Starting phenix.real_space_refine on Wed Mar 4 11:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xzc_10658/03_2026/6xzc_10658.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xzc_10658/03_2026/6xzc_10658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xzc_10658/03_2026/6xzc_10658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xzc_10658/03_2026/6xzc_10658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xzc_10658/03_2026/6xzc_10658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xzc_10658/03_2026/6xzc_10658.map" } resolution = 3.37 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= 0.001 sd= 0.100 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 49 5.16 5 C 8302 2.51 5 N 2359 2.21 5 O 2569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13279 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.44, per 1000 atoms: 0.11 Number of scatterers: 13279 At special positions: 0 Unit cell: (111.09, 110.032, 112.148, 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 49 16.00 O 2569 8.00 N 2359 7.00 C 8302 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: 0.84 Conformation dependent library (CDL) restraints added in 591.1 milliseconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 75.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.676A pdb=" N ILE A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 166 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 246 through 268 Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 155 " --> pdb=" O HIS C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 160 " --> pdb=" O TRP C 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.841A pdb=" N ASN C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 246 through 268 Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.676A pdb=" N ILE D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 160 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.841A pdb=" N ASN D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 246 through 268 Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY E 155 " --> pdb=" O HIS E 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN E 160 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 161 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 246 through 268 Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 166 removed outlier: 3.635A pdb=" N ASP F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 155 " --> pdb=" O HIS F 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 160 " --> pdb=" O TRP F 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 161 " --> pdb=" O ASN F 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA F 183 " --> pdb=" O ASP F 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 246 through 268 Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU G 133 " --> pdb=" O ASN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 155 " --> pdb=" O HIS G 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN G 160 " --> pdb=" O TRP G 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G 161 " --> pdb=" O ASN G 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP G 166 " --> pdb=" O THR G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA G 183 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 243 Processing helix chain 'G' and resid 246 through 268 952 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.12 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: 4566 1.34 - 1.46: 1663 1.46 - 1.57: 7267 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 13580 Sorted by residual: bond pdb=" CA GLU B 127 " pdb=" C GLU B 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.38e+00 bond pdb=" CA GLU G 127 " pdb=" C GLU G 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.36e+00 bond pdb=" CA GLU D 127 " pdb=" C GLU D 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.29e+00 bond pdb=" CA GLU C 127 " pdb=" C GLU C 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.26e+00 bond pdb=" CA GLU E 127 " pdb=" C GLU E 127 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.10e-02 2.27e+03 2.22e+00 ... (remaining 13575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 17388 1.17 - 2.35: 860 2.35 - 3.52: 185 3.52 - 4.70: 42 4.70 - 5.87: 19 Bond angle restraints: 18494 Sorted by residual: angle pdb=" CA GLU B 127 " pdb=" C GLU B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 7.02e+00 angle pdb=" CA GLU G 127 " pdb=" C GLU G 127 " pdb=" N PRO G 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 6.99e+00 angle pdb=" CA GLU F 127 " pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 6.99e+00 angle pdb=" CA GLU D 127 " pdb=" C GLU D 127 " pdb=" N PRO D 128 " ideal model delta sigma weight residual 116.90 120.86 -3.96 1.50e+00 4.44e-01 6.96e+00 angle pdb=" CA GLU C 127 " pdb=" C GLU C 127 " pdb=" N PRO C 128 " ideal model delta sigma weight residual 116.90 120.83 -3.93 1.50e+00 4.44e-01 6.86e+00 ... (remaining 18489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 7559 13.87 - 27.74: 575 27.74 - 41.62: 203 41.62 - 55.49: 42 55.49 - 69.36: 28 Dihedral angle restraints: 8407 sinusoidal: 3409 harmonic: 4998 Sorted by residual: dihedral pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " pdb=" OD1 ASP A 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.83 57.83 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP G 228 " pdb=" CB ASP G 228 " pdb=" CG ASP G 228 " pdb=" OD1 ASP G 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP C 228 " pdb=" CB ASP C 228 " pdb=" CG ASP C 228 " pdb=" OD1 ASP C 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 8404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1128 0.026 - 0.051: 558 0.051 - 0.077: 162 0.077 - 0.103: 99 0.103 - 0.129: 41 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CB ILE B 282 " pdb=" CA ILE B 282 " pdb=" CG1 ILE B 282 " pdb=" CG2 ILE B 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CB ILE C 282 " pdb=" CA ILE C 282 " pdb=" CG1 ILE C 282 " pdb=" CG2 ILE C 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CB ILE E 282 " pdb=" CA ILE E 282 " pdb=" CG1 ILE E 282 " pdb=" CG2 ILE E 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1985 not shown) Planarity restraints: 2513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 247 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO E 248 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 248 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 248 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 247 " 0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO F 248 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 248 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 248 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 247 " -0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 248 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.034 5.00e-02 4.00e+02 ... (remaining 2510 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4243 2.84 - 3.35: 12529 3.35 - 3.87: 21661 3.87 - 4.38: 23214 4.38 - 4.90: 40794 Nonbonded interactions: 102441 Sorted by model distance: nonbonded pdb=" OD1 ASN B 129 " pdb=" OH TYR B 250 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASN E 129 " pdb=" OH TYR E 250 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASN D 129 " pdb=" OH TYR D 250 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASN A 129 " pdb=" OH TYR A 250 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASN F 129 " pdb=" OH TYR F 250 " model vdw 2.323 3.040 ... (remaining 102436 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13580 Z= 0.196 Angle : 0.628 5.872 18494 Z= 0.372 Chirality : 0.038 0.129 1988 Planarity : 0.007 0.059 2513 Dihedral : 12.496 69.359 5145 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.06 % Allowed : 8.16 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.92 (0.16), residues: 1666 helix: -1.20 (0.11), residues: 1176 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 138 TYR 0.009 0.001 TYR C 236 PHE 0.017 0.002 PHE A 152 TRP 0.007 0.001 TRP C 156 HIS 0.006 0.002 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00427 (13580) covalent geometry : angle 0.62790 (18494) hydrogen bonds : bond 0.13092 ( 952) hydrogen bonds : angle 5.14013 ( 2793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.432 Fit side-chains REVERT: A 56 MET cc_start: 0.8450 (tpp) cc_final: 0.8180 (mmm) REVERT: A 59 TYR cc_start: 0.7567 (m-80) cc_final: 0.7312 (m-10) REVERT: B 239 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.6025 (p0) REVERT: C 25 MET cc_start: 0.7045 (mtp) cc_final: 0.6653 (mtt) REVERT: C 239 ASN cc_start: 0.5388 (OUTLIER) cc_final: 0.5133 (p0) REVERT: D 56 MET cc_start: 0.7297 (tpp) cc_final: 0.6868 (tpt) REVERT: D 131 MET cc_start: 0.6279 (mmm) cc_final: 0.5790 (mpp) REVERT: D 236 TYR cc_start: 0.5940 (t80) cc_final: 0.5553 (t80) REVERT: D 286 PRO cc_start: 0.8143 (Cg_exo) cc_final: 0.7625 (Cg_endo) REVERT: E 131 MET cc_start: 0.6574 (mmm) cc_final: 0.6243 (mpp) REVERT: E 286 PRO cc_start: 0.8418 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: F 131 MET cc_start: 0.6548 (mmm) cc_final: 0.6194 (mpp) REVERT: G 56 MET cc_start: 0.8239 (tpp) cc_final: 0.8027 (mmm) REVERT: G 255 GLN cc_start: 0.7426 (tt0) cc_final: 0.7223 (tm-30) outliers start: 42 outliers final: 1 residues processed: 357 average time/residue: 0.1220 time to fit residues: 61.8346 Evaluate side-chains 179 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain G residue 84 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS A 216 HIS B 216 HIS C 216 HIS C 274 ASN D 76 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN E 48 GLN E 129 ASN E 216 HIS E 245 GLN F 48 GLN F 175 ASN F 216 HIS G 216 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112448 restraints weight = 16008.628| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.48 r_work: 0.2951 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13580 Z= 0.172 Angle : 0.574 6.922 18494 Z= 0.298 Chirality : 0.036 0.154 1988 Planarity : 0.005 0.061 2513 Dihedral : 3.739 23.657 1839 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.38 % Allowed : 12.32 % Favored : 86.30 % 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: 1.78 (0.19), residues: 1666 helix: 1.75 (0.13), residues: 1204 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 67 TYR 0.035 0.002 TYR A 226 PHE 0.021 0.002 PHE A 152 TRP 0.013 0.001 TRP C 156 HIS 0.010 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00401 (13580) covalent geometry : angle 0.57382 (18494) hydrogen bonds : bond 0.04160 ( 952) hydrogen bonds : angle 3.21058 ( 2793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8708 (tpp) cc_final: 0.8356 (mmm) REVERT: A 59 TYR cc_start: 0.8452 (m-80) cc_final: 0.7944 (m-80) REVERT: A 254 GLN cc_start: 0.8523 (tp40) cc_final: 0.8229 (tp40) REVERT: B 239 ASN cc_start: 0.6713 (OUTLIER) cc_final: 0.6389 (p0) REVERT: C 239 ASN cc_start: 0.6281 (OUTLIER) cc_final: 0.6032 (p0) REVERT: D 131 MET cc_start: 0.6903 (mmm) cc_final: 0.6324 (mpp) REVERT: D 151 HIS cc_start: 0.7576 (t-90) cc_final: 0.7286 (t70) REVERT: E 56 MET cc_start: 0.9213 (tpp) cc_final: 0.8862 (tpp) REVERT: E 131 MET cc_start: 0.7380 (mmm) cc_final: 0.6892 (mpp) REVERT: E 198 MET cc_start: 0.7800 (mmm) cc_final: 0.7025 (mmt) REVERT: E 255 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8189 (tp40) REVERT: F 56 MET cc_start: 0.9188 (tpp) cc_final: 0.8791 (mmm) REVERT: F 131 MET cc_start: 0.7122 (mmm) cc_final: 0.6714 (mpp) REVERT: G 25 MET cc_start: 0.8717 (mtp) cc_final: 0.8491 (mtp) REVERT: G 235 LEU cc_start: 0.7778 (tp) cc_final: 0.7494 (tt) REVERT: G 255 GLN cc_start: 0.8287 (tt0) cc_final: 0.7894 (tp40) outliers start: 19 outliers final: 6 residues processed: 210 average time/residue: 0.0998 time to fit residues: 31.6864 Evaluate side-chains 161 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 137 optimal weight: 0.0040 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.0020 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 HIS D 216 HIS F 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107630 restraints weight = 16166.394| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.45 r_work: 0.2798 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13580 Z= 0.149 Angle : 0.526 8.308 18494 Z= 0.264 Chirality : 0.034 0.177 1988 Planarity : 0.004 0.034 2513 Dihedral : 3.511 19.647 1838 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.95 % Allowed : 13.63 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.20), residues: 1666 helix: 2.94 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.70 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 243 TYR 0.026 0.002 TYR G 226 PHE 0.022 0.002 PHE D 152 TRP 0.010 0.001 TRP B 156 HIS 0.013 0.002 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00366 (13580) covalent geometry : angle 0.52644 (18494) hydrogen bonds : bond 0.04030 ( 952) hydrogen bonds : angle 2.95185 ( 2793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.458 Fit side-chains REVERT: A 56 MET cc_start: 0.8912 (tpp) cc_final: 0.8579 (mmm) REVERT: A 198 MET cc_start: 0.8804 (mmm) cc_final: 0.8207 (mmt) REVERT: A 234 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7036 (tpp80) REVERT: A 285 ASP cc_start: 0.7944 (m-30) cc_final: 0.7395 (p0) REVERT: C 51 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8466 (mt) REVERT: C 284 ILE cc_start: 0.8752 (mm) cc_final: 0.8508 (mt) REVERT: D 68 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7956 (tt0) REVERT: D 131 MET cc_start: 0.6858 (mmm) cc_final: 0.6335 (mpp) REVERT: D 151 HIS cc_start: 0.8297 (t-90) cc_final: 0.8057 (t70) REVERT: D 171 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8020 (ptp90) REVERT: E 131 MET cc_start: 0.7362 (mmm) cc_final: 0.6868 (mpp) REVERT: E 198 MET cc_start: 0.8534 (mmm) cc_final: 0.8328 (mmt) REVERT: E 255 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7787 (tp40) REVERT: F 56 MET cc_start: 0.9205 (tpp) cc_final: 0.8628 (mmm) REVERT: F 131 MET cc_start: 0.7182 (mmm) cc_final: 0.6885 (mpp) REVERT: F 198 MET cc_start: 0.8729 (mmm) cc_final: 0.7991 (mmt) REVERT: F 285 ASP cc_start: 0.8411 (m-30) cc_final: 0.8029 (p0) REVERT: G 56 MET cc_start: 0.8770 (mmm) cc_final: 0.8187 (mmm) REVERT: G 198 MET cc_start: 0.8661 (mmt) cc_final: 0.8086 (mmt) REVERT: G 234 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.7176 (tpp80) REVERT: G 235 LEU cc_start: 0.7537 (tp) cc_final: 0.7312 (tt) REVERT: G 255 GLN cc_start: 0.8305 (tt0) cc_final: 0.7881 (tp40) REVERT: G 285 ASP cc_start: 0.8289 (m-30) cc_final: 0.7721 (p0) outliers start: 13 outliers final: 5 residues processed: 172 average time/residue: 0.1152 time to fit residues: 29.1732 Evaluate side-chains 142 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 37 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 17 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN F 175 ASN G 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107230 restraints weight = 15938.134| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.44 r_work: 0.2794 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13580 Z= 0.120 Angle : 0.470 7.463 18494 Z= 0.232 Chirality : 0.034 0.194 1988 Planarity : 0.003 0.031 2513 Dihedral : 3.300 13.100 1834 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.87 % Allowed : 14.87 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.21), residues: 1666 helix: 3.52 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.97 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 221 TYR 0.017 0.001 TYR G 226 PHE 0.016 0.002 PHE D 152 TRP 0.008 0.001 TRP D 156 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00280 (13580) covalent geometry : angle 0.46997 (18494) hydrogen bonds : bond 0.03431 ( 952) hydrogen bonds : angle 2.81137 ( 2793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.481 Fit side-chains REVERT: A 234 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.7039 (tpp80) REVERT: A 285 ASP cc_start: 0.8042 (m-30) cc_final: 0.7491 (p0) REVERT: B 12 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7531 (tp40) REVERT: B 239 ASN cc_start: 0.6840 (OUTLIER) cc_final: 0.6589 (p0) REVERT: C 284 ILE cc_start: 0.8871 (mm) cc_final: 0.8648 (mt) REVERT: D 68 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8107 (tt0) REVERT: D 131 MET cc_start: 0.6932 (mmm) cc_final: 0.6398 (mpp) REVERT: D 151 HIS cc_start: 0.8359 (t-90) cc_final: 0.8106 (t-90) REVERT: D 247 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7072 (tt) REVERT: D 252 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8222 (tm-30) REVERT: E 131 MET cc_start: 0.7325 (mmm) cc_final: 0.6880 (mpp) REVERT: E 254 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7429 (tt0) REVERT: F 56 MET cc_start: 0.9111 (tpp) cc_final: 0.8688 (mmm) REVERT: F 131 MET cc_start: 0.7152 (mmm) cc_final: 0.6827 (mpp) REVERT: F 198 MET cc_start: 0.8771 (mmm) cc_final: 0.8028 (mmt) REVERT: F 285 ASP cc_start: 0.8469 (m-30) cc_final: 0.8033 (p0) REVERT: G 200 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8187 (mtpp) REVERT: G 234 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7249 (tpp80) REVERT: G 235 LEU cc_start: 0.7539 (tp) cc_final: 0.7276 (tt) REVERT: G 255 GLN cc_start: 0.8314 (tt0) cc_final: 0.7850 (tp40) REVERT: G 285 ASP cc_start: 0.8318 (m-30) cc_final: 0.7784 (p0) outliers start: 12 outliers final: 5 residues processed: 158 average time/residue: 0.1028 time to fit residues: 24.1543 Evaluate side-chains 144 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 59 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 139 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 GLN F 48 GLN F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103442 restraints weight = 16174.887| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.44 r_work: 0.2732 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13580 Z= 0.159 Angle : 0.510 8.377 18494 Z= 0.249 Chirality : 0.036 0.202 1988 Planarity : 0.004 0.047 2513 Dihedral : 3.367 15.388 1834 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.60 % Allowed : 14.58 % Favored : 83.82 % 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: 4.40 (0.21), residues: 1666 helix: 3.60 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.08 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 221 TYR 0.021 0.001 TYR G 226 PHE 0.017 0.002 PHE D 152 TRP 0.010 0.001 TRP D 156 HIS 0.006 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00397 (13580) covalent geometry : angle 0.51025 (18494) hydrogen bonds : bond 0.03890 ( 952) hydrogen bonds : angle 2.83376 ( 2793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.494 Fit side-chains REVERT: A 200 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8330 (ttmm) REVERT: A 234 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7036 (tpp80) REVERT: A 285 ASP cc_start: 0.8162 (m-30) cc_final: 0.7700 (p0) REVERT: B 12 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7531 (tp40) REVERT: B 284 ILE cc_start: 0.8963 (mm) cc_final: 0.8721 (mt) REVERT: C 220 ARG cc_start: 0.8331 (tpt-90) cc_final: 0.7988 (tpt-90) REVERT: D 68 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8283 (tt0) REVERT: D 131 MET cc_start: 0.6864 (mmm) cc_final: 0.6595 (mpp) REVERT: D 247 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7030 (tt) REVERT: E 131 MET cc_start: 0.7296 (mmm) cc_final: 0.6791 (mpp) REVERT: E 252 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8394 (tm-30) REVERT: E 254 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7751 (tt0) REVERT: F 56 MET cc_start: 0.9055 (tpp) cc_final: 0.8736 (mmm) REVERT: F 131 MET cc_start: 0.7191 (mmm) cc_final: 0.6873 (mpp) REVERT: F 198 MET cc_start: 0.8956 (mmm) cc_final: 0.8262 (mmt) REVERT: F 235 LEU cc_start: 0.7636 (tp) cc_final: 0.7396 (tt) REVERT: F 285 ASP cc_start: 0.8511 (m-30) cc_final: 0.8048 (p0) REVERT: G 200 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8193 (mtpp) REVERT: G 234 ARG cc_start: 0.7500 (mmm-85) cc_final: 0.7180 (tpp80) REVERT: G 235 LEU cc_start: 0.7633 (tp) cc_final: 0.7348 (tt) REVERT: G 285 ASP cc_start: 0.8431 (m-30) cc_final: 0.7900 (p0) outliers start: 22 outliers final: 12 residues processed: 155 average time/residue: 0.1098 time to fit residues: 25.0513 Evaluate side-chains 139 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 14 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 145 optimal weight: 0.1980 chunk 147 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.087466 restraints weight = 16672.184| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.66 r_work: 0.2738 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13580 Z= 0.100 Angle : 0.459 7.677 18494 Z= 0.222 Chirality : 0.034 0.207 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.205 16.737 1834 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 0.95 % Allowed : 16.25 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.85 (0.21), residues: 1666 helix: 3.95 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.22 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 221 TYR 0.016 0.001 TYR G 226 PHE 0.018 0.001 PHE D 152 TRP 0.008 0.001 TRP A 156 HIS 0.002 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00232 (13580) covalent geometry : angle 0.45924 (18494) hydrogen bonds : bond 0.03228 ( 952) hydrogen bonds : angle 2.69045 ( 2793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.375 Fit side-chains REVERT: A 198 MET cc_start: 0.8856 (mmm) cc_final: 0.8084 (mmt) REVERT: A 234 ARG cc_start: 0.7454 (mmm-85) cc_final: 0.6918 (tpp80) REVERT: A 285 ASP cc_start: 0.8270 (m-30) cc_final: 0.7687 (p0) REVERT: B 12 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7461 (tp40) REVERT: B 284 ILE cc_start: 0.8961 (mm) cc_final: 0.8725 (mt) REVERT: D 131 MET cc_start: 0.6811 (mmm) cc_final: 0.6514 (mpp) REVERT: D 247 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6976 (tt) REVERT: E 131 MET cc_start: 0.7239 (mmm) cc_final: 0.6739 (mpp) REVERT: E 254 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7670 (tt0) REVERT: F 56 MET cc_start: 0.8940 (tpp) cc_final: 0.8698 (mmm) REVERT: F 131 MET cc_start: 0.6983 (mmm) cc_final: 0.6614 (mpp) REVERT: F 198 MET cc_start: 0.8903 (mmm) cc_final: 0.8263 (mmt) REVERT: F 235 LEU cc_start: 0.7505 (tp) cc_final: 0.7296 (tt) REVERT: F 285 ASP cc_start: 0.8522 (m-30) cc_final: 0.7991 (p0) REVERT: G 73 SER cc_start: 0.8926 (m) cc_final: 0.8616 (t) REVERT: G 234 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7115 (tpp80) REVERT: G 235 LEU cc_start: 0.7430 (tp) cc_final: 0.7152 (tt) REVERT: G 285 ASP cc_start: 0.8510 (m-30) cc_final: 0.7916 (p0) outliers start: 13 outliers final: 6 residues processed: 147 average time/residue: 0.1074 time to fit residues: 23.5716 Evaluate side-chains 136 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.084886 restraints weight = 16749.772| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.65 r_work: 0.2702 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13580 Z= 0.144 Angle : 0.487 7.861 18494 Z= 0.236 Chirality : 0.035 0.204 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.260 17.394 1834 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.58 % Allowed : 17.06 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.77 (0.21), residues: 1666 helix: 3.87 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.23 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 220 TYR 0.015 0.001 TYR G 226 PHE 0.017 0.002 PHE D 152 TRP 0.009 0.001 TRP D 156 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00358 (13580) covalent geometry : angle 0.48699 (18494) hydrogen bonds : bond 0.03591 ( 952) hydrogen bonds : angle 2.72095 ( 2793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.504 Fit side-chains REVERT: A 198 MET cc_start: 0.8836 (mmm) cc_final: 0.8218 (mmt) REVERT: A 285 ASP cc_start: 0.8317 (m-30) cc_final: 0.7733 (p0) REVERT: B 12 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7511 (tp40) REVERT: B 284 ILE cc_start: 0.8982 (mm) cc_final: 0.8774 (mt) REVERT: C 243 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7255 (ttm170) REVERT: D 131 MET cc_start: 0.6765 (mmm) cc_final: 0.6458 (mpp) REVERT: D 247 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6906 (tt) REVERT: D 252 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7824 (tm-30) REVERT: E 131 MET cc_start: 0.7200 (mmm) cc_final: 0.6667 (mpp) REVERT: E 254 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7614 (tt0) REVERT: F 56 MET cc_start: 0.8952 (tpp) cc_final: 0.8697 (mmm) REVERT: F 131 MET cc_start: 0.6986 (mmm) cc_final: 0.6641 (mpp) REVERT: F 198 MET cc_start: 0.8941 (mmm) cc_final: 0.8265 (mmt) REVERT: F 235 LEU cc_start: 0.7482 (tp) cc_final: 0.7251 (tt) REVERT: F 285 ASP cc_start: 0.8547 (m-30) cc_final: 0.8034 (p0) REVERT: G 73 SER cc_start: 0.8896 (m) cc_final: 0.8598 (t) REVERT: G 200 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8044 (mtpp) REVERT: G 234 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7164 (tpp80) REVERT: G 235 LEU cc_start: 0.7343 (tp) cc_final: 0.7064 (tt) REVERT: G 285 ASP cc_start: 0.8538 (m-30) cc_final: 0.7941 (p0) outliers start: 8 outliers final: 4 residues processed: 137 average time/residue: 0.1159 time to fit residues: 23.3981 Evaluate side-chains 134 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.0000 chunk 81 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.086932 restraints weight = 16575.716| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.66 r_work: 0.2736 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13580 Z= 0.102 Angle : 0.457 7.163 18494 Z= 0.221 Chirality : 0.034 0.216 1988 Planarity : 0.003 0.044 2513 Dihedral : 3.155 17.333 1834 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.66 % Allowed : 16.76 % Favored : 82.58 % 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: 5.06 (0.21), residues: 1666 helix: 4.11 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.30 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 220 TYR 0.015 0.001 TYR G 226 PHE 0.014 0.001 PHE D 152 TRP 0.007 0.001 TRP E 156 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00238 (13580) covalent geometry : angle 0.45691 (18494) hydrogen bonds : bond 0.03165 ( 952) hydrogen bonds : angle 2.62719 ( 2793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.513 Fit side-chains REVERT: A 38 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8230 (mm-30) REVERT: A 198 MET cc_start: 0.8812 (mmm) cc_final: 0.8335 (mmt) REVERT: A 285 ASP cc_start: 0.8349 (m-30) cc_final: 0.7750 (p0) REVERT: B 12 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7503 (tp40) REVERT: C 243 ARG cc_start: 0.7708 (ttm110) cc_final: 0.7250 (ttm170) REVERT: C 255 GLN cc_start: 0.8000 (tp40) cc_final: 0.7718 (tt0) REVERT: C 263 GLU cc_start: 0.8488 (tp30) cc_final: 0.8154 (tp30) REVERT: D 131 MET cc_start: 0.6765 (mmm) cc_final: 0.6452 (mpp) REVERT: D 247 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6888 (tt) REVERT: E 131 MET cc_start: 0.7229 (mmm) cc_final: 0.6701 (mpp) REVERT: E 235 LEU cc_start: 0.7489 (tp) cc_final: 0.7185 (tt) REVERT: E 254 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7646 (tt0) REVERT: F 131 MET cc_start: 0.6943 (mmm) cc_final: 0.6610 (mpp) REVERT: F 198 MET cc_start: 0.8918 (mmm) cc_final: 0.8368 (mmt) REVERT: F 235 LEU cc_start: 0.7489 (tp) cc_final: 0.7274 (tt) REVERT: F 254 GLN cc_start: 0.8049 (tp40) cc_final: 0.7801 (tt0) REVERT: F 285 ASP cc_start: 0.8523 (m-30) cc_final: 0.8010 (p0) REVERT: G 73 SER cc_start: 0.8889 (m) cc_final: 0.8615 (t) REVERT: G 234 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7113 (tpp80) REVERT: G 235 LEU cc_start: 0.7206 (tp) cc_final: 0.6928 (tt) REVERT: G 285 ASP cc_start: 0.8522 (m-30) cc_final: 0.7935 (p0) outliers start: 9 outliers final: 4 residues processed: 139 average time/residue: 0.1144 time to fit residues: 23.7192 Evaluate side-chains 133 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 166 optimal weight: 0.0030 chunk 45 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.086239 restraints weight = 16764.616| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.67 r_work: 0.2725 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13580 Z= 0.112 Angle : 0.464 7.481 18494 Z= 0.223 Chirality : 0.034 0.218 1988 Planarity : 0.003 0.062 2513 Dihedral : 3.147 17.415 1834 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.51 % Allowed : 16.69 % Favored : 82.80 % 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: 5.09 (0.21), residues: 1666 helix: 4.12 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.32 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 220 TYR 0.015 0.001 TYR G 226 PHE 0.014 0.001 PHE E 152 TRP 0.008 0.001 TRP E 156 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00268 (13580) covalent geometry : angle 0.46443 (18494) hydrogen bonds : bond 0.03216 ( 952) hydrogen bonds : angle 2.62057 ( 2793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.523 Fit side-chains REVERT: A 38 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8314 (mm-30) REVERT: A 198 MET cc_start: 0.8855 (mmm) cc_final: 0.8351 (mmt) REVERT: A 285 ASP cc_start: 0.8359 (m-30) cc_final: 0.7788 (p0) REVERT: B 12 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7496 (tp40) REVERT: C 243 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7215 (ttm170) REVERT: C 255 GLN cc_start: 0.8009 (tp40) cc_final: 0.7709 (tt0) REVERT: C 263 GLU cc_start: 0.8520 (tp30) cc_final: 0.8199 (tp30) REVERT: D 131 MET cc_start: 0.6746 (mmm) cc_final: 0.6420 (mpp) REVERT: E 131 MET cc_start: 0.7236 (mmm) cc_final: 0.6704 (mpp) REVERT: E 235 LEU cc_start: 0.7501 (tp) cc_final: 0.7193 (tt) REVERT: E 254 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7658 (tt0) REVERT: F 131 MET cc_start: 0.6935 (mmm) cc_final: 0.6600 (mpp) REVERT: F 198 MET cc_start: 0.8925 (mmm) cc_final: 0.8230 (mmt) REVERT: F 235 LEU cc_start: 0.7499 (tp) cc_final: 0.7278 (tt) REVERT: F 254 GLN cc_start: 0.8039 (tp40) cc_final: 0.7801 (tt0) REVERT: F 285 ASP cc_start: 0.8508 (m-30) cc_final: 0.8006 (p0) REVERT: G 73 SER cc_start: 0.8882 (m) cc_final: 0.8625 (t) REVERT: G 234 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7120 (tpp80) REVERT: G 235 LEU cc_start: 0.7211 (tp) cc_final: 0.6933 (tt) REVERT: G 285 ASP cc_start: 0.8525 (m-30) cc_final: 0.7952 (p0) outliers start: 7 outliers final: 4 residues processed: 136 average time/residue: 0.1119 time to fit residues: 22.6408 Evaluate side-chains 132 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 0.0570 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.085976 restraints weight = 16762.051| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.66 r_work: 0.2723 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13580 Z= 0.115 Angle : 0.471 7.736 18494 Z= 0.226 Chirality : 0.034 0.241 1988 Planarity : 0.003 0.056 2513 Dihedral : 3.149 17.862 1834 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.58 % Allowed : 16.62 % Favored : 82.80 % 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: 5.11 (0.21), residues: 1666 helix: 4.15 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.29 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 220 TYR 0.015 0.001 TYR G 226 PHE 0.014 0.001 PHE E 152 TRP 0.008 0.001 TRP E 156 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00277 (13580) covalent geometry : angle 0.47104 (18494) hydrogen bonds : bond 0.03242 ( 952) hydrogen bonds : angle 2.61324 ( 2793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.505 Fit side-chains REVERT: A 38 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8304 (mm-30) REVERT: A 198 MET cc_start: 0.8843 (mmm) cc_final: 0.8294 (mmt) REVERT: A 254 GLN cc_start: 0.8085 (tp40) cc_final: 0.7488 (tt0) REVERT: A 285 ASP cc_start: 0.8274 (m-30) cc_final: 0.7720 (p0) REVERT: B 200 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7935 (mttm) REVERT: C 243 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7210 (ttm170) REVERT: C 255 GLN cc_start: 0.8084 (tp40) cc_final: 0.7796 (tt0) REVERT: C 263 GLU cc_start: 0.8510 (tp30) cc_final: 0.8206 (tp30) REVERT: D 131 MET cc_start: 0.6781 (mmm) cc_final: 0.6437 (mpp) REVERT: E 131 MET cc_start: 0.7194 (mmm) cc_final: 0.6683 (mpp) REVERT: E 235 LEU cc_start: 0.7549 (tp) cc_final: 0.7228 (tt) REVERT: E 254 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7661 (tt0) REVERT: F 131 MET cc_start: 0.7006 (mmm) cc_final: 0.6634 (mpp) REVERT: F 198 MET cc_start: 0.8953 (mmm) cc_final: 0.8237 (mmt) REVERT: F 235 LEU cc_start: 0.7541 (tp) cc_final: 0.7311 (tt) REVERT: F 254 GLN cc_start: 0.8053 (tp40) cc_final: 0.7815 (tt0) REVERT: F 285 ASP cc_start: 0.8476 (m-30) cc_final: 0.7988 (p0) REVERT: G 73 SER cc_start: 0.8888 (m) cc_final: 0.8629 (t) REVERT: G 234 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.7119 (tpp80) REVERT: G 235 LEU cc_start: 0.7278 (tp) cc_final: 0.7000 (tt) REVERT: G 285 ASP cc_start: 0.8523 (m-30) cc_final: 0.7965 (p0) outliers start: 8 outliers final: 5 residues processed: 137 average time/residue: 0.1103 time to fit residues: 22.2753 Evaluate side-chains 133 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain G residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.085050 restraints weight = 16812.781| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.67 r_work: 0.2704 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13580 Z= 0.124 Angle : 0.481 8.345 18494 Z= 0.230 Chirality : 0.035 0.229 1988 Planarity : 0.004 0.058 2513 Dihedral : 3.175 18.018 1834 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.58 % Allowed : 16.55 % Favored : 82.87 % 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: 5.11 (0.21), residues: 1666 helix: 4.15 (0.13), residues: 1190 sheet: None (None), residues: 0 loop : 1.28 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 220 TYR 0.014 0.001 TYR G 226 PHE 0.014 0.001 PHE E 152 TRP 0.009 0.001 TRP E 156 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00303 (13580) covalent geometry : angle 0.48085 (18494) hydrogen bonds : bond 0.03382 ( 952) hydrogen bonds : angle 2.63843 ( 2793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.29 seconds wall clock time: 51 minutes 23.75 seconds (3083.75 seconds total)