Starting phenix.real_space_refine on Tue Aug 4 23:47:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tin_55962/08_2026/9tin_55962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tin_55962/08_2026/9tin_55962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tin_55962/08_2026/9tin_55962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tin_55962/08_2026/9tin_55962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tin_55962/08_2026/9tin_55962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tin_55962/08_2026/9tin_55962.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 12 5.16 5 C 4692 2.51 5 N 1195 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7390 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1327 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "B" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1327 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "C" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1327 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "D" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 861 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1279 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain breaks: 1 Chain: "F" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1269 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain breaks: 1 Time building chain proxies: 1.52, per 1000 atoms: 0.21 Number of scatterers: 7390 At special positions: 0 Unit cell: (115.037, 131.709, 101.699, 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 12 16.00 O 1491 8.00 N 1195 7.00 C 4692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 265.7 milliseconds 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 16 sheets defined 20.1% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.838A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.761A pdb=" N LEU B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP B 12 " --> pdb=" O PRO B 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 8 through 12' Processing helix chain 'B' and resid 15 through 18 Processing helix chain 'B' and resid 32 through 55 removed outlier: 3.703A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 43 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 removed outlier: 5.077A pdb=" N ALA B 121 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 18 Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.533A pdb=" N TYR C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.615A pdb=" N LEU C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 156 through 166 removed outlier: 4.506A pdb=" N ASP D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 removed outlier: 3.748A pdb=" N HIS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'F' and resid 5 through 19 removed outlier: 3.985A pdb=" N HIS F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 89 through 97 removed outlier: 4.286A pdb=" N LYS F 94 " --> pdb=" O PRO F 90 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 6.683A pdb=" N ARG A 20 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU B 143 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 22 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 140 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU B 104 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR B 159 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 106 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 63 removed outlier: 6.576A pdb=" N LYS A 60 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR A 82 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 62 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 165 removed outlier: 7.109A pdb=" N ILE A 106 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR A 159 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU A 104 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS C 22 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU A 143 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG C 20 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 24 removed outlier: 6.484A pdb=" N ARG B 20 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLU C 143 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 22 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 140 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 144 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 111 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 108 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR C 156 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 63 removed outlier: 4.189A pdb=" N ASP B 59 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 82 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR B 80 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 63 removed outlier: 3.659A pdb=" N ASP C 59 " --> pdb=" O TYR C 82 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR C 80 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.670A pdb=" N SER D 114 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP D 177 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE D 188 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.670A pdb=" N SER D 114 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP D 177 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP E 100 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU E 63 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 197 through 200 removed outlier: 3.684A pdb=" N TYR D 200 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 168 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU F 167 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER F 105 " --> pdb=" O GLU F 167 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 171 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 101 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER F 67 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N SER F 84 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.509A pdb=" N PHE F 151 " --> pdb=" O ILE E 3 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU F 148 " --> pdb=" O MET F 124 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET F 124 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE F 150 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE F 27 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY F 54 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 136 through 137 removed outlier: 3.711A pdb=" N GLY E 54 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL E 120 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE E 151 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE E 122 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB7, first strand: chain 'F' and resid 127 through 128 removed outlier: 7.050A pdb=" N VAL F 127 " --> pdb=" O GLU F 143 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 693 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: 0.94 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2405 1.34 - 1.46: 1449 1.46 - 1.57: 3658 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 7536 Sorted by residual: bond pdb=" N ILE A 87 " pdb=" CA ILE A 87 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" CA ILE B 87 " pdb=" CB ILE B 87 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.01e+00 bond pdb=" CA VAL C 130 " pdb=" CB VAL C 130 " ideal model delta sigma weight residual 1.547 1.537 0.010 1.10e-02 8.26e+03 8.11e-01 bond pdb=" C VAL B 130 " pdb=" O VAL B 130 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 7.31e-01 bond pdb=" CA LEU F 103 " pdb=" CB LEU F 103 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.35e-02 5.49e+03 6.31e-01 ... (remaining 7531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 9607 0.91 - 1.83: 519 1.83 - 2.74: 56 2.74 - 3.66: 37 3.66 - 4.57: 5 Bond angle restraints: 10224 Sorted by residual: angle pdb=" N ILE B 54 " pdb=" CA ILE B 54 " pdb=" C ILE B 54 " ideal model delta sigma weight residual 111.48 109.13 2.35 9.40e-01 1.13e+00 6.27e+00 angle pdb=" N ILE E 53 " pdb=" CA ILE E 53 " pdb=" C ILE E 53 " ideal model delta sigma weight residual 111.67 109.38 2.29 9.50e-01 1.11e+00 5.80e+00 angle pdb=" C GLY D 193 " pdb=" N LEU D 194 " pdb=" CA LEU D 194 " ideal model delta sigma weight residual 120.09 123.00 -2.91 1.25e+00 6.40e-01 5.40e+00 angle pdb=" CA ILE A 87 " pdb=" C ILE A 87 " pdb=" O ILE A 87 " ideal model delta sigma weight residual 122.63 120.85 1.78 8.70e-01 1.32e+00 4.18e+00 angle pdb=" N TYR D 141 " pdb=" CA TYR D 141 " pdb=" C TYR D 141 " ideal model delta sigma weight residual 112.93 110.80 2.13 1.12e+00 7.97e-01 3.61e+00 ... (remaining 10219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 4411 14.31 - 28.62: 88 28.62 - 42.93: 24 42.93 - 57.24: 5 57.24 - 71.55: 2 Dihedral angle restraints: 4530 sinusoidal: 1808 harmonic: 2722 Sorted by residual: dihedral pdb=" CA ASP D 152 " pdb=" C ASP D 152 " pdb=" N TYR D 153 " pdb=" CA TYR D 153 " ideal model delta harmonic sigma weight residual 180.00 164.69 15.31 0 5.00e+00 4.00e-02 9.38e+00 dihedral pdb=" N ARG D 183 " pdb=" CA ARG D 183 " pdb=" CB ARG D 183 " pdb=" CG ARG D 183 " ideal model delta sinusoidal sigma weight residual -180.00 -130.01 -49.99 3 1.50e+01 4.44e-03 8.84e+00 dihedral pdb=" CA ARG B 29 " pdb=" CB ARG B 29 " pdb=" CG ARG B 29 " pdb=" CD ARG B 29 " ideal model delta sinusoidal sigma weight residual -180.00 -136.59 -43.41 3 1.50e+01 4.44e-03 7.80e+00 ... (remaining 4527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 691 0.028 - 0.055: 303 0.055 - 0.083: 36 0.083 - 0.110: 90 0.110 - 0.138: 26 Chirality restraints: 1146 Sorted by residual: chirality pdb=" CA VAL E 138 " pdb=" N VAL E 138 " pdb=" C VAL E 138 " pdb=" CB VAL E 138 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE E 3 " pdb=" N ILE E 3 " pdb=" C ILE E 3 " pdb=" CB ILE E 3 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1143 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 154 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO D 155 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 155 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 155 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 138 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO E 139 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 139 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 139 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 31 " 0.014 5.00e-02 4.00e+02 2.12e-02 7.18e-01 pdb=" N PRO E 32 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO E 32 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 32 " 0.012 5.00e-02 4.00e+02 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 124 2.63 - 3.20: 6838 3.20 - 3.76: 10433 3.76 - 4.33: 15338 4.33 - 4.90: 25736 Nonbonded interactions: 58469 Sorted by model distance: nonbonded pdb=" OD1 ASP A 52 " pdb=" OH TYR A 82 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR E 5 " pdb=" O LEU F 148 " model vdw 2.077 3.040 nonbonded pdb=" OD1 ASP B 52 " pdb=" OH TYR B 82 " model vdw 2.080 3.040 nonbonded pdb=" OD2 ASP F 152 " pdb=" NZ LYS F 154 " model vdw 2.161 3.120 nonbonded pdb=" O SER F 30 " pdb=" NH1 ARG F 118 " model vdw 2.163 3.120 ... (remaining 58464 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' } ncs_group { reference = (chain 'E' and (resid 2 through 66 or resid 78 through 173)) selection = (chain 'F' and (resid 2 through 66 or resid 78 through 173)) } 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: 0.390 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.000 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.002 0.021 7536 Z= 0.107 Angle : 0.481 4.570 10224 Z= 0.296 Chirality : 0.042 0.138 1146 Planarity : 0.003 0.031 1328 Dihedral : 6.899 71.547 2790 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.24 % Allowed : 1.69 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.30), residues: 920 helix: 1.78 (0.49), residues: 131 sheet: 1.11 (0.37), residues: 212 loop : 0.84 (0.28), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.005 0.001 TYR C 133 PHE 0.004 0.000 PHE D 154 TRP 0.006 0.001 TRP D 190 HIS 0.001 0.000 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.11 ( 7536) covalent geometry : angle 0.48113 / 0.30 (10224) hydrogen bonds : bond 0.26120 / 17.01 ( 258) hydrogen bonds : angle 8.61208 / 6.06 ( 693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8750 (m) cc_final: 0.8490 (t) REVERT: B 114 ILE cc_start: 0.8687 (mt) cc_final: 0.8313 (mp) REVERT: C 12 ASP cc_start: 0.7914 (t70) cc_final: 0.7427 (t0) REVERT: C 14 PHE cc_start: 0.7743 (t80) cc_final: 0.7488 (t80) REVERT: C 61 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8511 (mm-40) REVERT: C 84 ASN cc_start: 0.8997 (t0) cc_final: 0.8485 (t0) REVERT: C 105 THR cc_start: 0.7667 (p) cc_final: 0.7385 (p) REVERT: C 140 ARG cc_start: 0.8233 (mpt180) cc_final: 0.7752 (mmt90) REVERT: E 135 PHE cc_start: 0.7924 (m-80) cc_final: 0.7627 (m-80) outliers start: 2 outliers final: 2 residues processed: 338 average time/residue: 0.0782 time to fit residues: 34.1454 Evaluate side-chains 201 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain E residue 150 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 77 ASN A 84 ASN B 84 ASN B 171 ASN C 126 GLN E 119 GLN E 155 GLN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131158 restraints weight = 11404.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.130908 restraints weight = 8769.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132154 restraints weight = 7092.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132648 restraints weight = 5127.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132800 restraints weight = 5005.354| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7536 Z= 0.133 Angle : 0.584 8.094 10224 Z= 0.309 Chirality : 0.047 0.184 1146 Planarity : 0.004 0.043 1328 Dihedral : 4.081 52.750 1015 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.30 % Allowed : 12.33 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.29), residues: 920 helix: 1.30 (0.45), residues: 142 sheet: 0.75 (0.35), residues: 226 loop : 0.72 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 13 TYR 0.015 0.001 TYR F 80 PHE 0.019 0.001 PHE E 156 TRP 0.008 0.001 TRP D 190 HIS 0.002 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7536) covalent geometry : angle 0.58396 / 0.31 (10224) hydrogen bonds : bond 0.05155 / 3.20 ( 258) hydrogen bonds : angle 5.93862 / 4.13 ( 693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.7928 (pt0) cc_final: 0.7459 (mm110) REVERT: B 116 THR cc_start: 0.8222 (p) cc_final: 0.7886 (t) REVERT: C 12 ASP cc_start: 0.7395 (t70) cc_final: 0.6776 (t0) REVERT: C 84 ASN cc_start: 0.8935 (t0) cc_final: 0.8485 (t0) REVERT: C 105 THR cc_start: 0.7846 (p) cc_final: 0.7535 (p) REVERT: C 140 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8097 (mmt90) REVERT: C 161 MET cc_start: 0.7794 (tpt) cc_final: 0.6634 (ttp) REVERT: D 110 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6508 (p0) REVERT: D 201 GLN cc_start: 0.4414 (mm-40) cc_final: 0.3927 (mm-40) REVERT: E 112 LEU cc_start: 0.8004 (mt) cc_final: 0.7797 (mt) REVERT: F 16 LEU cc_start: 0.7748 (mp) cc_final: 0.7486 (mt) REVERT: F 63 LEU cc_start: 0.8361 (mp) cc_final: 0.8156 (mt) outliers start: 19 outliers final: 8 residues processed: 229 average time/residue: 0.0700 time to fit residues: 22.0203 Evaluate side-chains 190 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 134 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN A 92 ASN B 49 ASN B 171 ASN C 26 ASN E 162 GLN F 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117688 restraints weight = 11757.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119812 restraints weight = 7020.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121192 restraints weight = 4824.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122072 restraints weight = 3678.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122710 restraints weight = 3034.066| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7536 Z= 0.140 Angle : 0.562 6.233 10224 Z= 0.294 Chirality : 0.046 0.189 1146 Planarity : 0.004 0.030 1328 Dihedral : 4.113 41.798 1013 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.78 % Allowed : 15.36 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 920 helix: 1.61 (0.47), residues: 130 sheet: 0.68 (0.34), residues: 241 loop : 0.61 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 140 TYR 0.011 0.001 TYR D 200 PHE 0.026 0.001 PHE C 14 TRP 0.010 0.001 TRP E 85 HIS 0.001 0.000 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7536) covalent geometry : angle 0.56180 / 0.29 (10224) hydrogen bonds : bond 0.04429 / 2.82 ( 258) hydrogen bonds : angle 5.45522 / 3.75 ( 693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 168 GLN cc_start: 0.8044 (pt0) cc_final: 0.7841 (mm-40) REVERT: B 5 PHE cc_start: 0.7656 (m-80) cc_final: 0.7242 (m-80) REVERT: B 33 GLN cc_start: 0.8946 (pm20) cc_final: 0.8606 (pm20) REVERT: B 143 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8028 (mt-10) REVERT: C 12 ASP cc_start: 0.7155 (t70) cc_final: 0.6757 (t0) REVERT: C 84 ASN cc_start: 0.9083 (t0) cc_final: 0.8653 (t0) REVERT: C 105 THR cc_start: 0.7840 (p) cc_final: 0.7553 (p) REVERT: C 161 MET cc_start: 0.7955 (tpt) cc_final: 0.6369 (ttt) REVERT: C 166 TYR cc_start: 0.7355 (m-10) cc_final: 0.6325 (m-10) REVERT: D 110 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6652 (p0) REVERT: D 189 LYS cc_start: 0.8092 (ptpp) cc_final: 0.7767 (mtpp) REVERT: F 27 ILE cc_start: 0.7532 (tp) cc_final: 0.7071 (tt) outliers start: 23 outliers final: 14 residues processed: 199 average time/residue: 0.0601 time to fit residues: 16.8916 Evaluate side-chains 185 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.0170 chunk 75 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 49 ASN B 171 ASN C 126 GLN E 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128644 restraints weight = 11677.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129243 restraints weight = 8712.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129994 restraints weight = 6777.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130269 restraints weight = 5532.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130670 restraints weight = 4821.394| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7536 Z= 0.118 Angle : 0.538 6.245 10224 Z= 0.281 Chirality : 0.046 0.184 1146 Planarity : 0.004 0.032 1328 Dihedral : 4.125 44.931 1013 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.39 % Allowed : 17.29 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.29), residues: 920 helix: 1.56 (0.47), residues: 130 sheet: 0.47 (0.34), residues: 246 loop : 0.56 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 88 TYR 0.011 0.001 TYR F 80 PHE 0.024 0.001 PHE C 14 TRP 0.007 0.001 TRP E 85 HIS 0.001 0.000 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7536) covalent geometry : angle 0.53766 / 0.28 (10224) hydrogen bonds : bond 0.04002 / 2.55 ( 258) hydrogen bonds : angle 5.21308 / 3.52 ( 693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 33 GLN cc_start: 0.8984 (pm20) cc_final: 0.8698 (pm20) REVERT: B 143 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7881 (mt-10) REVERT: C 12 ASP cc_start: 0.7101 (t70) cc_final: 0.6673 (t0) REVERT: C 84 ASN cc_start: 0.8913 (t0) cc_final: 0.8591 (t0) REVERT: C 105 THR cc_start: 0.7856 (p) cc_final: 0.7537 (p) REVERT: C 161 MET cc_start: 0.7989 (tpt) cc_final: 0.6426 (ttt) REVERT: C 166 TYR cc_start: 0.7365 (m-10) cc_final: 0.6428 (m-10) REVERT: D 110 ASP cc_start: 0.7134 (t0) cc_final: 0.6654 (p0) REVERT: E 25 LEU cc_start: 0.9181 (tp) cc_final: 0.8789 (tt) REVERT: F 21 ASP cc_start: 0.7647 (p0) cc_final: 0.7348 (p0) REVERT: F 167 GLU cc_start: 0.5333 (mm-30) cc_final: 0.4456 (mm-30) outliers start: 28 outliers final: 21 residues processed: 197 average time/residue: 0.0516 time to fit residues: 14.7835 Evaluate side-chains 197 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 171 ASN C 44 GLN C 126 GLN E 158 ASN F 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117942 restraints weight = 11821.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118389 restraints weight = 8386.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119002 restraints weight = 6163.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119355 restraints weight = 5621.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120499 restraints weight = 4823.872| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7536 Z= 0.152 Angle : 0.559 6.756 10224 Z= 0.293 Chirality : 0.046 0.194 1146 Planarity : 0.004 0.035 1328 Dihedral : 4.322 45.531 1013 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.23 % Allowed : 17.90 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 920 helix: 1.45 (0.46), residues: 130 sheet: 0.44 (0.34), residues: 246 loop : 0.43 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 140 TYR 0.009 0.001 TYR F 80 PHE 0.026 0.001 PHE C 14 TRP 0.008 0.001 TRP D 190 HIS 0.002 0.001 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 7536) covalent geometry : angle 0.55925 / 0.29 (10224) hydrogen bonds : bond 0.04150 / 2.66 ( 258) hydrogen bonds : angle 5.15073 / 3.49 ( 693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.172 Fit side-chains REVERT: A 153 THR cc_start: 0.8264 (p) cc_final: 0.7847 (m) REVERT: B 33 GLN cc_start: 0.9039 (pm20) cc_final: 0.8628 (pm20) REVERT: C 12 ASP cc_start: 0.7187 (t70) cc_final: 0.6741 (t0) REVERT: C 84 ASN cc_start: 0.8932 (t0) cc_final: 0.8597 (t0) REVERT: C 105 THR cc_start: 0.7935 (p) cc_final: 0.7625 (p) REVERT: C 161 MET cc_start: 0.7960 (tpt) cc_final: 0.6477 (ttt) REVERT: D 110 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6926 (p0) REVERT: E 25 LEU cc_start: 0.9139 (tp) cc_final: 0.8871 (tt) REVERT: E 172 GLU cc_start: 0.7362 (tt0) cc_final: 0.6957 (tt0) outliers start: 35 outliers final: 24 residues processed: 205 average time/residue: 0.0579 time to fit residues: 17.0404 Evaluate side-chains 194 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 171 ASN C 126 GLN E 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114539 restraints weight = 12107.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114479 restraints weight = 9034.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115271 restraints weight = 6691.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115716 restraints weight = 6107.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115915 restraints weight = 5027.356| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7536 Z= 0.151 Angle : 0.566 7.379 10224 Z= 0.295 Chirality : 0.047 0.258 1146 Planarity : 0.004 0.036 1328 Dihedral : 4.413 47.049 1013 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.23 % Allowed : 19.83 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.28), residues: 920 helix: 1.35 (0.46), residues: 130 sheet: 0.42 (0.34), residues: 245 loop : 0.31 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 13 TYR 0.011 0.001 TYR F 117 PHE 0.025 0.002 PHE C 14 TRP 0.007 0.001 TRP D 190 HIS 0.002 0.001 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 7536) covalent geometry : angle 0.56609 / 0.29 (10224) hydrogen bonds : bond 0.04113 / 2.64 ( 258) hydrogen bonds : angle 5.12149 / 3.47 ( 693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.218 Fit side-chains REVERT: A 153 THR cc_start: 0.8204 (p) cc_final: 0.7768 (m) REVERT: B 33 GLN cc_start: 0.9025 (pm20) cc_final: 0.8669 (pm20) REVERT: B 84 ASN cc_start: 0.8759 (t0) cc_final: 0.8470 (t0) REVERT: B 91 ASP cc_start: 0.7434 (t0) cc_final: 0.6917 (t70) REVERT: C 12 ASP cc_start: 0.7054 (t70) cc_final: 0.6648 (t0) REVERT: C 84 ASN cc_start: 0.8935 (t0) cc_final: 0.8598 (t0) REVERT: C 105 THR cc_start: 0.7962 (p) cc_final: 0.7641 (p) REVERT: C 161 MET cc_start: 0.7993 (tpt) cc_final: 0.6476 (ttt) REVERT: D 109 ASP cc_start: 0.7638 (t0) cc_final: 0.7036 (t0) REVERT: D 110 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6833 (p0) REVERT: E 25 LEU cc_start: 0.9307 (tp) cc_final: 0.8935 (tt) REVERT: E 172 GLU cc_start: 0.7261 (tt0) cc_final: 0.6793 (tt0) outliers start: 35 outliers final: 27 residues processed: 196 average time/residue: 0.0526 time to fit residues: 14.7589 Evaluate side-chains 201 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN C 126 GLN E 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115743 restraints weight = 11943.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115751 restraints weight = 9372.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116669 restraints weight = 6916.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117127 restraints weight = 6051.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117353 restraints weight = 4944.650| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7536 Z= 0.136 Angle : 0.555 7.963 10224 Z= 0.288 Chirality : 0.047 0.286 1146 Planarity : 0.004 0.037 1328 Dihedral : 4.387 48.569 1013 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.59 % Allowed : 19.23 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 920 helix: 1.33 (0.46), residues: 130 sheet: 0.38 (0.34), residues: 245 loop : 0.28 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 118 TYR 0.010 0.001 TYR F 80 PHE 0.025 0.001 PHE C 14 TRP 0.007 0.001 TRP D 190 HIS 0.001 0.001 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7536) covalent geometry : angle 0.55476 / 0.29 (10224) hydrogen bonds : bond 0.03991 / 2.56 ( 258) hydrogen bonds : angle 5.03871 / 3.39 ( 693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.208 Fit side-chains REVERT: A 133 TYR cc_start: 0.8043 (t80) cc_final: 0.7712 (t80) REVERT: A 153 THR cc_start: 0.8176 (p) cc_final: 0.7756 (m) REVERT: B 33 GLN cc_start: 0.8999 (pm20) cc_final: 0.8609 (pm20) REVERT: B 91 ASP cc_start: 0.7380 (t0) cc_final: 0.6874 (t70) REVERT: C 12 ASP cc_start: 0.6868 (t70) cc_final: 0.6449 (t0) REVERT: C 42 ILE cc_start: 0.8931 (mt) cc_final: 0.8701 (mm) REVERT: C 84 ASN cc_start: 0.8901 (t0) cc_final: 0.8572 (t0) REVERT: C 105 THR cc_start: 0.7942 (p) cc_final: 0.7630 (p) REVERT: D 109 ASP cc_start: 0.8022 (t0) cc_final: 0.7642 (t0) REVERT: D 110 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6852 (p0) REVERT: D 189 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8071 (mtpp) REVERT: E 25 LEU cc_start: 0.9272 (tp) cc_final: 0.8941 (tt) REVERT: E 172 GLU cc_start: 0.7386 (tt0) cc_final: 0.6681 (tt0) REVERT: F 124 MET cc_start: 0.5818 (ptp) cc_final: 0.5486 (ptp) REVERT: F 167 GLU cc_start: 0.5452 (mm-30) cc_final: 0.4911 (mm-30) outliers start: 38 outliers final: 30 residues processed: 203 average time/residue: 0.0556 time to fit residues: 16.3457 Evaluate side-chains 205 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN C 126 GLN E 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119089 restraints weight = 11924.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121067 restraints weight = 6879.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123078 restraints weight = 4451.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123241 restraints weight = 3236.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123353 restraints weight = 3008.868| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7536 Z= 0.113 Angle : 0.534 6.851 10224 Z= 0.278 Chirality : 0.046 0.237 1146 Planarity : 0.004 0.037 1328 Dihedral : 4.296 50.760 1013 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.23 % Allowed : 19.95 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.28), residues: 920 helix: 1.44 (0.46), residues: 130 sheet: 0.29 (0.33), residues: 249 loop : 0.31 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 168 TYR 0.016 0.001 TYR F 80 PHE 0.025 0.001 PHE C 14 TRP 0.008 0.001 TRP D 190 HIS 0.001 0.001 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 7536) covalent geometry : angle 0.53382 / 0.28 (10224) hydrogen bonds : bond 0.03760 / 2.40 ( 258) hydrogen bonds : angle 4.90534 / 3.28 ( 693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.266 Fit side-chains REVERT: A 133 TYR cc_start: 0.7739 (t80) cc_final: 0.7527 (t80) REVERT: A 153 THR cc_start: 0.8108 (p) cc_final: 0.7743 (m) REVERT: B 33 GLN cc_start: 0.8915 (pm20) cc_final: 0.8671 (pm20) REVERT: B 91 ASP cc_start: 0.7174 (t0) cc_final: 0.6641 (t70) REVERT: B 143 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 171 ASN cc_start: 0.6636 (m-40) cc_final: 0.6358 (m-40) REVERT: C 12 ASP cc_start: 0.6803 (t70) cc_final: 0.6396 (t0) REVERT: C 42 ILE cc_start: 0.9050 (mt) cc_final: 0.8767 (mm) REVERT: C 84 ASN cc_start: 0.8876 (t0) cc_final: 0.8573 (t0) REVERT: C 105 THR cc_start: 0.7923 (p) cc_final: 0.7617 (p) REVERT: D 109 ASP cc_start: 0.7985 (t0) cc_final: 0.7628 (t0) REVERT: D 110 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6798 (p0) REVERT: D 126 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8873 (m-40) REVERT: D 127 LYS cc_start: 0.8837 (ttpp) cc_final: 0.8555 (tttp) REVERT: E 135 PHE cc_start: 0.8135 (m-80) cc_final: 0.7711 (m-10) REVERT: E 172 GLU cc_start: 0.7387 (tt0) cc_final: 0.6710 (tt0) REVERT: F 167 GLU cc_start: 0.5248 (mm-30) cc_final: 0.4630 (mm-30) outliers start: 35 outliers final: 25 residues processed: 210 average time/residue: 0.0563 time to fit residues: 17.2307 Evaluate side-chains 201 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114154 restraints weight = 11930.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114549 restraints weight = 9667.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115086 restraints weight = 7124.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115559 restraints weight = 6540.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115856 restraints weight = 5434.249| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7536 Z= 0.169 Angle : 0.597 8.086 10224 Z= 0.310 Chirality : 0.048 0.298 1146 Planarity : 0.004 0.035 1328 Dihedral : 4.555 50.743 1013 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.99 % Allowed : 20.56 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.28), residues: 920 helix: 1.23 (0.47), residues: 130 sheet: 0.34 (0.33), residues: 247 loop : 0.15 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 159 TYR 0.017 0.002 TYR A 46 PHE 0.023 0.002 PHE C 14 TRP 0.009 0.001 TRP D 190 HIS 0.002 0.001 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 7536) covalent geometry : angle 0.59717 / 0.31 (10224) hydrogen bonds : bond 0.04146 / 2.63 ( 258) hydrogen bonds : angle 5.03976 / 3.40 ( 693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.260 Fit side-chains REVERT: A 133 TYR cc_start: 0.7935 (t80) cc_final: 0.7657 (t80) REVERT: A 153 THR cc_start: 0.8209 (p) cc_final: 0.7846 (m) REVERT: B 33 GLN cc_start: 0.9007 (pm20) cc_final: 0.8803 (pm20) REVERT: B 91 ASP cc_start: 0.7493 (t0) cc_final: 0.6977 (t70) REVERT: B 132 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8955 (p) REVERT: C 12 ASP cc_start: 0.6875 (t70) cc_final: 0.6649 (t0) REVERT: C 84 ASN cc_start: 0.8933 (t0) cc_final: 0.8592 (t0) REVERT: C 105 THR cc_start: 0.8024 (p) cc_final: 0.7729 (p) REVERT: D 109 ASP cc_start: 0.8101 (t0) cc_final: 0.7775 (t0) REVERT: D 110 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6843 (p0) REVERT: E 6 TYR cc_start: 0.6022 (t80) cc_final: 0.5633 (t80) REVERT: E 25 LEU cc_start: 0.9363 (tp) cc_final: 0.8993 (tt) REVERT: E 135 PHE cc_start: 0.8176 (m-80) cc_final: 0.7787 (m-10) REVERT: E 141 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8076 (mt-10) REVERT: E 172 GLU cc_start: 0.7458 (tt0) cc_final: 0.7020 (tt0) REVERT: F 167 GLU cc_start: 0.5215 (mm-30) cc_final: 0.4668 (mm-30) outliers start: 33 outliers final: 28 residues processed: 195 average time/residue: 0.0565 time to fit residues: 16.0213 Evaluate side-chains 207 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.0010 chunk 39 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117359 restraints weight = 11940.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117587 restraints weight = 9742.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118318 restraints weight = 7297.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118812 restraints weight = 6513.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119200 restraints weight = 5346.919| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7536 Z= 0.108 Angle : 0.549 8.225 10224 Z= 0.285 Chirality : 0.046 0.199 1146 Planarity : 0.004 0.032 1328 Dihedral : 4.315 53.834 1013 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.26 % Allowed : 21.40 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.28), residues: 920 helix: 1.40 (0.47), residues: 130 sheet: 0.49 (0.33), residues: 237 loop : 0.14 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 168 TYR 0.012 0.001 TYR A 46 PHE 0.022 0.001 PHE C 14 TRP 0.008 0.001 TRP D 190 HIS 0.002 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7536) covalent geometry : angle 0.54858 / 0.28 (10224) hydrogen bonds : bond 0.03702 / 2.36 ( 258) hydrogen bonds : angle 4.87399 / 3.23 ( 693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7774 (t80) cc_final: 0.7499 (t80) REVERT: A 153 THR cc_start: 0.8144 (p) cc_final: 0.7811 (m) REVERT: B 33 GLN cc_start: 0.8986 (pm20) cc_final: 0.8651 (pm20) REVERT: B 91 ASP cc_start: 0.7151 (t0) cc_final: 0.6645 (t70) REVERT: B 143 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 12 ASP cc_start: 0.6833 (t70) cc_final: 0.6552 (t0) REVERT: C 84 ASN cc_start: 0.8858 (t0) cc_final: 0.8553 (t0) REVERT: C 105 THR cc_start: 0.7939 (p) cc_final: 0.7606 (p) REVERT: C 126 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7318 (mm110) REVERT: C 161 MET cc_start: 0.7827 (tpt) cc_final: 0.6527 (ttt) REVERT: D 109 ASP cc_start: 0.8086 (t0) cc_final: 0.7801 (t0) REVERT: D 110 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6865 (p0) REVERT: E 6 TYR cc_start: 0.5933 (t80) cc_final: 0.5533 (t80) REVERT: E 112 LEU cc_start: 0.8267 (mp) cc_final: 0.7765 (mp) REVERT: E 135 PHE cc_start: 0.8166 (m-80) cc_final: 0.7786 (m-10) REVERT: F 167 GLU cc_start: 0.5108 (mm-30) cc_final: 0.4681 (mm-30) outliers start: 27 outliers final: 25 residues processed: 198 average time/residue: 0.0573 time to fit residues: 16.3236 Evaluate side-chains 199 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117437 restraints weight = 11936.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118263 restraints weight = 8825.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118737 restraints weight = 6351.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119050 restraints weight = 5882.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120128 restraints weight = 5035.621| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7536 Z= 0.111 Angle : 0.558 8.837 10224 Z= 0.289 Chirality : 0.046 0.201 1146 Planarity : 0.004 0.029 1328 Dihedral : 4.309 55.885 1013 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.02 % Allowed : 22.85 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.28), residues: 920 helix: 1.39 (0.47), residues: 130 sheet: 0.52 (0.33), residues: 237 loop : 0.07 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.013 0.001 TYR B 45 PHE 0.022 0.001 PHE C 14 TRP 0.009 0.001 TRP D 190 HIS 0.002 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7536) covalent geometry : angle 0.55755 / 0.29 (10224) hydrogen bonds : bond 0.03671 / 2.34 ( 258) hydrogen bonds : angle 4.82047 / 3.20 ( 693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1129.86 seconds wall clock time: 20 minutes 9.31 seconds (1209.31 seconds total)