Starting phenix.real_space_refine on Wed Aug 5 07:16:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21eo_67613/08_2026/21eo_67613.cif Found real_map, /net/cci-nas-00/data/ceres_data/21eo_67613/08_2026/21eo_67613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21eo_67613/08_2026/21eo_67613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21eo_67613/08_2026/21eo_67613.map" model { file = "/net/cci-nas-00/data/ceres_data/21eo_67613/08_2026/21eo_67613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21eo_67613/08_2026/21eo_67613.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 48 5.16 5 C 5430 2.51 5 N 1488 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 220} Chain: "B" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 220} Chain: "C" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 220} Chain: "D" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1112 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "E" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1112 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "F" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1112 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Time building chain proxies: 2.07, per 1000 atoms: 0.24 Number of scatterers: 8691 At special positions: 0 Unit cell: (150.4, 148.896, 67.68, 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 48 16.00 O 1725 8.00 N 1488 7.00 C 5430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.02 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 213 " distance=2.02 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=2.02 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 213 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 213 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 519.8 milliseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 21 sheets defined 7.4% alpha, 43.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 removed outlier: 3.765A pdb=" N TYR A 33 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.559A pdb=" N LEU A 208 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.770A pdb=" N TYR B 33 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.503A pdb=" N LYS B 66 " --> pdb=" O ASP B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.769A pdb=" N TYR C 33 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.555A pdb=" N THR F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.648A pdb=" N ALA A 93 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS A 39 " --> pdb=" O TRP A 48 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TRP A 48 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.648A pdb=" N ALA A 93 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 114 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.556A pdb=" N VAL A 158 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR A 174 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP A 160 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.516A pdb=" N GLN A 215 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 222 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 59 through 61 removed outlier: 5.439A pdb=" N TRP B 48 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS B 39 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 114 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 59 through 61 removed outlier: 5.439A pdb=" N TRP B 48 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS B 39 " --> pdb=" O TRP B 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 135 through 138 removed outlier: 6.487A pdb=" N VAL B 158 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 174 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP B 160 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 135 through 138 removed outlier: 3.546A pdb=" N GLN B 215 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 222 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.201A pdb=" N LYS C 39 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TRP C 48 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.954A pdb=" N VAL C 114 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AB8, first strand: chain 'C' and resid 135 through 138 removed outlier: 6.577A pdb=" N VAL C 158 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR C 174 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP C 160 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 135 through 138 removed outlier: 3.512A pdb=" N GLN C 215 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 222 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 83 through 89 removed outlier: 5.654A pdb=" N ASP D 83 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL D 47 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY D 85 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 45 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 44 " --> pdb=" O HIS D 120 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET D 117 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS D 146 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 119 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL D 148 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL D 8 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 6 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 83 through 89 removed outlier: 5.510A pdb=" N ASP E 83 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL E 47 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY E 85 " --> pdb=" O PHE E 45 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 45 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 44 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET E 117 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS E 146 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 119 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL E 148 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL E 8 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 6 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.627A pdb=" N ASP F 83 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL F 47 " --> pdb=" O ASP F 83 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY F 85 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY F 44 " --> pdb=" O HIS F 120 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL F 148 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL F 8 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 6 " --> pdb=" O GLY F 150 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 870 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: 1.47 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1987 1.32 - 1.44: 2098 1.44 - 1.57: 4714 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8871 Sorted by residual: bond pdb=" CB PRO C 100 " pdb=" CG PRO C 100 " ideal model delta sigma weight residual 1.492 1.293 0.199 5.00e-02 4.00e+02 1.59e+01 bond pdb=" CB PRO A 100 " pdb=" CG PRO A 100 " ideal model delta sigma weight residual 1.492 1.293 0.199 5.00e-02 4.00e+02 1.58e+01 bond pdb=" CB PRO B 100 " pdb=" CG PRO B 100 " ideal model delta sigma weight residual 1.492 1.296 0.196 5.00e-02 4.00e+02 1.54e+01 bond pdb=" CB PHE A 96 " pdb=" CG PHE A 96 " ideal model delta sigma weight residual 1.502 1.412 0.090 2.30e-02 1.89e+03 1.54e+01 bond pdb=" CB TYR A 161 " pdb=" CG TYR A 161 " ideal model delta sigma weight residual 1.512 1.426 0.086 2.20e-02 2.07e+03 1.54e+01 ... (remaining 8866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 11143 2.79 - 5.58: 738 5.58 - 8.36: 89 8.36 - 11.15: 24 11.15 - 13.94: 6 Bond angle restraints: 12000 Sorted by residual: angle pdb=" N ARG B 68 " pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 114.04 104.33 9.71 1.24e+00 6.50e-01 6.13e+01 angle pdb=" N ARG C 68 " pdb=" CA ARG C 68 " pdb=" C ARG C 68 " ideal model delta sigma weight residual 114.04 104.49 9.55 1.24e+00 6.50e-01 5.93e+01 angle pdb=" N ARG A 68 " pdb=" CA ARG A 68 " pdb=" C ARG A 68 " ideal model delta sigma weight residual 114.04 104.73 9.31 1.24e+00 6.50e-01 5.64e+01 angle pdb=" C ARG A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta sigma weight residual 122.79 112.08 10.71 1.70e+00 3.46e-01 3.97e+01 angle pdb=" N ARG A 68 " pdb=" CA ARG A 68 " pdb=" CB ARG A 68 " ideal model delta sigma weight residual 110.81 118.63 -7.82 1.48e+00 4.57e-01 2.79e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4967 17.66 - 35.32: 172 35.32 - 52.98: 64 52.98 - 70.64: 18 70.64 - 88.29: 8 Dihedral angle restraints: 5229 sinusoidal: 2019 harmonic: 3210 Sorted by residual: dihedral pdb=" CD ARG A 105 " pdb=" NE ARG A 105 " pdb=" CZ ARG A 105 " pdb=" NH1 ARG A 105 " ideal model delta sinusoidal sigma weight residual 0.00 71.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CA PHE A 96 " pdb=" C PHE A 96 " pdb=" N CYS A 97 " pdb=" CA CYS A 97 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PHE C 96 " pdb=" C PHE C 96 " pdb=" N CYS C 97 " pdb=" CA CYS C 97 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 840 0.067 - 0.134: 347 0.134 - 0.201: 97 0.201 - 0.268: 17 0.268 - 0.335: 7 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CA ASP B 113 " pdb=" N ASP B 113 " pdb=" C ASP B 113 " pdb=" CB ASP B 113 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA ASP A 113 " pdb=" N ASP A 113 " pdb=" C ASP A 113 " pdb=" CB ASP A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ASP C 113 " pdb=" N ASP C 113 " pdb=" C ASP C 113 " pdb=" CB ASP C 113 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1305 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 105 " -0.886 9.50e-02 1.11e+02 3.98e-01 1.09e+02 pdb=" NE ARG A 105 " 0.076 2.00e-02 2.50e+03 pdb=" CZ ARG A 105 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 105 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 105 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 143 " -0.452 9.50e-02 1.11e+02 2.04e-01 3.22e+01 pdb=" NE ARG B 143 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 143 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG B 143 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 143 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 143 " 0.313 9.50e-02 1.11e+02 1.42e-01 1.56e+01 pdb=" NE ARG A 143 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 143 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG A 143 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 143 " 0.000 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 152 2.61 - 3.18: 7908 3.18 - 3.76: 13087 3.76 - 4.33: 19219 4.33 - 4.90: 31225 Nonbonded interactions: 71591 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OE1 GLN B 214 " model vdw 2.039 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OE1 GLN A 214 " model vdw 2.041 3.040 nonbonded pdb=" OH TYR C 161 " pdb=" OE1 GLN C 214 " model vdw 2.049 3.040 nonbonded pdb=" OE1 GLN B 131 " pdb=" OG1 THR B 227 " model vdw 2.098 3.040 nonbonded pdb=" OE1 GLN A 131 " pdb=" OG1 THR A 227 " model vdw 2.138 3.040 ... (remaining 71586 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.200 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 : 0.020 0.199 8877 Z= 0.859 Angle : 1.537 13.940 12012 Z= 0.843 Chirality : 0.080 0.335 1308 Planarity : 0.016 0.398 1572 Dihedral : 11.863 88.294 3195 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.86 % Favored : 93.35 % Rotamer: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.22), residues: 1143 helix: -5.33 (0.17), residues: 18 sheet: -1.31 (0.22), residues: 510 loop : -1.96 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.004 ARG A 105 TYR 0.057 0.008 TYR A 61 PHE 0.048 0.008 PHE B 112 TRP 0.058 0.009 TRP B 37 HIS 0.012 0.004 HIS F 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01983 / 0.86 ( 8871) covalent geometry : angle 1.53484 / 0.84 (12000) SS BOND : bond 0.01122 / 0.53 ( 6) SS BOND : angle 2.91549 / 1.55 ( 12) hydrogen bonds : bond 0.15936 / 10.00 ( 327) hydrogen bonds : angle 9.31506 / 6.38 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7200 (mmtm) REVERT: A 215 GLN cc_start: 0.8456 (pp30) cc_final: 0.7718 (pp30) REVERT: B 149 LYS cc_start: 0.7340 (tttt) cc_final: 0.7007 (mtmt) REVERT: B 196 PHE cc_start: 0.8277 (m-80) cc_final: 0.8071 (m-10) REVERT: B 215 GLN cc_start: 0.8433 (pp30) cc_final: 0.7507 (pp30) REVERT: C 160 TRP cc_start: 0.8258 (m100) cc_final: 0.7875 (m100) REVERT: C 215 GLN cc_start: 0.8360 (pp30) cc_final: 0.7552 (pp30) REVERT: D 24 LYS cc_start: 0.8869 (mttt) cc_final: 0.8594 (ptpt) REVERT: D 49 GLN cc_start: 0.7868 (tp40) cc_final: 0.7551 (tm-30) REVERT: D 107 SER cc_start: 0.8608 (t) cc_final: 0.8394 (t) REVERT: E 24 LYS cc_start: 0.8831 (mttt) cc_final: 0.8565 (ptpt) REVERT: F 24 LYS cc_start: 0.8930 (mttt) cc_final: 0.8673 (ptpt) REVERT: F 49 GLN cc_start: 0.7966 (tp40) cc_final: 0.7728 (tm-30) REVERT: F 125 ASP cc_start: 0.7820 (p0) cc_final: 0.7523 (p0) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.0845 time to fit residues: 34.7884 Evaluate side-chains 152 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.0040 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 109 ASN B 109 ASN B 131 GLN C 163 GLN D 49 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.145024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113856 restraints weight = 18413.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112851 restraints weight = 19547.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114261 restraints weight = 20223.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114526 restraints weight = 14704.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115046 restraints weight = 12992.533| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8877 Z= 0.148 Angle : 0.665 6.966 12012 Z= 0.355 Chirality : 0.049 0.196 1308 Planarity : 0.005 0.035 1572 Dihedral : 5.635 22.406 1224 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 4.03 % Allowed : 8.81 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.24), residues: 1143 helix: -5.03 (0.15), residues: 21 sheet: -0.71 (0.22), residues: 510 loop : -0.94 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 123 TYR 0.014 0.001 TYR A 216 PHE 0.018 0.002 PHE A 196 TRP 0.016 0.001 TRP A 48 HIS 0.006 0.001 HIS E 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8871) covalent geometry : angle 0.66465 / 0.35 (12000) SS BOND : bond 0.00234 / 0.13 ( 6) SS BOND : angle 0.70627 / 0.40 ( 12) hydrogen bonds : bond 0.03890 / 2.59 ( 327) hydrogen bonds : angle 6.57572 / 4.57 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8562 (ptm) cc_final: 0.8181 (ppp) REVERT: A 11 ASP cc_start: 0.8101 (t0) cc_final: 0.7807 (m-30) REVERT: A 196 PHE cc_start: 0.7948 (m-80) cc_final: 0.7714 (m-10) REVERT: B 1 MET cc_start: 0.7396 (ptm) cc_final: 0.7015 (ppp) REVERT: B 11 ASP cc_start: 0.8015 (t0) cc_final: 0.7608 (m-30) REVERT: C 149 LYS cc_start: 0.7398 (tttt) cc_final: 0.7168 (mmtm) outliers start: 38 outliers final: 14 residues processed: 238 average time/residue: 0.0737 time to fit residues: 24.6523 Evaluate side-chains 156 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 111 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 167 GLN B 167 GLN C 109 ASN C 167 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.144440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112675 restraints weight = 18077.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112263 restraints weight = 15785.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.113389 restraints weight = 16517.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113827 restraints weight = 12070.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114073 restraints weight = 11105.729| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8877 Z= 0.130 Angle : 0.641 7.559 12012 Z= 0.337 Chirality : 0.047 0.155 1308 Planarity : 0.004 0.035 1572 Dihedral : 5.158 23.172 1224 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 3.29 % Allowed : 12.74 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1143 helix: -4.90 (0.20), residues: 21 sheet: -0.30 (0.23), residues: 501 loop : -0.85 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 123 TYR 0.014 0.001 TYR C 216 PHE 0.036 0.002 PHE F 45 TRP 0.016 0.002 TRP A 48 HIS 0.005 0.001 HIS E 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8871) covalent geometry : angle 0.63935 / 0.34 (12000) SS BOND : bond 0.00189 / 0.09 ( 6) SS BOND : angle 1.71693 / 0.97 ( 12) hydrogen bonds : bond 0.03354 / 2.29 ( 327) hydrogen bonds : angle 6.06099 / 4.20 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8344 (ptm) cc_final: 0.8084 (ppp) REVERT: A 11 ASP cc_start: 0.8157 (t0) cc_final: 0.7709 (m-30) REVERT: A 136 MET cc_start: 0.7324 (tmm) cc_final: 0.7080 (tmm) REVERT: A 196 PHE cc_start: 0.8031 (m-80) cc_final: 0.7808 (m-10) REVERT: B 1 MET cc_start: 0.7376 (ptm) cc_final: 0.7173 (ppp) outliers start: 31 outliers final: 18 residues processed: 199 average time/residue: 0.0903 time to fit residues: 24.5848 Evaluate side-chains 169 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain F residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.140421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111306 restraints weight = 18548.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109410 restraints weight = 19273.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110624 restraints weight = 18914.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110775 restraints weight = 14716.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111121 restraints weight = 14481.279| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8877 Z= 0.184 Angle : 0.650 10.209 12012 Z= 0.342 Chirality : 0.047 0.248 1308 Planarity : 0.004 0.034 1572 Dihedral : 5.239 22.446 1224 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 4.03 % Allowed : 12.74 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1143 helix: -4.73 (0.31), residues: 21 sheet: -0.17 (0.24), residues: 471 loop : -0.59 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 179 TYR 0.018 0.002 TYR B 28 PHE 0.035 0.003 PHE D 45 TRP 0.016 0.002 TRP B 48 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 8871) covalent geometry : angle 0.64851 / 0.34 (12000) SS BOND : bond 0.00245 / 0.12 ( 6) SS BOND : angle 1.49602 / 0.86 ( 12) hydrogen bonds : bond 0.03541 / 2.42 ( 327) hydrogen bonds : angle 6.07246 / 4.21 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8312 (ptm) cc_final: 0.8089 (ppp) REVERT: A 11 ASP cc_start: 0.8190 (t0) cc_final: 0.7679 (m-30) REVERT: A 136 MET cc_start: 0.7435 (tmm) cc_final: 0.6965 (tmm) REVERT: A 196 PHE cc_start: 0.8107 (m-80) cc_final: 0.7802 (m-10) REVERT: B 11 ASP cc_start: 0.8023 (t0) cc_final: 0.7763 (t0) REVERT: E 10 LYS cc_start: 0.7498 (mtpp) cc_final: 0.7122 (pttt) outliers start: 38 outliers final: 25 residues processed: 196 average time/residue: 0.0862 time to fit residues: 23.6015 Evaluate side-chains 175 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 111 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 55 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** 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 = 0.3999 r_free = 0.3999 target = 0.140672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110018 restraints weight = 18284.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107038 restraints weight = 21641.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108199 restraints weight = 22390.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109121 restraints weight = 16355.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109621 restraints weight = 14073.666| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8877 Z= 0.156 Angle : 0.640 7.989 12012 Z= 0.337 Chirality : 0.048 0.215 1308 Planarity : 0.004 0.032 1572 Dihedral : 5.081 21.241 1224 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 3.50 % Allowed : 15.29 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1143 helix: -4.66 (0.35), residues: 21 sheet: -0.07 (0.23), residues: 480 loop : -0.60 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 123 TYR 0.018 0.002 TYR B 28 PHE 0.025 0.002 PHE C 196 TRP 0.013 0.002 TRP B 48 HIS 0.003 0.001 HIS F 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 8871) covalent geometry : angle 0.63878 / 0.34 (12000) SS BOND : bond 0.00363 / 0.17 ( 6) SS BOND : angle 1.30937 / 0.76 ( 12) hydrogen bonds : bond 0.03420 / 2.35 ( 327) hydrogen bonds : angle 5.95697 / 4.14 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8297 (ptm) cc_final: 0.8084 (ppp) REVERT: A 11 ASP cc_start: 0.8161 (t0) cc_final: 0.7660 (m-30) REVERT: A 136 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7099 (tmm) REVERT: A 138 THR cc_start: 0.6336 (OUTLIER) cc_final: 0.6070 (p) REVERT: A 196 PHE cc_start: 0.8166 (m-80) cc_final: 0.7895 (m-10) REVERT: B 1 MET cc_start: 0.7391 (ppp) cc_final: 0.7182 (ppp) REVERT: B 11 ASP cc_start: 0.8015 (t0) cc_final: 0.7717 (t0) REVERT: D 112 ILE cc_start: 0.7850 (pt) cc_final: 0.7628 (mt) REVERT: D 132 GLU cc_start: 0.8333 (tt0) cc_final: 0.8025 (tp30) REVERT: D 136 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7236 (mm110) REVERT: E 10 LYS cc_start: 0.7670 (mtpp) cc_final: 0.7205 (pttt) outliers start: 33 outliers final: 23 residues processed: 187 average time/residue: 0.0723 time to fit residues: 19.0239 Evaluate side-chains 179 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 104 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.142263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112579 restraints weight = 18021.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110415 restraints weight = 18715.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.111321 restraints weight = 22138.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.112305 restraints weight = 15892.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112774 restraints weight = 13006.668| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8877 Z= 0.123 Angle : 0.621 6.721 12012 Z= 0.327 Chirality : 0.047 0.190 1308 Planarity : 0.004 0.030 1572 Dihedral : 4.827 21.584 1224 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 2.87 % Allowed : 16.77 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.24), residues: 1143 helix: -4.61 (0.36), residues: 21 sheet: -0.02 (0.24), residues: 471 loop : -0.63 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 115 TYR 0.019 0.001 TYR B 28 PHE 0.021 0.002 PHE B 196 TRP 0.012 0.002 TRP C 48 HIS 0.002 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8871) covalent geometry : angle 0.62029 / 0.33 (12000) SS BOND : bond 0.00184 / 0.08 ( 6) SS BOND : angle 1.12638 / 0.67 ( 12) hydrogen bonds : bond 0.03266 / 2.25 ( 327) hydrogen bonds : angle 5.74865 / 3.99 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8126 (t0) cc_final: 0.7648 (m-30) REVERT: A 136 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7174 (tmm) REVERT: A 138 THR cc_start: 0.6156 (OUTLIER) cc_final: 0.5886 (p) REVERT: A 196 PHE cc_start: 0.8136 (m-80) cc_final: 0.7858 (m-10) REVERT: B 1 MET cc_start: 0.7574 (ppp) cc_final: 0.7355 (ppp) REVERT: B 11 ASP cc_start: 0.7987 (t0) cc_final: 0.7681 (t0) REVERT: D 132 GLU cc_start: 0.8277 (tt0) cc_final: 0.8006 (tp30) REVERT: D 136 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7247 (mm110) REVERT: E 10 LYS cc_start: 0.7538 (mtpp) cc_final: 0.7154 (pttt) outliers start: 27 outliers final: 19 residues processed: 181 average time/residue: 0.0820 time to fit residues: 20.5270 Evaluate side-chains 172 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 76 optimal weight: 0.0070 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN E 139 ASN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.143123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.113861 restraints weight = 18388.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111767 restraints weight = 19308.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.112905 restraints weight = 21626.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.113659 restraints weight = 15531.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113804 restraints weight = 14075.990| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8877 Z= 0.123 Angle : 0.630 7.734 12012 Z= 0.330 Chirality : 0.047 0.194 1308 Planarity : 0.004 0.051 1572 Dihedral : 4.774 19.933 1224 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 3.08 % Allowed : 17.52 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.24), residues: 1143 helix: -4.55 (0.38), residues: 21 sheet: 0.06 (0.24), residues: 474 loop : -0.64 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 123 TYR 0.017 0.001 TYR B 28 PHE 0.034 0.002 PHE E 45 TRP 0.009 0.001 TRP C 48 HIS 0.003 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8871) covalent geometry : angle 0.62976 / 0.33 (12000) SS BOND : bond 0.00153 / 0.07 ( 6) SS BOND : angle 1.05113 / 0.62 ( 12) hydrogen bonds : bond 0.03201 / 2.22 ( 327) hydrogen bonds : angle 5.67901 / 3.95 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8173 (t0) cc_final: 0.7839 (t0) REVERT: A 136 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7224 (tmm) REVERT: A 138 THR cc_start: 0.6161 (OUTLIER) cc_final: 0.5916 (p) REVERT: A 196 PHE cc_start: 0.8133 (m-80) cc_final: 0.7877 (m-10) REVERT: B 11 ASP cc_start: 0.7981 (t0) cc_final: 0.7654 (t0) REVERT: D 132 GLU cc_start: 0.8311 (tt0) cc_final: 0.7980 (tp30) REVERT: D 136 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7263 (mm110) REVERT: E 10 LYS cc_start: 0.7534 (mtpp) cc_final: 0.7176 (pttt) REVERT: F 132 GLU cc_start: 0.8321 (tt0) cc_final: 0.8016 (tp30) outliers start: 29 outliers final: 24 residues processed: 188 average time/residue: 0.0853 time to fit residues: 22.2308 Evaluate side-chains 179 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.139093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108336 restraints weight = 18573.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.106648 restraints weight = 19538.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107864 restraints weight = 19484.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108193 restraints weight = 14127.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108563 restraints weight = 13045.680| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8877 Z= 0.278 Angle : 0.756 13.669 12012 Z= 0.398 Chirality : 0.050 0.215 1308 Planarity : 0.005 0.047 1572 Dihedral : 5.478 23.282 1224 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 4.03 % Allowed : 18.05 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.24), residues: 1143 helix: -4.46 (0.32), residues: 21 sheet: -0.09 (0.24), residues: 465 loop : -0.80 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 123 TYR 0.021 0.002 TYR C 216 PHE 0.027 0.003 PHE B 196 TRP 0.040 0.003 TRP C 160 HIS 0.007 0.002 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.28 ( 8871) covalent geometry : angle 0.75481 / 0.40 (12000) SS BOND : bond 0.00157 / 0.08 ( 6) SS BOND : angle 1.35896 / 0.78 ( 12) hydrogen bonds : bond 0.04019 / 2.77 ( 327) hydrogen bonds : angle 6.20990 / 4.34 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8221 (t0) cc_final: 0.7952 (t0) REVERT: A 196 PHE cc_start: 0.8190 (m-80) cc_final: 0.7984 (m-10) REVERT: B 11 ASP cc_start: 0.8056 (t0) cc_final: 0.7721 (t0) REVERT: E 10 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7074 (pttt) REVERT: F 132 GLU cc_start: 0.8213 (tt0) cc_final: 0.7861 (tp30) outliers start: 38 outliers final: 26 residues processed: 179 average time/residue: 0.0892 time to fit residues: 21.9089 Evaluate side-chains 171 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** F 63 HIS ** 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 = 0.4016 r_free = 0.4016 target = 0.141682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111625 restraints weight = 18694.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109842 restraints weight = 21664.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111265 restraints weight = 20033.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111755 restraints weight = 14864.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.112125 restraints weight = 13777.600| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8877 Z= 0.192 Angle : 0.716 10.809 12012 Z= 0.374 Chirality : 0.049 0.192 1308 Planarity : 0.004 0.050 1572 Dihedral : 5.227 21.248 1224 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 2.87 % Allowed : 19.32 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1143 helix: -4.39 (0.29), residues: 21 sheet: -0.10 (0.24), residues: 468 loop : -0.96 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 179 TYR 0.018 0.002 TYR C 216 PHE 0.024 0.003 PHE C 196 TRP 0.065 0.003 TRP C 160 HIS 0.005 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 8871) covalent geometry : angle 0.71354 / 0.37 (12000) SS BOND : bond 0.00391 / 0.14 ( 6) SS BOND : angle 1.86329 / 1.14 ( 12) hydrogen bonds : bond 0.03745 / 2.60 ( 327) hydrogen bonds : angle 6.12530 / 4.29 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8173 (t0) cc_final: 0.7953 (t0) REVERT: A 136 MET cc_start: 0.7193 (tmm) cc_final: 0.6818 (tmm) REVERT: A 144 VAL cc_start: 0.8289 (t) cc_final: 0.7995 (m) REVERT: B 11 ASP cc_start: 0.8009 (t0) cc_final: 0.7671 (t0) REVERT: E 10 LYS cc_start: 0.7379 (mtpp) cc_final: 0.7061 (pttt) outliers start: 27 outliers final: 23 residues processed: 168 average time/residue: 0.0803 time to fit residues: 18.6721 Evaluate side-chains 167 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.142684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112310 restraints weight = 18719.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110948 restraints weight = 21443.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.112050 restraints weight = 21220.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112929 restraints weight = 15040.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113010 restraints weight = 13939.105| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8877 Z= 0.169 Angle : 0.721 9.970 12012 Z= 0.374 Chirality : 0.048 0.181 1308 Planarity : 0.004 0.039 1572 Dihedral : 5.097 20.216 1224 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 2.65 % Allowed : 19.32 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1143 helix: -4.34 (0.28), residues: 21 sheet: -0.13 (0.24), residues: 468 loop : -0.95 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 123 TYR 0.019 0.002 TYR A 216 PHE 0.042 0.003 PHE D 45 TRP 0.091 0.003 TRP C 160 HIS 0.004 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 8871) covalent geometry : angle 0.71747 / 0.37 (12000) SS BOND : bond 0.00583 / 0.20 ( 6) SS BOND : angle 2.27572 / 1.40 ( 12) hydrogen bonds : bond 0.03594 / 2.53 ( 327) hydrogen bonds : angle 6.08765 / 4.27 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8184 (t0) cc_final: 0.7949 (t0) REVERT: B 11 ASP cc_start: 0.8024 (t0) cc_final: 0.7687 (t0) REVERT: E 10 LYS cc_start: 0.7449 (mtpp) cc_final: 0.7070 (pttt) REVERT: F 132 GLU cc_start: 0.8393 (tt0) cc_final: 0.8020 (tp30) outliers start: 25 outliers final: 23 residues processed: 167 average time/residue: 0.0858 time to fit residues: 19.7851 Evaluate side-chains 167 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.146793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.117706 restraints weight = 18520.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116592 restraints weight = 17839.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118027 restraints weight = 16934.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118356 restraints weight = 13015.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.118678 restraints weight = 11446.143| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8877 Z= 0.135 Angle : 0.701 9.268 12012 Z= 0.360 Chirality : 0.048 0.174 1308 Planarity : 0.004 0.038 1572 Dihedral : 4.813 20.843 1224 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 2.12 % Allowed : 20.28 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1143 helix: -4.20 (0.34), residues: 21 sheet: -0.10 (0.24), residues: 471 loop : -0.82 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 123 TYR 0.018 0.001 TYR B 28 PHE 0.028 0.002 PHE A 196 TRP 0.094 0.003 TRP C 160 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8871) covalent geometry : angle 0.69807 / 0.36 (12000) SS BOND : bond 0.00612 / 0.21 ( 6) SS BOND : angle 2.22224 / 1.36 ( 12) hydrogen bonds : bond 0.03328 / 2.36 ( 327) hydrogen bonds : angle 5.92899 / 4.16 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.46 seconds wall clock time: 26 minutes 3.80 seconds (1563.80 seconds total)