Starting phenix.real_space_refine on Mon Dec 30 12:37:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xzc_10658/12_2024/6xzc_10658.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xzc_10658/12_2024/6xzc_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_10658/12_2024/6xzc_10658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xzc_10658/12_2024/6xzc_10658.map" model { file = "/net/cci-nas-00/data/ceres_data/6xzc_10658/12_2024/6xzc_10658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xzc_10658/12_2024/6xzc_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.29, per 1000 atoms: 0.17 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: 3.07 Conformation dependent library (CDL) restraints added in 1.8 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: 1.16 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: 3.88 Time building geometry restraints manager: 3.61 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 13.990 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: 0.000 Extract box with map and model: 5.330 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.700 Find NCS groups from input model: 0.470 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- 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= 0.280 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 *********************** 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 : 1.626 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: 0.2907 time to fit residues: 145.1189 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 : 1.478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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= 0.245 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 *********************** 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 : 1.556 Fit side-chains revert: symmetry clash REVERT: A 16 ASN cc_start: 0.8058 (m-40) cc_final: 0.7854 (m-40) REVERT: A 56 MET cc_start: 0.8312 (tpp) cc_final: 0.7898 (mmm) REVERT: A 59 TYR cc_start: 0.8272 (m-80) cc_final: 0.7759 (m-80) REVERT: A 254 GLN cc_start: 0.8158 (tp40) cc_final: 0.7844 (tp40) REVERT: B 239 ASN cc_start: 0.6520 (OUTLIER) cc_final: 0.6236 (p0) REVERT: D 131 MET cc_start: 0.6383 (mmm) cc_final: 0.5973 (mpp) REVERT: D 151 HIS cc_start: 0.7000 (t-90) cc_final: 0.6788 (t70) REVERT: E 56 MET cc_start: 0.9007 (tpp) cc_final: 0.8631 (tpp) REVERT: E 131 MET cc_start: 0.6780 (mmm) cc_final: 0.6371 (mpp) REVERT: E 198 MET cc_start: 0.7481 (mmm) cc_final: 0.6705 (mmt) REVERT: E 255 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7795 (tp40) REVERT: F 56 MET cc_start: 0.9009 (tpp) cc_final: 0.8641 (mmm) REVERT: F 131 MET cc_start: 0.6538 (mmm) cc_final: 0.6218 (mpp) REVERT: G 235 LEU cc_start: 0.7662 (tp) cc_final: 0.7396 (tt) REVERT: G 255 GLN cc_start: 0.7946 (tt0) cc_final: 0.7587 (tp40) outliers start: 18 outliers final: 5 residues processed: 209 average time/residue: 0.2344 time to fit residues: 73.4292 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 : 1.700 ------------------------------------------------------------------------------- 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 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 122 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 151 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN F 245 GLN G 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13580 Z= 0.246 Angle : 0.530 8.347 18494 Z= 0.267 Chirality : 0.035 0.203 1988 Planarity : 0.004 0.047 2513 Dihedral : 3.463 19.529 1836 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.31 % Allowed : 13.19 % Favored : 85.50 % 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: 3.41 (0.20), residues: 1666 helix: 2.88 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.67 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 156 HIS 0.014 0.002 HIS B 151 PHE 0.028 0.002 PHE E 130 TYR 0.026 0.002 TYR G 226 ARG 0.005 0.001 ARG D 75 *********************** 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 181 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.457 Fit side-chains REVERT: A 16 ASN cc_start: 0.8304 (m-40) cc_final: 0.7923 (m-40) REVERT: A 56 MET cc_start: 0.8698 (tpp) cc_final: 0.8328 (mmm) REVERT: A 198 MET cc_start: 0.8605 (mmm) cc_final: 0.7963 (mmt) REVERT: A 285 ASP cc_start: 0.7636 (m-30) cc_final: 0.7274 (p0) REVERT: C 51 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8300 (mt) REVERT: C 284 ILE cc_start: 0.8678 (mm) cc_final: 0.8442 (mt) REVERT: D 68 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7804 (tt0) REVERT: D 131 MET cc_start: 0.6473 (mmm) cc_final: 0.6144 (mpp) REVERT: D 151 HIS cc_start: 0.7842 (t-90) cc_final: 0.7642 (t70) REVERT: D 171 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7805 (ptp90) REVERT: E 131 MET cc_start: 0.6856 (mmm) cc_final: 0.6450 (mpp) REVERT: E 250 TYR cc_start: 0.7566 (t80) cc_final: 0.7028 (t80) REVERT: E 255 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7499 (tp40) REVERT: F 198 MET cc_start: 0.8501 (mmm) cc_final: 0.7618 (mmt) REVERT: F 285 ASP cc_start: 0.8159 (m-30) cc_final: 0.7933 (p0) REVERT: G 25 MET cc_start: 0.8990 (mtp) cc_final: 0.8729 (mtt) REVERT: G 56 MET cc_start: 0.8536 (mmm) cc_final: 0.7794 (mmm) REVERT: G 198 MET cc_start: 0.8431 (mmt) cc_final: 0.7724 (mmt) REVERT: G 234 ARG cc_start: 0.7442 (mmm-85) cc_final: 0.7147 (tpp80) REVERT: G 235 LEU cc_start: 0.7516 (tp) cc_final: 0.7315 (tt) REVERT: G 255 GLN cc_start: 0.8007 (tt0) cc_final: 0.7660 (tp40) REVERT: G 285 ASP cc_start: 0.8015 (m-30) cc_final: 0.7601 (p0) outliers start: 18 outliers final: 11 residues processed: 179 average time/residue: 0.2539 time to fit residues: 66.3446 Evaluate side-chains 148 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS 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 37 CYS Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 162 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13580 Z= 0.224 Angle : 0.488 7.862 18494 Z= 0.240 Chirality : 0.035 0.203 1988 Planarity : 0.004 0.031 2513 Dihedral : 3.344 14.812 1834 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.17 % Allowed : 14.58 % 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 (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: 3.42 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.92 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 156 HIS 0.004 0.001 HIS D 216 PHE 0.018 0.002 PHE C 152 TYR 0.018 0.001 TYR G 226 ARG 0.006 0.000 ARG F 221 *********************** 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 165 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.615 Fit side-chains REVERT: A 234 ARG cc_start: 0.7362 (mmm-85) cc_final: 0.7008 (tpp80) REVERT: A 285 ASP cc_start: 0.7717 (m-30) cc_final: 0.7414 (p0) REVERT: B 12 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7522 (tp40) REVERT: B 284 ILE cc_start: 0.8740 (mm) cc_final: 0.8459 (mt) REVERT: C 51 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8324 (mt) REVERT: C 284 ILE cc_start: 0.8809 (mm) cc_final: 0.8588 (mt) REVERT: D 68 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7927 (tt0) REVERT: D 131 MET cc_start: 0.6570 (mmm) cc_final: 0.6229 (mpp) REVERT: D 151 HIS cc_start: 0.7948 (t-90) cc_final: 0.7745 (t-90) REVERT: D 247 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7066 (tt) REVERT: D 252 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8130 (tm-30) REVERT: E 131 MET cc_start: 0.6834 (mmm) cc_final: 0.6477 (mpp) REVERT: E 254 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7176 (tt0) REVERT: F 56 MET cc_start: 0.8836 (tpp) cc_final: 0.8470 (mmm) REVERT: F 198 MET cc_start: 0.8567 (mmm) cc_final: 0.7710 (mmt) REVERT: F 285 ASP cc_start: 0.8201 (m-30) cc_final: 0.7910 (p0) REVERT: G 200 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7868 (mtpp) REVERT: G 234 ARG cc_start: 0.7494 (mmm-85) cc_final: 0.7247 (tpp80) REVERT: G 235 LEU cc_start: 0.7566 (tp) cc_final: 0.7304 (tt) REVERT: G 255 GLN cc_start: 0.7949 (tt0) cc_final: 0.7592 (tp40) REVERT: G 285 ASP cc_start: 0.8091 (m-30) cc_final: 0.7736 (p0) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 0.2602 time to fit residues: 61.7432 Evaluate side-chains 144 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 262 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 200 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 40 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: C 245 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13580 Z= 0.207 Angle : 0.478 7.784 18494 Z= 0.232 Chirality : 0.034 0.191 1988 Planarity : 0.003 0.031 2513 Dihedral : 3.256 16.360 1834 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.17 % Allowed : 14.80 % Favored : 84.04 % 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: 4.54 (0.21), residues: 1666 helix: 3.72 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.12 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.005 0.001 HIS D 216 PHE 0.016 0.002 PHE C 152 TYR 0.020 0.001 TYR G 226 ARG 0.006 0.000 ARG A 243 *********************** 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 153 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.379 Fit side-chains REVERT: A 198 MET cc_start: 0.8430 (mmt) cc_final: 0.7707 (mmt) REVERT: A 234 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.6997 (tpp80) REVERT: A 285 ASP cc_start: 0.7833 (m-30) cc_final: 0.7546 (p0) REVERT: B 12 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7486 (tp40) REVERT: B 284 ILE cc_start: 0.8928 (mm) cc_final: 0.8687 (mt) REVERT: C 151 HIS cc_start: 0.7976 (t70) cc_final: 0.7626 (m-70) REVERT: D 247 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7011 (tt) REVERT: D 252 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7916 (tm-30) REVERT: E 131 MET cc_start: 0.6815 (mmm) cc_final: 0.6396 (mpp) REVERT: E 252 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8233 (tm-30) REVERT: E 254 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7368 (tt0) REVERT: F 56 MET cc_start: 0.8810 (tpp) cc_final: 0.8494 (mmm) REVERT: F 198 MET cc_start: 0.8684 (mmm) cc_final: 0.7936 (mmt) REVERT: F 285 ASP cc_start: 0.8233 (m-30) cc_final: 0.7936 (p0) REVERT: G 234 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.7158 (tpp80) REVERT: G 235 LEU cc_start: 0.7656 (tp) cc_final: 0.7392 (tt) REVERT: G 285 ASP cc_start: 0.8087 (m-30) cc_final: 0.7733 (p0) outliers start: 16 outliers final: 11 residues processed: 149 average time/residue: 0.2282 time to fit residues: 51.5507 Evaluate side-chains 137 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 D residue 10 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13580 Z= 0.232 Angle : 0.492 7.933 18494 Z= 0.238 Chirality : 0.035 0.193 1988 Planarity : 0.003 0.030 2513 Dihedral : 3.302 17.472 1834 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.38 % Allowed : 16.03 % 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 (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: 4.61 (0.21), residues: 1666 helix: 3.75 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.19 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 156 HIS 0.005 0.001 HIS C 216 PHE 0.020 0.002 PHE D 152 TYR 0.015 0.001 TYR G 226 ARG 0.012 0.000 ARG G 67 *********************** 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: 19 poor density : 134 time to evaluate : 1.555 Fit side-chains REVERT: A 198 MET cc_start: 0.8581 (mmt) cc_final: 0.7844 (mmt) REVERT: A 200 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8000 (ttmm) REVERT: A 234 ARG cc_start: 0.7368 (mmm-85) cc_final: 0.6978 (tpp80) REVERT: A 285 ASP cc_start: 0.7902 (m-30) cc_final: 0.7619 (p0) REVERT: B 12 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7499 (tp40) REVERT: B 200 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7697 (mttm) REVERT: B 284 ILE cc_start: 0.8988 (mm) cc_final: 0.8761 (mt) REVERT: C 151 HIS cc_start: 0.7891 (t70) cc_final: 0.7618 (m-70) REVERT: C 243 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7303 (ttm170) REVERT: D 247 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7088 (tt) REVERT: D 252 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 131 MET cc_start: 0.6850 (mmm) cc_final: 0.6443 (mpp) REVERT: E 254 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7361 (tt0) REVERT: E 255 GLN cc_start: 0.7794 (tp40) cc_final: 0.7479 (tt0) REVERT: F 56 MET cc_start: 0.8777 (tpp) cc_final: 0.8510 (mmm) REVERT: F 198 MET cc_start: 0.8701 (mmm) cc_final: 0.7960 (mmt) REVERT: F 285 ASP cc_start: 0.8207 (m-30) cc_final: 0.7937 (p0) REVERT: G 73 SER cc_start: 0.8936 (m) cc_final: 0.8560 (t) REVERT: G 200 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7802 (mtpp) REVERT: G 234 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7187 (tpp80) REVERT: G 235 LEU cc_start: 0.7663 (tp) cc_final: 0.7375 (tt) REVERT: G 285 ASP cc_start: 0.8191 (m-30) cc_final: 0.7864 (p0) outliers start: 19 outliers final: 9 residues processed: 149 average time/residue: 0.2662 time to fit residues: 57.7820 Evaluate side-chains 140 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 B residue 200 LYS 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 273 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13580 Z= 0.165 Angle : 0.460 7.272 18494 Z= 0.221 Chirality : 0.034 0.205 1988 Planarity : 0.003 0.028 2513 Dihedral : 3.179 17.287 1834 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.51 % Allowed : 16.62 % 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: 4.93 (0.21), residues: 1666 helix: 3.99 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.30 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 156 HIS 0.004 0.001 HIS D 216 PHE 0.016 0.001 PHE D 152 TYR 0.017 0.001 TYR G 226 ARG 0.005 0.000 ARG F 243 *********************** 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 143 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.483 Fit side-chains REVERT: A 234 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.6969 (tpp80) REVERT: A 285 ASP cc_start: 0.7921 (m-30) cc_final: 0.7655 (p0) REVERT: B 12 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7545 (tp40) REVERT: C 243 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7281 (ttm170) REVERT: D 247 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.7040 (tt) REVERT: E 131 MET cc_start: 0.6909 (mmm) cc_final: 0.6472 (mpp) REVERT: E 252 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8161 (tm-30) REVERT: E 254 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7417 (tt0) REVERT: E 255 GLN cc_start: 0.7815 (tp40) cc_final: 0.7518 (tt0) REVERT: F 198 MET cc_start: 0.8712 (mmm) cc_final: 0.8039 (mmt) REVERT: F 285 ASP cc_start: 0.8166 (m-30) cc_final: 0.7918 (p0) REVERT: G 73 SER cc_start: 0.9001 (m) cc_final: 0.8674 (t) REVERT: G 234 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.7182 (tpp80) REVERT: G 235 LEU cc_start: 0.7596 (tp) cc_final: 0.7312 (tt) REVERT: G 285 ASP cc_start: 0.8184 (m-30) cc_final: 0.7870 (p0) outliers start: 7 outliers final: 5 residues processed: 141 average time/residue: 0.2823 time to fit residues: 59.3811 Evaluate side-chains 127 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 E residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 147 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.038 13580 Z= 0.208 Angle : 0.486 8.036 18494 Z= 0.233 Chirality : 0.035 0.217 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.220 18.718 1834 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.51 % Allowed : 16.76 % Favored : 82.73 % 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: 4.90 (0.21), residues: 1666 helix: 3.97 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.28 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 156 HIS 0.005 0.001 HIS C 216 PHE 0.016 0.001 PHE D 152 TYR 0.014 0.001 TYR G 226 ARG 0.005 0.000 ARG E 220 *********************** 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 139 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 1.471 Fit side-chains REVERT: A 198 MET cc_start: 0.8754 (mmt) cc_final: 0.7826 (mmt) REVERT: A 234 ARG cc_start: 0.7355 (mmm-85) cc_final: 0.7152 (tpt-90) REVERT: A 285 ASP cc_start: 0.7962 (m-30) cc_final: 0.7695 (p0) REVERT: C 243 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7313 (ttm170) REVERT: E 131 MET cc_start: 0.6896 (mmm) cc_final: 0.6467 (mpp) REVERT: E 235 LEU cc_start: 0.7760 (tp) cc_final: 0.7476 (tt) REVERT: E 252 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8126 (tm-30) REVERT: E 254 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7445 (tt0) REVERT: E 255 GLN cc_start: 0.7791 (tp40) cc_final: 0.7482 (tt0) REVERT: F 73 SER cc_start: 0.9045 (t) cc_final: 0.8811 (t) REVERT: F 254 GLN cc_start: 0.7791 (tp40) cc_final: 0.7487 (tt0) REVERT: F 285 ASP cc_start: 0.8157 (m-30) cc_final: 0.7922 (p0) REVERT: G 73 SER cc_start: 0.9007 (m) cc_final: 0.8694 (t) REVERT: G 234 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7255 (tpp80) REVERT: G 235 LEU cc_start: 0.7626 (tp) cc_final: 0.7332 (tt) REVERT: G 285 ASP cc_start: 0.8190 (m-30) cc_final: 0.7894 (p0) outliers start: 7 outliers final: 4 residues processed: 138 average time/residue: 0.2508 time to fit residues: 51.2317 Evaluate side-chains 129 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 136 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.6986 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= 0.175 Angle : 0.470 7.564 18494 Z= 0.225 Chirality : 0.035 0.219 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.159 17.980 1834 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.36 % Allowed : 16.91 % Favored : 82.73 % 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: 5.05 (0.21), residues: 1666 helix: 4.09 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.29 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 218 HIS 0.004 0.001 HIS D 216 PHE 0.014 0.001 PHE D 152 TYR 0.015 0.001 TYR G 226 ARG 0.005 0.000 ARG E 220 *********************** 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 131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 1.511 Fit side-chains REVERT: A 198 MET cc_start: 0.8696 (mmt) cc_final: 0.7798 (mmt) REVERT: A 234 ARG cc_start: 0.7377 (mmm-85) cc_final: 0.7129 (tpt-90) REVERT: A 254 GLN cc_start: 0.7838 (tp40) cc_final: 0.7205 (tt0) REVERT: A 285 ASP cc_start: 0.7883 (m-30) cc_final: 0.7654 (p0) REVERT: C 243 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7324 (ttm170) REVERT: C 255 GLN cc_start: 0.7888 (tp40) cc_final: 0.7600 (tt0) REVERT: E 131 MET cc_start: 0.6799 (mmm) cc_final: 0.6399 (mpp) REVERT: E 235 LEU cc_start: 0.7826 (tp) cc_final: 0.7555 (tt) REVERT: E 252 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 254 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7325 (tt0) REVERT: E 255 GLN cc_start: 0.7782 (tp40) cc_final: 0.7541 (tt0) REVERT: F 73 SER cc_start: 0.9034 (t) cc_final: 0.8779 (t) REVERT: F 198 MET cc_start: 0.8512 (mmt) cc_final: 0.7893 (mmt) REVERT: F 254 GLN cc_start: 0.7774 (tp40) cc_final: 0.7492 (tt0) REVERT: G 73 SER cc_start: 0.9013 (m) cc_final: 0.8692 (t) REVERT: G 234 ARG cc_start: 0.7530 (mmm-85) cc_final: 0.7216 (tpp80) REVERT: G 235 LEU cc_start: 0.7564 (tp) cc_final: 0.7273 (tt) REVERT: G 285 ASP cc_start: 0.8184 (m-30) cc_final: 0.7904 (p0) outliers start: 5 outliers final: 5 residues processed: 129 average time/residue: 0.2599 time to fit residues: 49.3512 Evaluate side-chains 126 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 E residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 167 optimal weight: 0.0020 chunk 154 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13580 Z= 0.181 Angle : 0.474 7.814 18494 Z= 0.225 Chirality : 0.035 0.237 1988 Planarity : 0.003 0.036 2513 Dihedral : 3.150 18.163 1834 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.36 % Allowed : 16.91 % Favored : 82.73 % 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: 5.07 (0.21), residues: 1666 helix: 4.11 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.29 (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 C 216 PHE 0.014 0.001 PHE D 152 TYR 0.015 0.001 TYR G 226 ARG 0.007 0.000 ARG A 243 ********************** 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 127 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 1.522 Fit side-chains REVERT: A 198 MET cc_start: 0.8679 (mmt) cc_final: 0.7742 (mmt) REVERT: A 254 GLN cc_start: 0.7868 (tp40) cc_final: 0.7226 (tt0) REVERT: A 285 ASP cc_start: 0.7895 (m-30) cc_final: 0.7673 (p0) REVERT: C 243 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7237 (ttm170) REVERT: C 255 GLN cc_start: 0.7908 (tp40) cc_final: 0.7621 (tt0) REVERT: E 131 MET cc_start: 0.6815 (mmm) cc_final: 0.6414 (mpp) REVERT: E 235 LEU cc_start: 0.7815 (tp) cc_final: 0.7530 (tt) REVERT: E 254 GLN cc_start: 0.7791 (tp-100) cc_final: 0.7322 (tt0) REVERT: E 255 GLN cc_start: 0.7774 (tp40) cc_final: 0.7556 (tt0) REVERT: F 73 SER cc_start: 0.9047 (t) cc_final: 0.8799 (t) REVERT: F 198 MET cc_start: 0.8568 (mmt) cc_final: 0.7901 (mmt) REVERT: F 254 GLN cc_start: 0.7791 (tp40) cc_final: 0.7539 (tt0) REVERT: G 73 SER cc_start: 0.9005 (m) cc_final: 0.8708 (t) REVERT: G 234 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.7209 (tpp80) REVERT: G 235 LEU cc_start: 0.7672 (tp) cc_final: 0.7369 (tt) REVERT: G 285 ASP cc_start: 0.8142 (m-30) cc_final: 0.7877 (p0) outliers start: 5 outliers final: 5 residues processed: 125 average time/residue: 0.2718 time to fit residues: 49.7517 Evaluate side-chains 123 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 1.960 ------------------------------------------------------------------------------- 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 E residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 0.4980 chunk 19 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.087426 restraints weight = 16547.566| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.67 r_work: 0.2744 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13580 Z= 0.152 Angle : 0.460 7.313 18494 Z= 0.219 Chirality : 0.034 0.234 1988 Planarity : 0.003 0.038 2513 Dihedral : 3.087 17.375 1834 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.36 % Allowed : 16.84 % 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 (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: 5.21 (0.21), residues: 1666 helix: 4.24 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.30 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 156 HIS 0.004 0.001 HIS D 216 PHE 0.013 0.001 PHE E 152 TYR 0.015 0.001 TYR G 226 ARG 0.005 0.000 ARG E 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.71 seconds wall clock time: 48 minutes 53.73 seconds (2933.73 seconds total)