Starting phenix.real_space_refine on Thu Jul 31 05:16:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xzc_10658/07_2025/6xzc_10658.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xzc_10658/07_2025/6xzc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xzc_10658/07_2025/6xzc_10658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xzc_10658/07_2025/6xzc_10658.map" model { file = "/net/cci-nas-00/data/ceres_data/6xzc_10658/07_2025/6xzc_10658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xzc_10658/07_2025/6xzc_10658.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, G, F Time building chain proxies: 5.82, per 1000 atoms: 0.44 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: 3.98 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.31 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: 3.51 Time building geometry restraints manager: 4.49 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 4.060 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.910 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (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 TRP 0.007 0.001 TRP C 156 HIS 0.006 0.002 HIS D 216 PHE 0.017 0.002 PHE A 152 TYR 0.009 0.001 TYR C 236 ARG 0.003 0.000 ARG E 138 Details of bonding type rmsd hydrogen bonds : bond 0.13092 ( 952) hydrogen bonds : angle 5.14013 ( 2793) covalent geometry : bond 0.00427 (13580) covalent geometry : angle 0.62790 (18494) *********************** 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 : 1.496 Fit side-chains REVERT: A 56 MET cc_start: 0.8450 (tpp) cc_final: 0.8180 (mmm) REVERT: A 59 TYR cc_start: 0.7568 (m-80) cc_final: 0.7312 (m-10) REVERT: B 239 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.6026 (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: 0.2774 time to fit residues: 138.7232 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 : 1.541 ------------------------------------------------------------------------------- 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 141 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 0.0370 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 152 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.113540 restraints weight = 15922.388| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.47 r_work: 0.2882 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13580 Z= 0.160 Angle : 0.574 6.749 18494 Z= 0.296 Chirality : 0.036 0.157 1988 Planarity : 0.005 0.076 2513 Dihedral : 3.715 23.024 1839 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.31 % Allowed : 12.03 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1666 helix: 1.82 (0.13), residues: 1204 sheet: None (None), residues: 0 loop : -0.22 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.010 0.001 HIS B 151 PHE 0.019 0.002 PHE A 152 TYR 0.036 0.002 TYR A 226 ARG 0.006 0.001 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 952) hydrogen bonds : angle 3.20787 ( 2793) covalent geometry : bond 0.00371 (13580) covalent geometry : angle 0.57355 (18494) *********************** 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 211 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8650 (tpp) cc_final: 0.8306 (mmm) REVERT: A 59 TYR cc_start: 0.8381 (m-80) cc_final: 0.7882 (m-80) REVERT: A 254 GLN cc_start: 0.8468 (tp40) cc_final: 0.8202 (tp40) REVERT: B 239 ASN cc_start: 0.6734 (OUTLIER) cc_final: 0.6407 (p0) REVERT: D 131 MET cc_start: 0.6821 (mmm) cc_final: 0.6233 (mpp) REVERT: D 151 HIS cc_start: 0.7498 (t-90) cc_final: 0.7203 (t70) REVERT: E 56 MET cc_start: 0.9181 (tpp) cc_final: 0.8823 (tpp) REVERT: E 131 MET cc_start: 0.7340 (mmm) cc_final: 0.6837 (mpp) REVERT: E 198 MET cc_start: 0.7693 (mmm) cc_final: 0.6926 (mmt) REVERT: E 255 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8123 (tp40) REVERT: E 285 ASP cc_start: 0.8125 (m-30) cc_final: 0.7904 (p0) REVERT: F 56 MET cc_start: 0.9180 (tpp) cc_final: 0.8798 (mmm) REVERT: F 131 MET cc_start: 0.7045 (mmm) cc_final: 0.6628 (mpp) REVERT: G 25 MET cc_start: 0.8658 (mtp) cc_final: 0.8446 (mtp) REVERT: G 235 LEU cc_start: 0.7694 (tp) cc_final: 0.7413 (tt) REVERT: G 255 GLN cc_start: 0.8260 (tt0) cc_final: 0.7810 (tp40) outliers start: 18 outliers final: 5 residues processed: 209 average time/residue: 0.2231 time to fit residues: 69.7965 Evaluate side-chains 159 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 108 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 165 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN F 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.110724 restraints weight = 15988.779| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.44 r_work: 0.2846 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13580 Z= 0.125 Angle : 0.497 7.420 18494 Z= 0.248 Chirality : 0.034 0.159 1988 Planarity : 0.004 0.036 2513 Dihedral : 3.349 19.450 1836 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.44 % Allowed : 13.78 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.21), residues: 1666 helix: 3.04 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.74 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 156 HIS 0.012 0.001 HIS B 151 PHE 0.025 0.002 PHE E 130 TYR 0.025 0.001 TYR G 226 ARG 0.004 0.000 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 952) hydrogen bonds : angle 2.85890 ( 2793) covalent geometry : bond 0.00298 (13580) covalent geometry : angle 0.49686 (18494) *********************** 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 177 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 1.698 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8832 (tpp) cc_final: 0.7930 (mmm) REVERT: A 198 MET cc_start: 0.8691 (mmm) cc_final: 0.8021 (mmt) REVERT: A 243 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7631 (ttm170) REVERT: B 25 MET cc_start: 0.8364 (mtt) cc_final: 0.8096 (mtt) REVERT: B 56 MET cc_start: 0.8892 (mmt) cc_final: 0.8250 (mmt) REVERT: C 284 ILE cc_start: 0.8533 (mm) cc_final: 0.8287 (mt) REVERT: D 131 MET cc_start: 0.6746 (mmm) cc_final: 0.6303 (mpp) REVERT: D 151 HIS cc_start: 0.8108 (t-90) cc_final: 0.7845 (t-90) REVERT: E 131 MET cc_start: 0.7384 (mmm) cc_final: 0.6878 (mpp) REVERT: E 198 MET cc_start: 0.8249 (mmm) cc_final: 0.7157 (mmt) REVERT: E 250 TYR cc_start: 0.7677 (t80) cc_final: 0.7182 (t80) REVERT: E 255 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7833 (tp40) REVERT: E 285 ASP cc_start: 0.8146 (m-30) cc_final: 0.7832 (p0) REVERT: F 56 MET cc_start: 0.9210 (tpp) cc_final: 0.8634 (mmm) REVERT: F 131 MET cc_start: 0.7009 (mmm) cc_final: 0.6724 (mpp) REVERT: F 198 MET cc_start: 0.8518 (mmm) cc_final: 0.7838 (mmt) REVERT: F 285 ASP cc_start: 0.8408 (m-30) cc_final: 0.8023 (p0) REVERT: G 234 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.7155 (tpp80) REVERT: G 255 GLN cc_start: 0.8243 (tt0) cc_final: 0.7858 (tp40) REVERT: G 285 ASP cc_start: 0.8251 (m-30) cc_final: 0.7679 (p0) outliers start: 6 outliers final: 2 residues processed: 176 average time/residue: 0.2820 time to fit residues: 73.1110 Evaluate side-chains 144 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 119 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN D 216 HIS F 48 GLN F 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106521 restraints weight = 15955.809| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.43 r_work: 0.2784 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13580 Z= 0.143 Angle : 0.526 8.161 18494 Z= 0.258 Chirality : 0.036 0.229 1988 Planarity : 0.004 0.046 2513 Dihedral : 3.351 13.842 1834 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.38 % Allowed : 14.50 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.21), residues: 1666 helix: 3.41 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.95 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 156 HIS 0.005 0.001 HIS B 151 PHE 0.023 0.002 PHE C 152 TYR 0.024 0.001 TYR A 226 ARG 0.008 0.001 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 952) hydrogen bonds : angle 2.85959 ( 2793) covalent geometry : bond 0.00347 (13580) covalent geometry : angle 0.52602 (18494) *********************** 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 169 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.463 Fit side-chains REVERT: A 198 MET cc_start: 0.8911 (mmm) cc_final: 0.8105 (mmt) REVERT: A 243 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7578 (ttm170) REVERT: B 12 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7380 (tp40) REVERT: B 56 MET cc_start: 0.8878 (mmt) cc_final: 0.8388 (mmt) REVERT: B 284 ILE cc_start: 0.8811 (mm) cc_final: 0.8555 (mt) REVERT: C 284 ILE cc_start: 0.8839 (mm) cc_final: 0.8589 (mt) REVERT: D 68 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8103 (tt0) REVERT: D 131 MET cc_start: 0.6867 (mmm) cc_final: 0.6397 (mpp) REVERT: D 151 HIS cc_start: 0.8423 (t-90) cc_final: 0.8213 (t-90) REVERT: D 252 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8105 (tm-30) REVERT: E 131 MET cc_start: 0.7287 (mmm) cc_final: 0.6850 (mpp) REVERT: E 198 MET cc_start: 0.8587 (mmm) cc_final: 0.7600 (mmt) REVERT: E 254 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7481 (tt0) REVERT: E 285 ASP cc_start: 0.8177 (m-30) cc_final: 0.7850 (p0) REVERT: F 56 MET cc_start: 0.9091 (tpp) cc_final: 0.8754 (mmm) REVERT: F 131 MET cc_start: 0.7036 (mmm) cc_final: 0.6698 (mpp) REVERT: F 198 MET cc_start: 0.8774 (mmm) cc_final: 0.8072 (mmt) REVERT: F 285 ASP cc_start: 0.8487 (m-30) cc_final: 0.8045 (p0) REVERT: G 200 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8201 (mtpp) REVERT: G 234 ARG cc_start: 0.7470 (mmm-85) cc_final: 0.7038 (tpp80) REVERT: G 255 GLN cc_start: 0.8277 (tt0) cc_final: 0.7820 (tp40) REVERT: G 285 ASP cc_start: 0.8373 (m-30) cc_final: 0.7853 (p0) outliers start: 19 outliers final: 11 residues processed: 166 average time/residue: 0.2441 time to fit residues: 59.5186 Evaluate side-chains 148 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 123 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 0.0570 chunk 157 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 33 optimal weight: 0.0570 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN B 16 ASN D 175 ASN E 48 GLN G 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106898 restraints weight = 16034.492| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.43 r_work: 0.2783 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13580 Z= 0.112 Angle : 0.468 7.613 18494 Z= 0.226 Chirality : 0.034 0.180 1988 Planarity : 0.003 0.031 2513 Dihedral : 3.182 13.015 1834 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.66 % Allowed : 15.45 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.21), residues: 1666 helix: 3.77 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.15 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 156 HIS 0.003 0.001 HIS B 216 PHE 0.016 0.002 PHE D 152 TYR 0.020 0.001 TYR G 226 ARG 0.005 0.000 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 952) hydrogen bonds : angle 2.69975 ( 2793) covalent geometry : bond 0.00266 (13580) covalent geometry : angle 0.46804 (18494) *********************** 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 156 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 3.022 Fit side-chains REVERT: A 198 MET cc_start: 0.8793 (mmm) cc_final: 0.8052 (mmt) REVERT: B 12 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7521 (tp40) REVERT: B 284 ILE cc_start: 0.8887 (mm) cc_final: 0.8624 (mt) REVERT: C 247 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6962 (tt) REVERT: D 68 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8201 (tt0) REVERT: D 131 MET cc_start: 0.6853 (mmm) cc_final: 0.6584 (mpp) REVERT: D 252 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8016 (tm-30) REVERT: E 131 MET cc_start: 0.7285 (mmm) cc_final: 0.6812 (mpp) REVERT: E 198 MET cc_start: 0.8609 (mmm) cc_final: 0.7569 (mmt) REVERT: E 254 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7658 (tt0) REVERT: E 285 ASP cc_start: 0.8181 (m-30) cc_final: 0.7848 (p0) REVERT: F 56 MET cc_start: 0.9043 (tpp) cc_final: 0.8724 (mmm) REVERT: F 131 MET cc_start: 0.6983 (mmm) cc_final: 0.6733 (mpp) REVERT: F 198 MET cc_start: 0.8828 (mmm) cc_final: 0.8220 (mmt) REVERT: F 285 ASP cc_start: 0.8514 (m-30) cc_final: 0.8062 (p0) REVERT: G 234 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.7066 (tpp80) REVERT: G 285 ASP cc_start: 0.8377 (m-30) cc_final: 0.7831 (p0) outliers start: 9 outliers final: 5 residues processed: 152 average time/residue: 0.3212 time to fit residues: 74.8689 Evaluate side-chains 137 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 271 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 118 optimal weight: 0.1980 chunk 129 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.133481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106228 restraints weight = 16142.191| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.42 r_work: 0.2776 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6035 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= 0.116 Angle : 0.471 7.560 18494 Z= 0.229 Chirality : 0.034 0.193 1988 Planarity : 0.003 0.030 2513 Dihedral : 3.143 14.166 1834 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.73 % Allowed : 15.82 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.77 (0.21), residues: 1666 helix: 3.88 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.23 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 156 HIS 0.004 0.001 HIS C 216 PHE 0.018 0.001 PHE D 152 TYR 0.019 0.001 TYR G 226 ARG 0.007 0.000 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 952) hydrogen bonds : angle 2.65606 ( 2793) covalent geometry : bond 0.00274 (13580) covalent geometry : angle 0.47109 (18494) *********************** 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 149 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 3.593 Fit side-chains REVERT: A 56 MET cc_start: 0.8793 (tpp) cc_final: 0.8511 (mmm) REVERT: A 198 MET cc_start: 0.8812 (mmm) cc_final: 0.8040 (mmt) REVERT: A 234 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7306 (tpt90) REVERT: B 12 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7414 (tp40) REVERT: B 284 ILE cc_start: 0.8955 (mm) cc_final: 0.8706 (mt) REVERT: C 151 HIS cc_start: 0.8500 (t70) cc_final: 0.7640 (m-70) REVERT: C 247 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6918 (tt) REVERT: D 68 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8248 (tt0) REVERT: D 131 MET cc_start: 0.6841 (mmm) cc_final: 0.6568 (mpp) REVERT: D 252 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7965 (tm-30) REVERT: E 131 MET cc_start: 0.7255 (mmm) cc_final: 0.6792 (mpp) REVERT: E 198 MET cc_start: 0.8596 (mmm) cc_final: 0.7617 (mmt) REVERT: E 252 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8331 (tm-30) REVERT: E 254 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7710 (tt0) REVERT: E 285 ASP cc_start: 0.8153 (m-30) cc_final: 0.7832 (p0) REVERT: F 56 MET cc_start: 0.8997 (tpp) cc_final: 0.8693 (mmm) REVERT: F 131 MET cc_start: 0.7006 (mmm) cc_final: 0.6746 (mpp) REVERT: F 198 MET cc_start: 0.8866 (mmm) cc_final: 0.8177 (mmt) REVERT: F 285 ASP cc_start: 0.8474 (m-30) cc_final: 0.8022 (p0) REVERT: G 73 SER cc_start: 0.8948 (m) cc_final: 0.8594 (t) REVERT: G 234 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.7062 (tpp80) REVERT: G 285 ASP cc_start: 0.8368 (m-30) cc_final: 0.7848 (p0) outliers start: 10 outliers final: 5 residues processed: 146 average time/residue: 0.2580 time to fit residues: 56.7994 Evaluate side-chains 141 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 145 optimal weight: 0.0470 chunk 128 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN ** 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 = 0.3309 r_free = 0.3309 target = 0.118607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.087494 restraints weight = 16790.398| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.67 r_work: 0.2739 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13580 Z= 0.111 Angle : 0.467 7.539 18494 Z= 0.224 Chirality : 0.034 0.195 1988 Planarity : 0.003 0.028 2513 Dihedral : 3.127 14.418 1834 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.36 % Allowed : 16.47 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.94 (0.21), residues: 1666 helix: 4.00 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.29 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 156 HIS 0.004 0.001 HIS C 216 PHE 0.016 0.001 PHE D 152 TYR 0.018 0.001 TYR G 226 ARG 0.004 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 952) hydrogen bonds : angle 2.62902 ( 2793) covalent geometry : bond 0.00266 (13580) covalent geometry : angle 0.46741 (18494) *********************** 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 142 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 1.650 Fit side-chains REVERT: A 198 MET cc_start: 0.8836 (mmm) cc_final: 0.7994 (mmt) REVERT: A 234 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7300 (tpt90) REVERT: A 243 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7702 (ttm170) REVERT: B 12 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7423 (tp40) REVERT: B 284 ILE cc_start: 0.8932 (mm) cc_final: 0.8701 (mt) REVERT: C 56 MET cc_start: 0.8960 (tpp) cc_final: 0.8603 (tpp) REVERT: C 247 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6918 (tt) REVERT: C 255 GLN cc_start: 0.8086 (tp40) cc_final: 0.7874 (tt0) REVERT: D 68 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8232 (tt0) REVERT: D 131 MET cc_start: 0.6780 (mmm) cc_final: 0.6493 (mpp) REVERT: D 252 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7961 (tm-30) REVERT: E 131 MET cc_start: 0.7187 (mmm) cc_final: 0.6710 (mpp) REVERT: E 198 MET cc_start: 0.8673 (mmm) cc_final: 0.7676 (mmt) REVERT: E 254 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7640 (tt0) REVERT: E 255 GLN cc_start: 0.7911 (tp40) cc_final: 0.7578 (tt0) REVERT: E 285 ASP cc_start: 0.8253 (m-30) cc_final: 0.7845 (p0) REVERT: F 56 MET cc_start: 0.8938 (tpp) cc_final: 0.8671 (mmm) REVERT: F 131 MET cc_start: 0.6970 (mmm) cc_final: 0.6704 (mpp) REVERT: F 198 MET cc_start: 0.8895 (mmm) cc_final: 0.8215 (mmt) REVERT: F 285 ASP cc_start: 0.8504 (m-30) cc_final: 0.7998 (p0) REVERT: G 73 SER cc_start: 0.8928 (m) cc_final: 0.8598 (t) REVERT: G 234 ARG cc_start: 0.7355 (mmm-85) cc_final: 0.6934 (tpp80) REVERT: G 285 ASP cc_start: 0.8486 (m-30) cc_final: 0.7902 (p0) outliers start: 5 outliers final: 4 residues processed: 140 average time/residue: 0.2274 time to fit residues: 48.2108 Evaluate side-chains 136 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 133 optimal weight: 0.0970 chunk 112 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 159 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.087814 restraints weight = 16707.165| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.67 r_work: 0.2750 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13580 Z= 0.104 Angle : 0.464 7.383 18494 Z= 0.222 Chirality : 0.034 0.229 1988 Planarity : 0.003 0.028 2513 Dihedral : 3.089 14.379 1834 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.08 (0.21), residues: 1666 helix: 4.11 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.34 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 156 HIS 0.004 0.001 HIS C 216 PHE 0.014 0.001 PHE D 152 TYR 0.017 0.001 TYR G 226 ARG 0.006 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 952) hydrogen bonds : angle 2.59093 ( 2793) covalent geometry : bond 0.00246 (13580) covalent geometry : angle 0.46422 (18494) *********************** 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: 8 poor density : 134 time to evaluate : 1.878 Fit side-chains REVERT: A 56 MET cc_start: 0.8754 (tpp) cc_final: 0.8524 (mmm) REVERT: A 198 MET cc_start: 0.8820 (mmm) cc_final: 0.8016 (mmt) REVERT: A 243 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7684 (ttm170) REVERT: B 12 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7399 (tp40) REVERT: B 284 ILE cc_start: 0.8950 (mm) cc_final: 0.8702 (mt) REVERT: C 255 GLN cc_start: 0.8018 (tp40) cc_final: 0.7742 (tt0) REVERT: D 68 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8221 (tt0) REVERT: D 131 MET cc_start: 0.6740 (mmm) cc_final: 0.6438 (mpp) REVERT: E 131 MET cc_start: 0.7114 (mmm) cc_final: 0.6636 (mpp) REVERT: E 198 MET cc_start: 0.8676 (mmm) cc_final: 0.7764 (mmt) REVERT: E 254 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7587 (tt0) REVERT: E 255 GLN cc_start: 0.7962 (tp40) cc_final: 0.7644 (tt0) REVERT: E 285 ASP cc_start: 0.8277 (m-30) cc_final: 0.7836 (p0) REVERT: F 131 MET cc_start: 0.6914 (mmm) cc_final: 0.6660 (mpp) REVERT: F 198 MET cc_start: 0.8902 (mmm) cc_final: 0.8332 (mmt) REVERT: F 285 ASP cc_start: 0.8516 (m-30) cc_final: 0.7985 (p0) REVERT: G 73 SER cc_start: 0.8860 (m) cc_final: 0.8566 (t) REVERT: G 234 ARG cc_start: 0.7328 (mmm-85) cc_final: 0.6889 (tpp80) REVERT: G 285 ASP cc_start: 0.8502 (m-30) cc_final: 0.7911 (p0) outliers start: 8 outliers final: 3 residues processed: 139 average time/residue: 0.3155 time to fit residues: 65.2345 Evaluate side-chains 131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 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 F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.084852 restraints weight = 16848.698| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.66 r_work: 0.2698 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13580 Z= 0.142 Angle : 0.502 8.159 18494 Z= 0.239 Chirality : 0.036 0.208 1988 Planarity : 0.003 0.035 2513 Dihedral : 3.207 15.580 1834 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.44 % Allowed : 16.55 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.92 (0.21), residues: 1666 helix: 3.99 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.27 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 156 HIS 0.006 0.001 HIS C 216 PHE 0.015 0.002 PHE E 152 TYR 0.009 0.001 TYR A 226 ARG 0.005 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 952) hydrogen bonds : angle 2.67634 ( 2793) covalent geometry : bond 0.00353 (13580) covalent geometry : angle 0.50178 (18494) *********************** 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: 6 poor density : 133 time to evaluate : 1.702 Fit side-chains REVERT: A 198 MET cc_start: 0.8879 (mmm) cc_final: 0.7961 (mmt) REVERT: A 243 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7731 (ttm170) REVERT: B 284 ILE cc_start: 0.9019 (mm) cc_final: 0.8776 (mt) REVERT: C 243 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7247 (ttm170) REVERT: C 255 GLN cc_start: 0.8074 (tp40) cc_final: 0.7748 (tt0) REVERT: C 263 GLU cc_start: 0.8645 (tp30) cc_final: 0.8355 (tp30) REVERT: D 68 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8332 (tt0) REVERT: D 131 MET cc_start: 0.6801 (mmm) cc_final: 0.6465 (mpp) REVERT: E 131 MET cc_start: 0.7192 (mmm) cc_final: 0.6732 (mpp) REVERT: E 235 LEU cc_start: 0.7604 (tp) cc_final: 0.7288 (tt) REVERT: E 252 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8221 (tm-30) REVERT: E 254 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7675 (tt0) REVERT: E 255 GLN cc_start: 0.7974 (tp40) cc_final: 0.7627 (tt0) REVERT: E 285 ASP cc_start: 0.8310 (m-30) cc_final: 0.7910 (p0) REVERT: F 131 MET cc_start: 0.7038 (mmm) cc_final: 0.6686 (mpp) REVERT: F 285 ASP cc_start: 0.8510 (m-30) cc_final: 0.8013 (p0) REVERT: G 73 SER cc_start: 0.8943 (m) cc_final: 0.8654 (t) REVERT: G 234 ARG cc_start: 0.7368 (mmm-85) cc_final: 0.6907 (tpp80) REVERT: G 285 ASP cc_start: 0.8507 (m-30) cc_final: 0.7966 (p0) outliers start: 6 outliers final: 4 residues processed: 137 average time/residue: 0.4469 time to fit residues: 90.3511 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 : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 10 ASP 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 74 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 119 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 97 optimal weight: 0.0040 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106518 restraints weight = 15844.529| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.43 r_work: 0.2778 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13580 Z= 0.099 Angle : 0.467 7.454 18494 Z= 0.223 Chirality : 0.034 0.237 1988 Planarity : 0.003 0.053 2513 Dihedral : 3.091 14.531 1834 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.29 % Allowed : 16.55 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.20 (0.21), residues: 1666 helix: 4.21 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.34 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 156 HIS 0.003 0.001 HIS C 216 PHE 0.013 0.001 PHE D 152 TYR 0.011 0.001 TYR A 226 ARG 0.005 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 952) hydrogen bonds : angle 2.58803 ( 2793) covalent geometry : bond 0.00229 (13580) covalent geometry : angle 0.46689 (18494) ********************** 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 131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.425 Fit side-chains REVERT: A 56 MET cc_start: 0.8737 (tpp) cc_final: 0.8497 (mmm) REVERT: A 198 MET cc_start: 0.8841 (mmm) cc_final: 0.8085 (mmt) REVERT: A 243 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7776 (ttm170) REVERT: B 284 ILE cc_start: 0.9076 (mm) cc_final: 0.8855 (mt) REVERT: C 243 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7275 (ttm170) REVERT: C 255 GLN cc_start: 0.8054 (tp40) cc_final: 0.7802 (tt0) REVERT: D 131 MET cc_start: 0.6838 (mmm) cc_final: 0.6531 (mpp) REVERT: E 131 MET cc_start: 0.7273 (mmm) cc_final: 0.6790 (mpp) REVERT: E 235 LEU cc_start: 0.7747 (tp) cc_final: 0.7448 (tt) REVERT: E 254 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7594 (tt0) REVERT: E 255 GLN cc_start: 0.7934 (tp40) cc_final: 0.7653 (tt0) REVERT: E 285 ASP cc_start: 0.8241 (m-30) cc_final: 0.7917 (p0) REVERT: F 131 MET cc_start: 0.6891 (mmm) cc_final: 0.6590 (mpp) REVERT: F 198 MET cc_start: 0.8700 (mmt) cc_final: 0.8176 (mmt) REVERT: F 254 GLN cc_start: 0.8186 (tp40) cc_final: 0.7934 (tt0) REVERT: F 285 ASP cc_start: 0.8446 (m-30) cc_final: 0.8044 (p0) REVERT: G 73 SER cc_start: 0.8994 (m) cc_final: 0.8735 (t) REVERT: G 234 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.6944 (tpp80) REVERT: G 285 ASP cc_start: 0.8450 (m-30) cc_final: 0.7961 (p0) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.3093 time to fit residues: 58.9650 Evaluate side-chains 121 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL 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 92 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 167 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.086646 restraints weight = 16706.875| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.68 r_work: 0.2731 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13580 Z= 0.106 Angle : 0.471 7.614 18494 Z= 0.222 Chirality : 0.034 0.220 1988 Planarity : 0.003 0.065 2513 Dihedral : 3.080 14.497 1834 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.29 % Allowed : 16.55 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.22 (0.21), residues: 1666 helix: 4.22 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.35 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 156 HIS 0.004 0.001 HIS B 216 PHE 0.014 0.001 PHE E 152 TYR 0.011 0.001 TYR A 226 ARG 0.005 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 952) hydrogen bonds : angle 2.57348 ( 2793) covalent geometry : bond 0.00254 (13580) covalent geometry : angle 0.47083 (18494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6427.33 seconds wall clock time: 118 minutes 27.19 seconds (7107.19 seconds total)