Starting phenix.real_space_refine on Mon Dec 30 14:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vym_21464/12_2024/6vym_21464.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vym_21464/12_2024/6vym_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vym_21464/12_2024/6vym_21464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vym_21464/12_2024/6vym_21464.map" model { file = "/net/cci-nas-00/data/ceres_data/6vym_21464/12_2024/6vym_21464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vym_21464/12_2024/6vym_21464.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.43, per 1000 atoms: 0.55 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: 3.39 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.35 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: 4.18 Time building geometry restraints manager: 3.92 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: 0.00 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.520 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- 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= 0.423 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.002 TRP E 240 PHE 0.010 0.003 PHE B 130 TYR 0.008 0.001 TYR B 194 ARG 0.002 0.000 ARG A 219 *********************** 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 : 1.466 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: 0.2708 time to fit residues: 162.0475 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 : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13748 Z= 0.196 Angle : 0.581 8.417 18641 Z= 0.305 Chirality : 0.046 0.306 2282 Planarity : 0.004 0.034 2366 Dihedral : 5.296 23.451 1939 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.98 % Allowed : 15.88 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.17), residues: 1764 helix: -0.50 (0.16), residues: 903 sheet: -2.17 (0.29), residues: 238 loop : -3.18 (0.19), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 240 PHE 0.017 0.001 PHE D 277 TYR 0.008 0.001 TYR G 135 ARG 0.006 0.000 ARG B 180 *********************** 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 371 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 1.554 Fit side-chains REVERT: A 161 LYS cc_start: 0.9180 (mtmt) cc_final: 0.8830 (mtmm) REVERT: A 209 ILE cc_start: 0.8975 (pt) cc_final: 0.8744 (mt) REVERT: A 210 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8266 (mm-40) REVERT: A 273 MET cc_start: 0.8211 (ttm) cc_final: 0.7412 (ttm) REVERT: B 47 MET cc_start: 0.3766 (ttt) cc_final: 0.3423 (mtt) REVERT: B 273 MET cc_start: 0.8187 (ttm) cc_final: 0.7571 (ttm) REVERT: C 47 MET cc_start: 0.4266 (ttt) cc_final: 0.3958 (mtt) REVERT: C 126 MET cc_start: 0.7484 (ttt) cc_final: 0.7203 (ttt) REVERT: C 127 PHE cc_start: 0.6815 (t80) cc_final: 0.6478 (t80) REVERT: C 138 LEU cc_start: 0.8877 (mp) cc_final: 0.8541 (mp) REVERT: C 157 THR cc_start: 0.9521 (t) cc_final: 0.9112 (m) REVERT: C 272 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8754 (mm-40) REVERT: C 273 MET cc_start: 0.8100 (ttm) cc_final: 0.7770 (ttm) REVERT: C 274 ASP cc_start: 0.8109 (t0) cc_final: 0.7678 (t70) REVERT: D 47 MET cc_start: 0.3311 (ttt) cc_final: 0.2850 (mtt) REVERT: D 127 PHE cc_start: 0.6844 (t80) cc_final: 0.6532 (t80) REVERT: D 151 PHE cc_start: 0.8665 (m-80) cc_final: 0.8390 (m-80) REVERT: D 203 GLN cc_start: 0.8447 (tp40) cc_final: 0.8142 (tp40) REVERT: D 270 TYR cc_start: 0.9059 (m-80) cc_final: 0.8580 (m-80) REVERT: D 272 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8697 (mm-40) REVERT: D 273 MET cc_start: 0.7665 (ttm) cc_final: 0.7319 (ttm) REVERT: D 277 PHE cc_start: 0.8000 (m-10) cc_final: 0.7742 (m-80) REVERT: D 278 LYS cc_start: 0.8118 (mttp) cc_final: 0.7803 (mttp) REVERT: E 47 MET cc_start: 0.3069 (ttt) cc_final: 0.2838 (ttt) REVERT: E 161 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8893 (mtmm) REVERT: E 181 GLU cc_start: 0.8538 (tp30) cc_final: 0.8327 (tp30) REVERT: E 273 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7491 (mtm) REVERT: F 47 MET cc_start: 0.4235 (ttt) cc_final: 0.3821 (mtt) REVERT: F 115 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8686 (tt) REVERT: F 157 THR cc_start: 0.9297 (t) cc_final: 0.8948 (m) REVERT: F 210 GLN cc_start: 0.8761 (tp40) cc_final: 0.8540 (mm110) REVERT: F 272 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8430 (mm-40) REVERT: G 157 THR cc_start: 0.9418 (t) cc_final: 0.9032 (m) REVERT: G 274 ASP cc_start: 0.8111 (t0) cc_final: 0.7774 (t70) outliers start: 43 outliers final: 16 residues processed: 355 average time/residue: 0.2222 time to fit residues: 119.3957 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 : 1.484 ------------------------------------------------------------------------------- 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 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 F residue 239 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 88 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13748 Z= 0.314 Angle : 0.624 8.478 18641 Z= 0.328 Chirality : 0.047 0.401 2282 Planarity : 0.004 0.033 2366 Dihedral : 5.259 23.543 1939 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.54 % Allowed : 17.34 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 1764 helix: 0.39 (0.17), residues: 896 sheet: -2.21 (0.27), residues: 273 loop : -3.01 (0.20), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 240 PHE 0.016 0.001 PHE E 178 TYR 0.008 0.001 TYR B 135 ARG 0.006 0.000 ARG D 256 *********************** 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 318 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 1.499 Fit side-chains REVERT: A 112 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 273 MET cc_start: 0.8149 (ttm) cc_final: 0.7372 (ttm) REVERT: B 47 MET cc_start: 0.3792 (ttt) cc_final: 0.3507 (mtt) REVERT: B 212 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 273 MET cc_start: 0.8214 (ttm) cc_final: 0.7529 (ttm) REVERT: C 47 MET cc_start: 0.4256 (ttt) cc_final: 0.3954 (mtt) REVERT: C 115 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8861 (tp) REVERT: C 126 MET cc_start: 0.7603 (ttt) cc_final: 0.7319 (ttt) REVERT: C 127 PHE cc_start: 0.6839 (t80) cc_final: 0.6442 (t80) REVERT: C 157 THR cc_start: 0.9547 (t) cc_final: 0.9238 (m) REVERT: C 212 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7923 (tm-30) REVERT: C 272 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8707 (mm-40) REVERT: C 273 MET cc_start: 0.8073 (ttm) cc_final: 0.7814 (ttm) REVERT: D 47 MET cc_start: 0.3248 (ttt) cc_final: 0.2808 (mtt) REVERT: D 203 GLN cc_start: 0.8505 (tp40) cc_final: 0.8202 (tp40) REVERT: D 212 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7867 (tp30) REVERT: D 270 TYR cc_start: 0.9093 (m-80) cc_final: 0.8637 (m-80) REVERT: E 47 MET cc_start: 0.2996 (ttt) cc_final: 0.2792 (ttt) REVERT: E 126 MET cc_start: 0.7897 (ttt) cc_final: 0.7676 (ttt) REVERT: E 181 GLU cc_start: 0.8574 (tp30) cc_final: 0.8354 (tp30) REVERT: E 273 MET cc_start: 0.8034 (mtm) cc_final: 0.7809 (mtp) REVERT: F 47 MET cc_start: 0.4387 (ttt) cc_final: 0.3978 (mtt) REVERT: F 115 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8890 (tt) REVERT: F 157 THR cc_start: 0.9487 (t) cc_final: 0.9118 (m) REVERT: G 157 THR cc_start: 0.9489 (t) cc_final: 0.9125 (m) REVERT: G 273 MET cc_start: 0.7987 (ttm) cc_final: 0.7284 (ttm) REVERT: G 274 ASP cc_start: 0.8077 (t0) cc_final: 0.7677 (t70) outliers start: 51 outliers final: 29 residues processed: 306 average time/residue: 0.2117 time to fit residues: 101.6094 Evaluate side-chains 265 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 C residue 227 GLU Chi-restraints excluded: chain D residue 138 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 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 225 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 111 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 152 SER 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 157 optimal weight: 3.9990 chunk 119 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.3464 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13748 Z= 0.325 Angle : 0.611 8.547 18641 Z= 0.320 Chirality : 0.047 0.400 2282 Planarity : 0.003 0.036 2366 Dihedral : 5.142 23.251 1939 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.16 % Allowed : 17.06 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1764 helix: 0.80 (0.17), residues: 896 sheet: -1.76 (0.31), residues: 224 loop : -2.97 (0.19), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 240 PHE 0.014 0.001 PHE C 277 TYR 0.010 0.001 TYR B 135 ARG 0.004 0.000 ARG D 256 *********************** 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 310 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 1.442 Fit side-chains REVERT: A 112 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 203 GLN cc_start: 0.8554 (tp40) cc_final: 0.8241 (tp40) REVERT: A 212 GLU cc_start: 0.8457 (tp30) cc_final: 0.8191 (tm-30) REVERT: A 272 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8811 (mm-40) REVERT: A 273 MET cc_start: 0.8151 (ttm) cc_final: 0.7284 (ttm) REVERT: B 47 MET cc_start: 0.3741 (ttt) cc_final: 0.3465 (mtt) REVERT: B 115 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8968 (tt) REVERT: B 273 MET cc_start: 0.8153 (ttm) cc_final: 0.7459 (ttm) REVERT: C 47 MET cc_start: 0.4228 (ttt) cc_final: 0.3984 (mtt) REVERT: C 115 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8960 (tp) REVERT: C 126 MET cc_start: 0.7869 (ttt) cc_final: 0.7574 (ttt) REVERT: C 127 PHE cc_start: 0.6838 (t80) cc_final: 0.6427 (t80) REVERT: C 157 THR cc_start: 0.9562 (t) cc_final: 0.9253 (m) REVERT: C 273 MET cc_start: 0.8017 (ttm) cc_final: 0.7726 (ttm) REVERT: C 274 ASP cc_start: 0.8036 (t0) cc_final: 0.7627 (t0) REVERT: D 47 MET cc_start: 0.3266 (ttt) cc_final: 0.2819 (mtt) REVERT: D 203 GLN cc_start: 0.8551 (tp40) cc_final: 0.8281 (tp40) REVERT: D 270 TYR cc_start: 0.9099 (m-80) cc_final: 0.8605 (m-80) REVERT: D 272 GLN cc_start: 0.9141 (mm110) cc_final: 0.8837 (mm-40) REVERT: E 47 MET cc_start: 0.3120 (ttt) cc_final: 0.2904 (ttt) REVERT: E 134 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7119 (mp0) REVERT: E 181 GLU cc_start: 0.8557 (tp30) cc_final: 0.8330 (tp30) REVERT: E 212 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7761 (tp30) REVERT: F 47 MET cc_start: 0.4218 (ttt) cc_final: 0.3818 (mtt) REVERT: F 115 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8945 (tt) REVERT: F 157 THR cc_start: 0.9493 (t) cc_final: 0.9178 (m) REVERT: F 212 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7857 (tp30) REVERT: G 157 THR cc_start: 0.9479 (t) cc_final: 0.9147 (m) REVERT: G 212 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7765 (tp30) REVERT: G 274 ASP cc_start: 0.7992 (t0) cc_final: 0.7522 (t70) outliers start: 60 outliers final: 35 residues processed: 291 average time/residue: 0.2072 time to fit residues: 95.2185 Evaluate side-chains 274 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 199 ASP 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 115 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 ASP 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 C residue 227 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 127 PHE 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 F residue 233 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 152 SER 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 140 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 chunk 69 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 116 optimal weight: 0.0570 chunk 0 optimal weight: 40.0000 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.3702 ------------------------------------------------------------------------------- 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 E 200 GLN F 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13748 Z= 0.221 Angle : 0.576 9.021 18641 Z= 0.298 Chirality : 0.045 0.390 2282 Planarity : 0.003 0.034 2366 Dihedral : 4.933 21.309 1939 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.40 % Allowed : 19.35 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1764 helix: 1.04 (0.17), residues: 896 sheet: -1.54 (0.32), residues: 224 loop : -2.88 (0.19), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 240 PHE 0.012 0.001 PHE E 178 TYR 0.008 0.001 TYR F 135 ARG 0.003 0.000 ARG D 256 *********************** 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 313 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 1.498 Fit side-chains REVERT: A 112 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 210 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8394 (mm-40) REVERT: A 212 GLU cc_start: 0.8404 (tp30) cc_final: 0.8177 (tm-30) REVERT: A 272 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8762 (mm-40) REVERT: A 273 MET cc_start: 0.8037 (ttm) cc_final: 0.7173 (ttm) REVERT: B 47 MET cc_start: 0.3766 (ttt) cc_final: 0.3467 (mtt) REVERT: B 273 MET cc_start: 0.8087 (ttm) cc_final: 0.7399 (ttm) REVERT: C 47 MET cc_start: 0.4253 (ttt) cc_final: 0.3984 (mtt) REVERT: C 115 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8945 (tp) REVERT: C 126 MET cc_start: 0.7847 (ttt) cc_final: 0.7556 (ttt) REVERT: C 157 THR cc_start: 0.9522 (t) cc_final: 0.9209 (m) REVERT: C 273 MET cc_start: 0.8061 (ttm) cc_final: 0.7775 (ttm) REVERT: D 47 MET cc_start: 0.3390 (ttt) cc_final: 0.2951 (mtt) REVERT: D 115 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8919 (tp) REVERT: D 203 GLN cc_start: 0.8547 (tp40) cc_final: 0.8282 (tp40) REVERT: D 212 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7694 (tp30) REVERT: E 47 MET cc_start: 0.3283 (ttt) cc_final: 0.3083 (ttt) REVERT: E 69 LEU cc_start: 0.8805 (mm) cc_final: 0.8545 (tp) REVERT: E 134 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7095 (mp0) REVERT: E 150 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9143 (tp) REVERT: E 181 GLU cc_start: 0.8472 (tp30) cc_final: 0.8252 (tp30) REVERT: E 212 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7928 (tp30) REVERT: E 267 SER cc_start: 0.8952 (t) cc_final: 0.8583 (p) REVERT: F 47 MET cc_start: 0.4242 (ttt) cc_final: 0.3827 (mtt) REVERT: F 112 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8265 (tm-30) REVERT: F 115 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8952 (tt) REVERT: F 157 THR cc_start: 0.9477 (t) cc_final: 0.9155 (m) REVERT: G 112 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8681 (tm-30) REVERT: G 157 THR cc_start: 0.9445 (t) cc_final: 0.9152 (m) REVERT: G 274 ASP cc_start: 0.8037 (t0) cc_final: 0.7543 (t70) outliers start: 49 outliers final: 29 residues processed: 302 average time/residue: 0.2188 time to fit residues: 101.7217 Evaluate side-chains 274 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 223 VAL 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 149 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 115 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 150 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 GLU 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 138 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 152 SER 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 56 optimal weight: 40.0000 chunk 152 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN G 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13748 Z= 0.375 Angle : 0.633 7.222 18641 Z= 0.330 Chirality : 0.047 0.389 2282 Planarity : 0.003 0.034 2366 Dihedral : 5.060 23.302 1939 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.23 % Allowed : 20.18 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1764 helix: 1.11 (0.17), residues: 896 sheet: -1.90 (0.31), residues: 210 loop : -2.68 (0.20), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 240 PHE 0.013 0.001 PHE C 277 TYR 0.011 0.001 TYR B 135 ARG 0.007 0.000 ARG D 238 *********************** 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 302 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 1.460 Fit side-chains REVERT: A 112 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8453 (tm-30) REVERT: A 203 GLN cc_start: 0.8507 (tp40) cc_final: 0.8239 (tp40) REVERT: A 212 GLU cc_start: 0.8385 (tp30) cc_final: 0.8162 (tm-30) REVERT: A 273 MET cc_start: 0.8024 (ttm) cc_final: 0.7590 (ttm) REVERT: B 47 MET cc_start: 0.3807 (ttt) cc_final: 0.3523 (mtt) REVERT: B 212 GLU cc_start: 0.8421 (tp30) cc_final: 0.8182 (tm-30) REVERT: B 273 MET cc_start: 0.8137 (ttm) cc_final: 0.7440 (ttm) REVERT: C 47 MET cc_start: 0.4244 (ttt) cc_final: 0.3961 (mtt) REVERT: C 112 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 126 MET cc_start: 0.7854 (ttt) cc_final: 0.7545 (ttt) REVERT: C 273 MET cc_start: 0.8035 (ttm) cc_final: 0.7743 (ttm) REVERT: D 47 MET cc_start: 0.3417 (ttt) cc_final: 0.2974 (mtt) REVERT: D 112 GLN cc_start: 0.8440 (tt0) cc_final: 0.8099 (tm-30) REVERT: D 115 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8874 (tp) REVERT: D 203 GLN cc_start: 0.8578 (tp40) cc_final: 0.8328 (tp40) REVERT: D 278 LYS cc_start: 0.8336 (mmmm) cc_final: 0.7961 (mmtp) REVERT: E 47 MET cc_start: 0.3391 (ttt) cc_final: 0.3180 (ttt) REVERT: E 69 LEU cc_start: 0.8812 (mm) cc_final: 0.8504 (tp) REVERT: E 134 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7118 (mp0) REVERT: E 150 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9175 (tp) REVERT: E 181 GLU cc_start: 0.8558 (tp30) cc_final: 0.8332 (tp30) REVERT: E 212 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7979 (tp30) REVERT: E 267 SER cc_start: 0.9006 (t) cc_final: 0.8647 (p) REVERT: F 47 MET cc_start: 0.4172 (ttt) cc_final: 0.3781 (mtt) REVERT: F 112 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8295 (tm-30) REVERT: F 115 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8983 (tt) REVERT: F 157 THR cc_start: 0.9497 (t) cc_final: 0.9130 (m) REVERT: F 212 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7825 (tp30) REVERT: G 112 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8706 (tm-30) REVERT: G 212 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7853 (tm-30) outliers start: 61 outliers final: 32 residues processed: 288 average time/residue: 0.2211 time to fit residues: 98.0145 Evaluate side-chains 265 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 199 ASP 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 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 C residue 227 GLU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 199 ASP 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 223 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 164 VAL 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 19 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13748 Z= 0.259 Angle : 0.602 10.181 18641 Z= 0.309 Chirality : 0.045 0.235 2282 Planarity : 0.003 0.033 2366 Dihedral : 4.936 21.290 1939 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.26 % Allowed : 21.98 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1764 helix: 1.23 (0.17), residues: 896 sheet: -1.66 (0.32), residues: 210 loop : -2.63 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 240 PHE 0.012 0.001 PHE E 178 TYR 0.011 0.001 TYR D 135 ARG 0.005 0.000 ARG D 238 *********************** 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 309 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.433 Fit side-chains REVERT: A 112 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8481 (tm-30) REVERT: A 134 GLU cc_start: 0.7840 (pm20) cc_final: 0.7640 (pm20) REVERT: A 203 GLN cc_start: 0.8578 (tp40) cc_final: 0.8239 (tp40) REVERT: A 273 MET cc_start: 0.7994 (ttm) cc_final: 0.7605 (ttm) REVERT: B 47 MET cc_start: 0.3806 (ttt) cc_final: 0.3498 (mtt) REVERT: B 112 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 212 GLU cc_start: 0.8406 (tp30) cc_final: 0.8173 (tm-30) REVERT: B 273 MET cc_start: 0.8107 (ttm) cc_final: 0.7419 (ttm) REVERT: C 47 MET cc_start: 0.4124 (ttt) cc_final: 0.3845 (mtt) REVERT: C 112 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8314 (tm-30) REVERT: C 126 MET cc_start: 0.7839 (ttt) cc_final: 0.7571 (ttt) REVERT: C 212 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7749 (tp30) REVERT: C 273 MET cc_start: 0.8102 (ttm) cc_final: 0.7748 (ttm) REVERT: D 47 MET cc_start: 0.3410 (ttt) cc_final: 0.2981 (mtt) REVERT: D 115 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8845 (tp) REVERT: D 203 GLN cc_start: 0.8563 (tp40) cc_final: 0.8302 (tp40) REVERT: D 212 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7651 (tp30) REVERT: E 47 MET cc_start: 0.3467 (ttt) cc_final: 0.3229 (ttt) REVERT: E 150 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9109 (tp) REVERT: E 181 GLU cc_start: 0.8477 (tp30) cc_final: 0.8250 (tp30) REVERT: E 212 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8015 (tp30) REVERT: E 267 SER cc_start: 0.8989 (t) cc_final: 0.8625 (p) REVERT: F 47 MET cc_start: 0.4226 (ttt) cc_final: 0.3844 (mtt) REVERT: F 112 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8367 (tm-30) REVERT: F 115 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8964 (tt) REVERT: F 157 THR cc_start: 0.9484 (t) cc_final: 0.9127 (m) REVERT: F 159 ASP cc_start: 0.8800 (p0) cc_final: 0.8371 (p0) REVERT: F 212 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7801 (tp30) REVERT: F 245 ASP cc_start: 0.8384 (m-30) cc_final: 0.8173 (m-30) REVERT: G 112 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8703 (tm-30) outliers start: 47 outliers final: 33 residues processed: 296 average time/residue: 0.1992 time to fit residues: 93.8372 Evaluate side-chains 278 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 VAL 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 136 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 115 LEU 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 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 199 ASP 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 126 MET Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 152 SER 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 67 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 50 optimal weight: 40.0000 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13748 Z= 0.276 Angle : 0.633 9.787 18641 Z= 0.321 Chirality : 0.048 0.447 2282 Planarity : 0.003 0.031 2366 Dihedral : 4.949 20.908 1939 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.54 % Allowed : 22.19 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1764 helix: 1.26 (0.16), residues: 896 sheet: -1.60 (0.31), residues: 210 loop : -2.60 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 240 PHE 0.019 0.001 PHE E 277 TYR 0.011 0.001 TYR F 135 ARG 0.005 0.000 ARG G 256 *********************** 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 296 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 1.559 Fit side-chains REVERT: A 112 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 273 MET cc_start: 0.8036 (ttm) cc_final: 0.7240 (ttm) REVERT: B 47 MET cc_start: 0.3905 (ttt) cc_final: 0.3613 (mtt) REVERT: B 112 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 212 GLU cc_start: 0.8413 (tp30) cc_final: 0.8209 (tm-30) REVERT: B 273 MET cc_start: 0.8186 (ttm) cc_final: 0.7430 (ttm) REVERT: C 47 MET cc_start: 0.4128 (ttt) cc_final: 0.3846 (mtt) REVERT: C 112 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8451 (tm-30) REVERT: C 126 MET cc_start: 0.7860 (ttt) cc_final: 0.7610 (ttt) REVERT: C 212 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7896 (tp30) REVERT: C 273 MET cc_start: 0.8096 (ttm) cc_final: 0.7665 (ttm) REVERT: D 47 MET cc_start: 0.3443 (ttt) cc_final: 0.3002 (mtt) REVERT: D 203 GLN cc_start: 0.8566 (tp40) cc_final: 0.8292 (tp40) REVERT: D 212 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7471 (tp30) REVERT: E 47 MET cc_start: 0.3450 (ttt) cc_final: 0.3226 (ttt) REVERT: E 69 LEU cc_start: 0.8836 (mm) cc_final: 0.8542 (tp) REVERT: E 181 GLU cc_start: 0.8484 (tp30) cc_final: 0.8247 (tp30) REVERT: E 212 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8005 (tp30) REVERT: E 267 SER cc_start: 0.8895 (t) cc_final: 0.8552 (p) REVERT: F 47 MET cc_start: 0.4220 (ttt) cc_final: 0.3854 (mtt) REVERT: F 112 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8395 (tm-30) REVERT: F 115 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8966 (tt) REVERT: F 157 THR cc_start: 0.9491 (t) cc_final: 0.9135 (m) REVERT: F 212 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7692 (tm-30) REVERT: G 112 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8665 (tm-30) REVERT: G 212 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7762 (tp30) outliers start: 51 outliers final: 37 residues processed: 282 average time/residue: 0.1934 time to fit residues: 86.8743 Evaluate side-chains 277 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 VAL 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 164 VAL 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 109 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE 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 199 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 199 ASP 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 126 MET Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 152 SER 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 161 optimal weight: 2.9990 chunk 147 optimal weight: 0.1980 chunk 157 optimal weight: 7.9990 chunk 94 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 13748 Z= 0.166 Angle : 0.608 10.520 18641 Z= 0.301 Chirality : 0.047 0.459 2282 Planarity : 0.003 0.034 2366 Dihedral : 4.706 17.811 1939 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.36 % Allowed : 23.51 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1764 helix: 1.39 (0.17), residues: 896 sheet: -0.88 (0.33), residues: 224 loop : -2.69 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 240 PHE 0.012 0.001 PHE E 277 TYR 0.011 0.001 TYR F 135 ARG 0.005 0.000 ARG D 238 *********************** 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 302 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 1.364 Fit side-chains REVERT: A 112 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8488 (tm-30) REVERT: A 187 GLU cc_start: 0.7509 (tt0) cc_final: 0.7057 (tt0) REVERT: A 203 GLN cc_start: 0.8539 (tp40) cc_final: 0.8305 (tp40) REVERT: A 273 MET cc_start: 0.7916 (ttm) cc_final: 0.7673 (ttm) REVERT: B 47 MET cc_start: 0.4011 (ttt) cc_final: 0.3754 (mtt) REVERT: B 127 PHE cc_start: 0.6602 (t80) cc_final: 0.6264 (t80) REVERT: B 273 MET cc_start: 0.8083 (ttm) cc_final: 0.7862 (ttm) REVERT: B 274 ASP cc_start: 0.8022 (t70) cc_final: 0.7794 (m-30) REVERT: C 47 MET cc_start: 0.4137 (ttt) cc_final: 0.3836 (mtt) REVERT: C 112 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8506 (tm-30) REVERT: C 126 MET cc_start: 0.7770 (ttt) cc_final: 0.7528 (ttt) REVERT: C 134 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7245 (pt0) REVERT: C 212 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7955 (tp30) REVERT: D 47 MET cc_start: 0.3446 (ttt) cc_final: 0.3023 (mtt) REVERT: D 203 GLN cc_start: 0.8533 (tp40) cc_final: 0.8253 (tp40) REVERT: D 212 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7645 (tp30) REVERT: E 69 LEU cc_start: 0.8764 (mm) cc_final: 0.8437 (tp) REVERT: E 212 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7952 (tp30) REVERT: E 267 SER cc_start: 0.8669 (t) cc_final: 0.8395 (p) REVERT: F 47 MET cc_start: 0.4092 (ttt) cc_final: 0.3726 (mtt) REVERT: F 112 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8438 (tm-30) REVERT: F 115 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8916 (tt) REVERT: F 157 THR cc_start: 0.9424 (t) cc_final: 0.9122 (m) REVERT: G 112 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8653 (tm-30) REVERT: G 212 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7809 (tp30) outliers start: 34 outliers final: 28 residues processed: 292 average time/residue: 0.2141 time to fit residues: 96.9650 Evaluate side-chains 268 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 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 109 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 95 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 152 SER 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 166 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13748 Z= 0.178 Angle : 0.640 11.637 18641 Z= 0.312 Chirality : 0.047 0.457 2282 Planarity : 0.003 0.037 2366 Dihedral : 4.685 18.445 1939 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.15 % Allowed : 24.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1764 helix: 1.48 (0.16), residues: 896 sheet: -0.77 (0.33), residues: 224 loop : -2.63 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 240 PHE 0.011 0.001 PHE E 277 TYR 0.015 0.001 TYR F 135 ARG 0.010 0.000 ARG A 238 ********************** 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 280 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 1.633 Fit side-chains REVERT: A 112 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8489 (tm-30) REVERT: A 238 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8091 (mtt90) REVERT: A 273 MET cc_start: 0.7899 (ttm) cc_final: 0.7529 (ttm) REVERT: B 47 MET cc_start: 0.4063 (ttt) cc_final: 0.3815 (mtt) REVERT: B 127 PHE cc_start: 0.6484 (t80) cc_final: 0.6193 (t80) REVERT: B 273 MET cc_start: 0.8046 (ttm) cc_final: 0.7751 (ttm) REVERT: B 274 ASP cc_start: 0.8040 (t70) cc_final: 0.7583 (t70) REVERT: C 47 MET cc_start: 0.4182 (ttt) cc_final: 0.3906 (mtt) REVERT: C 112 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 126 MET cc_start: 0.7690 (ttt) cc_final: 0.7434 (ttt) REVERT: C 134 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7232 (pt0) REVERT: C 212 GLU cc_start: 0.8209 (tm-30) cc_final: 0.8000 (tp30) REVERT: D 47 MET cc_start: 0.3485 (ttt) cc_final: 0.3045 (mtt) REVERT: D 203 GLN cc_start: 0.8520 (tp40) cc_final: 0.8266 (tp40) REVERT: D 212 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7508 (tp30) REVERT: E 65 VAL cc_start: 0.8541 (p) cc_final: 0.8319 (p) REVERT: E 69 LEU cc_start: 0.8784 (mm) cc_final: 0.8461 (tp) REVERT: E 212 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7872 (tp30) REVERT: E 267 SER cc_start: 0.8628 (t) cc_final: 0.8334 (p) REVERT: F 47 MET cc_start: 0.4145 (ttt) cc_final: 0.3749 (mtt) REVERT: F 112 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8423 (tm-30) REVERT: F 115 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8898 (tt) REVERT: F 157 THR cc_start: 0.9438 (t) cc_final: 0.9142 (m) REVERT: F 272 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8859 (mm110) REVERT: G 112 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8642 (tm-30) REVERT: G 212 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7844 (tp30) outliers start: 31 outliers final: 25 residues processed: 270 average time/residue: 0.2077 time to fit residues: 88.2582 Evaluate side-chains 268 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 223 VAL 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 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 138 LEU 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 147 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 40.0000 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 40.0000 chunk 122 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4014 r_free = 0.4014 target = 0.163701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112408 restraints weight = 19063.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116541 restraints weight = 9599.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119211 restraints weight = 6347.373| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13748 Z= 0.181 Angle : 0.638 11.646 18641 Z= 0.315 Chirality : 0.047 0.458 2282 Planarity : 0.003 0.032 2366 Dihedral : 4.653 18.338 1939 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.94 % Allowed : 24.41 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1764 helix: 1.49 (0.16), residues: 896 sheet: -0.69 (0.33), residues: 224 loop : -2.58 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 240 PHE 0.012 0.001 PHE E 68 TYR 0.015 0.001 TYR F 135 ARG 0.008 0.000 ARG F 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.57 seconds wall clock time: 49 minutes 59.51 seconds (2999.51 seconds total)