraints weight = 6761.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116669 restraints weight = 5138.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116658 restraints weight = 4843.213| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13748 Z= 0.178 Angle : 0.640 10.333 18641 Z= 0.320 Chirality : 0.048 0.463 2282 Planarity : 0.003 0.032 2366 Dihedral : 4.771 20.298 1939 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.91 % Allowed : 23.02 % Favored : 74.06 % 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: -0.37 (0.19), residues: 1764 helix: 1.43 (0.16), residues: 889 sheet: -1.23 (0.32), residues: 210 loop : -2.32 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 256 TYR 0.014 0.001 TYR F 135 PHE 0.012 0.001 PHE E 68 TRP 0.002 0.001 TRP G 240 Details of bonding type rmsd covalent geometry : bond 0.00405 (13748) covalent geometry : angle 0.63971 (18641) hydrogen bonds : bond 0.03869 ( 911) hydrogen bonds : angle 4.37696 ( 2667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.544 Fit side-chains REVERT: A 112 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 134 GLU cc_start: 0.7707 (pt0) cc_final: 0.7486 (pt0) REVERT: B 212 GLU cc_start: 0.8655 (tp30) cc_final: 0.8159 (tm-30) REVERT: B 273 MET cc_start: 0.8203 (ttm) cc_final: 0.7727 (ttm) REVERT: B 274 ASP cc_start: 0.8109 (t70) cc_final: 0.7626 (t70) REVERT: C 112 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 126 MET cc_start: 0.7835 (ttt) cc_final: 0.7590 (ttt) REVERT: C 149 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: C 212 GLU cc_start: 0.8641 (tp30) cc_final: 0.8409 (tm-30) REVERT: D 47 MET cc_start: 0.3083 (ttt) cc_final: 0.2842 (mtt) REVERT: D 134 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: D 151 PHE cc_start: 0.8939 (m-80) cc_final: 0.8690 (m-80) REVERT: D 187 GLU cc_start: 0.7711 (tt0) cc_final: 0.7443 (tp30) REVERT: D 203 GLN cc_start: 0.8671 (tp40) cc_final: 0.8373 (tp40) REVERT: D 212 GLU cc_start: 0.8632 (tp30) cc_final: 0.8149 (tm-30) REVERT: E 150 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9136 (tp) REVERT: E 212 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8094 (tp30) REVERT: E 267 SER cc_start: 0.8791 (t) cc_final: 0.8467 (p) REVERT: F 47 MET cc_start: 0.3876 (ttt) cc_final: 0.3579 (mtt) REVERT: F 112 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8338 (tm-30) REVERT: F 115 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8936 (tt) REVERT: F 149 GLN cc_start: 0.8558 (mt0) cc_final: 0.8225 (mt0) REVERT: F 212 GLU cc_start: 0.8592 (tp30) cc_final: 0.8262 (tm-30) REVERT: G 112 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8556 (tm-30) REVERT: G 114 SER cc_start: 0.9383 (m) cc_final: 0.8732 (t) outliers start: 42 outliers final: 31 residues processed: 286 average time/residue: 0.0837 time to fit residues: 38.9489 Evaluate side-chains 274 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 86 optimal weight: 0.0270 chunk 30 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN E 210 GLN G 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114133 restraints weight = 19217.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116895 restraints weight = 10112.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119095 restraints weight = 6792.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120390 restraints weight = 5508.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120574 restraints weight = 4739.700| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13748 Z= 0.122 Angle : 0.625 10.851 18641 Z= 0.306 Chirality : 0.046 0.456 2282 Planarity : 0.003 0.032 2366 Dihedral : 4.657 17.998 1939 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.43 % Allowed : 23.79 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.25 (0.19), residues: 1764 helix: 1.48 (0.16), residues: 903 sheet: -0.72 (0.33), residues: 224 loop : -2.48 (0.21), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 256 TYR 0.014 0.001 TYR F 135 PHE 0.010 0.001 PHE E 68 TRP 0.002 0.000 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00276 (13748) covalent geometry : angle 0.62481 (18641) hydrogen bonds : bond 0.03792 ( 911) hydrogen bonds : angle 4.30795 ( 2667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.65 seconds wall clock time: 36 minutes 3.20 seconds (2163.20 seconds total)