Starting phenix.real_space_refine on Sun Aug 24 16:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6n_29775/08_2025/8g6n_29775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6n_29775/08_2025/8g6n_29775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g6n_29775/08_2025/8g6n_29775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6n_29775/08_2025/8g6n_29775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g6n_29775/08_2025/8g6n_29775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6n_29775/08_2025/8g6n_29775.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6800 2.51 5 N 1875 2.21 5 O 2026 1.98 5 H 10672 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21450 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3057 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3115 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2721 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3269 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3116 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3115 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3057 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 4.19, per 1000 atoms: 0.20 Number of scatterers: 21450 At special positions: 0 Unit cell: (109.2, 135.2, 126.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 O 2026 8.00 N 1875 7.00 C 6800 6.00 H 10672 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 589.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 1 sheets defined 76.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.757A pdb=" N LYS G 30 " --> pdb=" O VAL G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.746A pdb=" N TYR G 130 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 176 removed outlier: 3.509A pdb=" N GLN G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.007A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.719A pdb=" N ASP A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.855A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.593A pdb=" N THR A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 174 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.446A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.924A pdb=" N ALA C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 60 removed outlier: 3.548A pdb=" N THR C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.538A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 4.219A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.991A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 194 removed outlier: 4.287A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.923A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 103 through 107 removed outlier: 4.224A pdb=" N THR E 107 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 160 through 176 removed outlier: 3.559A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.320A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.937A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 30 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 146 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.844A pdb=" N GLN F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.773A pdb=" N TRP F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 4.169A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 715 hydrogen bonds defined for protein. 2124 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: 5.46 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10660 1.03 - 1.23: 30 1.23 - 1.42: 4397 1.42 - 1.62: 6458 1.62 - 1.82: 142 Bond restraints: 21687 Sorted by residual: bond pdb=" N HIS F 12 " pdb=" CA HIS F 12 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N HIS G 12 " pdb=" CA HIS G 12 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" CB MET C 144 " pdb=" CG MET C 144 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" N HIS G 12 " pdb=" H HIS G 12 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" N HIS F 12 " pdb=" H HIS F 12 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 21682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 38941 2.62 - 5.24: 354 5.24 - 7.86: 19 7.86 - 10.48: 4 10.48 - 13.10: 1 Bond angle restraints: 39319 Sorted by residual: angle pdb=" CB MET D 68 " pdb=" CG MET D 68 " pdb=" SD MET D 68 " ideal model delta sigma weight residual 112.70 99.60 13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CA MET E 144 " pdb=" CB MET E 144 " pdb=" CG MET E 144 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA MET D 68 " pdb=" CB MET D 68 " pdb=" CG MET D 68 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.71e+00 angle pdb=" CB MET A 68 " pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 112.70 103.51 9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" CB MET F 118 " pdb=" CG MET F 118 " pdb=" SD MET F 118 " ideal model delta sigma weight residual 112.70 121.66 -8.96 3.00e+00 1.11e-01 8.92e+00 ... (remaining 39314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 8752 17.49 - 34.98: 1001 34.98 - 52.47: 389 52.47 - 69.96: 81 69.96 - 87.45: 19 Dihedral angle restraints: 10242 sinusoidal: 5703 harmonic: 4539 Sorted by residual: dihedral pdb=" CA ALA D 174 " pdb=" C ALA D 174 " pdb=" N GLU D 175 " pdb=" CA GLU D 175 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TRP D 117 " pdb=" C TRP D 117 " pdb=" N MET D 118 " pdb=" CA MET D 118 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASP F 163 " pdb=" CB ASP F 163 " pdb=" CG ASP F 163 " pdb=" OD1 ASP F 163 " ideal model delta sinusoidal sigma weight residual -30.00 -85.42 55.42 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 10239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1186 0.035 - 0.071: 358 0.071 - 0.106: 101 0.106 - 0.141: 28 0.141 - 0.177: 5 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA MET E 215 " pdb=" N MET E 215 " pdb=" C MET E 215 " pdb=" CB MET E 215 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU C 202 " pdb=" CB LEU C 202 " pdb=" CD1 LEU C 202 " pdb=" CD2 LEU C 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE E 124 " pdb=" N ILE E 124 " pdb=" C ILE E 124 " pdb=" CB ILE E 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 1675 not shown) Planarity restraints: 3210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 122 " -0.062 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO E 123 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 132 " 0.180 9.50e-02 1.11e+02 6.07e-02 5.10e+00 pdb=" NE ARG B 132 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 132 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 132 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 132 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 132 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B 132 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG B 132 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 132 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 100 " -0.189 9.50e-02 1.11e+02 6.35e-02 4.88e+00 pdb=" NE ARG D 100 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 100 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 100 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 100 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG D 100 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG D 100 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 100 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 100 " 0.000 2.00e-02 2.50e+03 ... (remaining 3207 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 3684 2.28 - 2.86: 47946 2.86 - 3.44: 57668 3.44 - 4.02: 72827 4.02 - 4.60: 113226 Nonbonded interactions: 295351 Sorted by model distance: nonbonded pdb=" O GLY F 156 " pdb="HD22 ASN F 195 " model vdw 1.702 2.450 nonbonded pdb="HD22 ASN D 53 " pdb=" O ALA D 105 " model vdw 1.718 2.450 nonbonded pdb=" OE2 GLU B 98 " pdb=" HE ARG B 100 " model vdw 1.720 2.450 nonbonded pdb=" OE1 GLU G 79 " pdb="HH21 ARG G 82 " model vdw 1.720 2.450 nonbonded pdb=" HG1 THR A 210 " pdb=" OE1 GLU A 213 " model vdw 1.722 2.450 ... (remaining 295346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 67 through 85 or (resid \ 96 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 97 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 101 through 119 or (resid 120 and ( \ name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 121 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 159 through 161 \ or (resid 162 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 163 through 181 or (resid 182 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 183 through 193)) selection = (chain 'B' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 65 or (resid 66 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 67 through 85 or (resid 96 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 97 through 99 or (res \ id 100 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 101 through 119 or (resid 120 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 \ through 157 or (resid 158 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 159 through 161 or (resid 162 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 163 throu \ gh 193)) selection = (chain 'C' and (resid 12 through 85 or (resid 96 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 97 through 99 or (resid \ 100 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 101 through 119 or (resid 120 and (name N or name CA or name C or nam \ e O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or nam \ e H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 th \ rough 157 or (resid 158 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 159 through 181 or (resid 182 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 183 through \ 186 or (resid 187 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 188 through 193)) selection = (chain 'D' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 61 or (resid 62 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 63 through 65 or \ (resid 66 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 67 through 83 or (resid 84 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) \ or resid 85 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 101 through 119 or (resid 120 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 121 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 159 through 161 \ or (resid 162 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 163 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 183 through 186 or (re \ sid 187 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 188 through 193)) selection = (chain 'E' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 65 or (resid 66 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 67 through 85 or (resid 96 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 97 through 99 or (res \ id 100 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 101 through 119 or (resid 120 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 \ through 157 or (resid 158 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 159 through 161 or (resid 162 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 163 throu \ gh 181 or (resid 182 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 183 through 193)) selection = (chain 'F' and (resid 12 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 67 through 119 or (resid \ 120 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name H \ B3 or name HD2 or name HE1)) or resid 121 through 161 or (resid 162 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 163 t \ hrough 193)) selection = (chain 'G' and (resid 12 through 85 or (resid 96 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 97 through 119 or (resid \ 120 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name H \ B3 or name HD2 or name HE1)) or resid 121 through 161 or (resid 162 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 163 t \ hrough 193)) } 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.770 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11015 Z= 0.175 Angle : 0.739 13.102 14969 Z= 0.358 Chirality : 0.039 0.177 1678 Planarity : 0.006 0.093 1941 Dihedral : 16.670 87.445 4132 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.17 % Allowed : 14.80 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 1.92 (0.23), residues: 1351 helix: 1.79 (0.17), residues: 989 sheet: -2.96 (1.11), residues: 9 loop : 0.02 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 132 TYR 0.022 0.002 TYR E 145 PHE 0.035 0.002 PHE B 168 TRP 0.029 0.001 TRP G 184 HIS 0.005 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00417 (11015) covalent geometry : angle 0.73939 (14969) hydrogen bonds : bond 0.09327 ( 715) hydrogen bonds : angle 4.32482 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 MET cc_start: 0.7304 (mtm) cc_final: 0.7082 (mtm) outliers start: 2 outliers final: 2 residues processed: 154 average time/residue: 0.3017 time to fit residues: 62.7215 Evaluate side-chains 138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 171 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN C 139 ASN C 176 GLN F 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.079235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061501 restraints weight = 112243.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064022 restraints weight = 46020.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065582 restraints weight = 27823.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066534 restraints weight = 20803.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067106 restraints weight = 17536.414| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11015 Z= 0.128 Angle : 0.506 7.728 14969 Z= 0.259 Chirality : 0.036 0.156 1678 Planarity : 0.004 0.061 1941 Dihedral : 3.900 23.100 1463 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.12 % Allowed : 14.72 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.18 (0.23), residues: 1351 helix: 2.01 (0.16), residues: 986 sheet: -3.38 (1.06), residues: 9 loop : 0.03 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.009 0.001 TYR B 169 PHE 0.008 0.001 PHE B 168 TRP 0.007 0.001 TRP G 184 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00285 (11015) covalent geometry : angle 0.50642 (14969) hydrogen bonds : bond 0.03760 ( 715) hydrogen bonds : angle 3.93159 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.641 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: C 214 MET cc_start: 0.8448 (mtm) cc_final: 0.8039 (mtm) REVERT: E 144 MET cc_start: 0.8207 (tmm) cc_final: 0.7862 (tmm) REVERT: F 133 TRP cc_start: 0.8512 (m-10) cc_final: 0.8295 (m-10) REVERT: F 144 MET cc_start: 0.8329 (ttt) cc_final: 0.8079 (ttm) outliers start: 13 outliers final: 6 residues processed: 154 average time/residue: 0.2525 time to fit residues: 54.0148 Evaluate side-chains 142 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS C 21 ASN C 139 ASN C 176 GLN E 50 GLN F 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.077706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059937 restraints weight = 112687.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.062347 restraints weight = 46804.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063865 restraints weight = 28593.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064792 restraints weight = 21545.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065345 restraints weight = 18207.333| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11015 Z= 0.187 Angle : 0.534 7.532 14969 Z= 0.279 Chirality : 0.037 0.149 1678 Planarity : 0.005 0.055 1941 Dihedral : 3.882 15.104 1460 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.64 % Allowed : 14.80 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.01 (0.23), residues: 1351 helix: 1.92 (0.16), residues: 987 sheet: -3.88 (1.15), residues: 9 loop : -0.11 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 100 TYR 0.011 0.001 TYR D 169 PHE 0.009 0.001 PHE A 32 TRP 0.006 0.001 TRP E 184 HIS 0.003 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00404 (11015) covalent geometry : angle 0.53371 (14969) hydrogen bonds : bond 0.03839 ( 715) hydrogen bonds : angle 4.06946 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.625 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: G 120 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7179 (t-90) REVERT: C 39 MET cc_start: 0.8521 (mtt) cc_final: 0.8256 (mtm) REVERT: C 214 MET cc_start: 0.8616 (mtm) cc_final: 0.8282 (mtm) REVERT: E 144 MET cc_start: 0.8192 (tmm) cc_final: 0.7842 (tmm) REVERT: F 133 TRP cc_start: 0.8597 (m-10) cc_final: 0.8245 (m-10) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.2735 time to fit residues: 55.9621 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 163 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.077882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060054 restraints weight = 112428.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062492 restraints weight = 46571.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064019 restraints weight = 28471.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064945 restraints weight = 21428.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065506 restraints weight = 18128.206| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11015 Z= 0.148 Angle : 0.495 5.244 14969 Z= 0.255 Chirality : 0.036 0.143 1678 Planarity : 0.004 0.050 1941 Dihedral : 3.816 14.318 1460 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.29 % Allowed : 15.49 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.10 (0.23), residues: 1351 helix: 1.99 (0.16), residues: 991 sheet: -3.79 (1.17), residues: 9 loop : -0.13 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.010 0.001 TYR D 169 PHE 0.009 0.001 PHE G 161 TRP 0.007 0.001 TRP G 80 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00325 (11015) covalent geometry : angle 0.49470 (14969) hydrogen bonds : bond 0.03596 ( 715) hydrogen bonds : angle 3.95084 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.503 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: G 120 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7151 (t-90) REVERT: C 214 MET cc_start: 0.8558 (mtm) cc_final: 0.8216 (mtm) REVERT: E 210 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8297 (p) REVERT: F 133 TRP cc_start: 0.8587 (m-10) cc_final: 0.8232 (m-10) outliers start: 15 outliers final: 12 residues processed: 147 average time/residue: 0.2829 time to fit residues: 57.1566 Evaluate side-chains 146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 176 GLN F 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.077171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059308 restraints weight = 111745.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061714 restraints weight = 46957.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063222 restraints weight = 28818.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.064104 restraints weight = 21735.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064660 restraints weight = 18461.153| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11015 Z= 0.202 Angle : 0.532 5.511 14969 Z= 0.281 Chirality : 0.037 0.145 1678 Planarity : 0.004 0.052 1941 Dihedral : 3.935 15.151 1460 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 15.40 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 1.83 (0.23), residues: 1351 helix: 1.77 (0.16), residues: 995 sheet: -3.97 (1.21), residues: 9 loop : -0.17 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.010 0.001 TYR D 169 PHE 0.009 0.001 PHE C 161 TRP 0.007 0.001 TRP B 184 HIS 0.003 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00436 (11015) covalent geometry : angle 0.53223 (14969) hydrogen bonds : bond 0.03804 ( 715) hydrogen bonds : angle 4.14095 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.622 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: G 120 HIS cc_start: 0.7532 (OUTLIER) cc_final: 0.7256 (t-90) REVERT: C 214 MET cc_start: 0.8596 (mtm) cc_final: 0.8307 (mtm) REVERT: E 210 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8376 (p) REVERT: F 133 TRP cc_start: 0.8609 (m-10) cc_final: 0.8199 (m-10) outliers start: 21 outliers final: 17 residues processed: 148 average time/residue: 0.2747 time to fit residues: 55.9999 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 41 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059252 restraints weight = 112699.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061658 restraints weight = 46996.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.063164 restraints weight = 28743.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064071 restraints weight = 21685.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064617 restraints weight = 18381.262| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11015 Z= 0.181 Angle : 0.521 6.885 14969 Z= 0.272 Chirality : 0.037 0.151 1678 Planarity : 0.004 0.055 1941 Dihedral : 3.923 14.869 1460 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.89 % Allowed : 16.09 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 1.85 (0.23), residues: 1351 helix: 1.78 (0.16), residues: 996 sheet: -3.79 (1.23), residues: 9 loop : -0.17 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.013 0.001 TYR D 164 PHE 0.010 0.001 PHE A 32 TRP 0.008 0.001 TRP B 184 HIS 0.004 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00394 (11015) covalent geometry : angle 0.52140 (14969) hydrogen bonds : bond 0.03707 ( 715) hydrogen bonds : angle 4.10213 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.648 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: G 120 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.7215 (t-90) REVERT: C 214 MET cc_start: 0.8603 (mtm) cc_final: 0.8319 (mtm) REVERT: E 28 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: E 145 TYR cc_start: 0.8044 (m-80) cc_final: 0.7778 (m-80) REVERT: E 210 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8409 (p) REVERT: F 133 TRP cc_start: 0.8595 (m-10) cc_final: 0.8137 (m-10) outliers start: 22 outliers final: 18 residues processed: 149 average time/residue: 0.2695 time to fit residues: 55.8937 Evaluate side-chains 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 163 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.078059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060181 restraints weight = 111590.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062639 restraints weight = 46184.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.064167 restraints weight = 28202.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065112 restraints weight = 21211.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065583 restraints weight = 17891.174| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11015 Z= 0.109 Angle : 0.483 5.950 14969 Z= 0.246 Chirality : 0.035 0.141 1678 Planarity : 0.004 0.055 1941 Dihedral : 3.751 14.801 1460 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 16.01 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.29 (0.23), residues: 1351 helix: 2.11 (0.16), residues: 991 sheet: -3.62 (1.24), residues: 9 loop : -0.01 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.013 0.001 TYR D 164 PHE 0.008 0.001 PHE A 32 TRP 0.008 0.001 TRP G 80 HIS 0.002 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00247 (11015) covalent geometry : angle 0.48307 (14969) hydrogen bonds : bond 0.03451 ( 715) hydrogen bonds : angle 3.85211 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.776 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: G 120 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.7253 (t-90) REVERT: B 96 MET cc_start: 0.4672 (ppp) cc_final: 0.4333 (ppp) REVERT: C 214 MET cc_start: 0.8595 (mtm) cc_final: 0.8307 (mtm) REVERT: E 28 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: E 145 TYR cc_start: 0.7856 (m-80) cc_final: 0.7601 (m-80) REVERT: E 210 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8364 (p) REVERT: F 133 TRP cc_start: 0.8571 (m-10) cc_final: 0.8050 (m-10) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.2767 time to fit residues: 57.6348 Evaluate side-chains 146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.077703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059801 restraints weight = 112310.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062244 restraints weight = 46608.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063775 restraints weight = 28446.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064707 restraints weight = 21395.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065235 restraints weight = 18086.432| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11015 Z= 0.129 Angle : 0.497 5.146 14969 Z= 0.255 Chirality : 0.036 0.142 1678 Planarity : 0.004 0.057 1941 Dihedral : 3.733 14.659 1460 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.64 % Allowed : 16.44 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.30 (0.23), residues: 1351 helix: 2.11 (0.16), residues: 995 sheet: -3.52 (1.27), residues: 9 loop : 0.03 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 100 TYR 0.013 0.001 TYR D 164 PHE 0.008 0.001 PHE A 32 TRP 0.008 0.001 TRP B 184 HIS 0.004 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00287 (11015) covalent geometry : angle 0.49747 (14969) hydrogen bonds : bond 0.03469 ( 715) hydrogen bonds : angle 3.86806 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.632 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: G 120 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.7134 (t-90) REVERT: B 96 MET cc_start: 0.4673 (ppp) cc_final: 0.4333 (ppp) REVERT: C 214 MET cc_start: 0.8593 (mtm) cc_final: 0.8294 (mtm) REVERT: E 28 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: E 145 TYR cc_start: 0.8007 (m-80) cc_final: 0.7732 (m-80) REVERT: E 210 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8368 (p) REVERT: F 133 TRP cc_start: 0.8569 (m-10) cc_final: 0.8118 (m-10) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.2636 time to fit residues: 53.9488 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.078175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060348 restraints weight = 112062.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.062819 restraints weight = 46005.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064360 restraints weight = 27946.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065296 restraints weight = 20967.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065854 restraints weight = 17682.275| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11015 Z= 0.107 Angle : 0.486 4.829 14969 Z= 0.246 Chirality : 0.035 0.139 1678 Planarity : 0.004 0.059 1941 Dihedral : 3.666 14.616 1460 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.72 % Allowed : 16.44 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.46 (0.23), residues: 1351 helix: 2.21 (0.17), residues: 996 sheet: -3.43 (1.26), residues: 9 loop : 0.10 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 100 TYR 0.014 0.001 TYR D 164 PHE 0.007 0.001 PHE A 32 TRP 0.011 0.001 TRP B 184 HIS 0.004 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00241 (11015) covalent geometry : angle 0.48598 (14969) hydrogen bonds : bond 0.03361 ( 715) hydrogen bonds : angle 3.76334 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.740 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: G 120 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.7162 (t-90) REVERT: G 154 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7279 (mmm-85) REVERT: B 96 MET cc_start: 0.4664 (ppp) cc_final: 0.4327 (ppp) REVERT: B 185 MET cc_start: 0.8006 (mtt) cc_final: 0.7526 (mtp) REVERT: C 214 MET cc_start: 0.8656 (mtm) cc_final: 0.8333 (mtm) REVERT: E 28 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: E 145 TYR cc_start: 0.8010 (m-80) cc_final: 0.7710 (m-80) REVERT: E 210 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8367 (p) REVERT: F 133 TRP cc_start: 0.8590 (m-10) cc_final: 0.8132 (m-10) REVERT: F 145 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6989 (m-80) outliers start: 20 outliers final: 14 residues processed: 152 average time/residue: 0.2767 time to fit residues: 57.9373 Evaluate side-chains 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 55 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.078121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060298 restraints weight = 112417.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062766 restraints weight = 46190.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064308 restraints weight = 28079.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065236 restraints weight = 21067.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065731 restraints weight = 17761.197| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11015 Z= 0.115 Angle : 0.491 4.738 14969 Z= 0.249 Chirality : 0.035 0.145 1678 Planarity : 0.004 0.060 1941 Dihedral : 3.646 14.510 1460 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.55 % Allowed : 16.95 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.45 (0.23), residues: 1351 helix: 2.20 (0.16), residues: 996 sheet: -3.32 (1.31), residues: 9 loop : 0.12 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 100 TYR 0.014 0.001 TYR D 164 PHE 0.007 0.001 PHE A 32 TRP 0.011 0.001 TRP B 184 HIS 0.005 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00258 (11015) covalent geometry : angle 0.49078 (14969) hydrogen bonds : bond 0.03353 ( 715) hydrogen bonds : angle 3.78838 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.598 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: G 120 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7118 (t-90) REVERT: G 154 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.7176 (mmm-85) REVERT: B 96 MET cc_start: 0.4658 (ppp) cc_final: 0.4323 (ppp) REVERT: B 176 GLN cc_start: 0.8263 (mp10) cc_final: 0.8039 (mp10) REVERT: C 214 MET cc_start: 0.8598 (mtm) cc_final: 0.8264 (mtm) REVERT: E 28 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: E 145 TYR cc_start: 0.8023 (m-80) cc_final: 0.7726 (m-80) REVERT: E 210 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8516 (p) REVERT: F 133 TRP cc_start: 0.8560 (m-10) cc_final: 0.8110 (m-10) REVERT: F 145 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6972 (m-80) outliers start: 18 outliers final: 14 residues processed: 149 average time/residue: 0.2748 time to fit residues: 56.5979 Evaluate side-chains 150 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060419 restraints weight = 112219.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062882 restraints weight = 46123.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064422 restraints weight = 28054.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065337 restraints weight = 21040.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065899 restraints weight = 17777.827| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11015 Z= 0.112 Angle : 0.490 5.680 14969 Z= 0.248 Chirality : 0.035 0.144 1678 Planarity : 0.004 0.060 1941 Dihedral : 3.608 14.474 1460 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.81 % Allowed : 16.70 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: 2.53 (0.23), residues: 1351 helix: 2.26 (0.16), residues: 995 sheet: -3.22 (1.33), residues: 9 loop : 0.16 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 100 TYR 0.014 0.001 TYR D 164 PHE 0.007 0.001 PHE A 32 TRP 0.010 0.001 TRP B 184 HIS 0.004 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00253 (11015) covalent geometry : angle 0.49023 (14969) hydrogen bonds : bond 0.03316 ( 715) hydrogen bonds : angle 3.75633 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.14 seconds wall clock time: 66 minutes 43.77 seconds (4003.77 seconds total)